diff --git a/404.html b/404.html
index 1c671a92..21162bb5 100644
--- a/404.html
+++ b/404.html
@@ -85,7 +85,7 @@ <h6 class="dropdown-header" data-toc-skip>User Guides</h6>
 
     <footer><div class="pkgdown-footer-left">
   <p></p>
-<p>Developed by Aaron Clark, Jeff Thompson, Robert Krajcik, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
+<p>Developed by Aaron Clark, Robert Krajcik, Jeff Thompson, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
 </div>
 
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diff --git a/LICENSE-text.html b/LICENSE-text.html
index 1d565afd..352c87be 100644
--- a/LICENSE-text.html
+++ b/LICENSE-text.html
@@ -476,7 +476,7 @@ <h6 class="dropdown-header" data-toc-skip>User Guides</h6>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Aaron Clark, Jeff Thompson, Robert Krajcik, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
+  <p></p><p>Developed by Aaron Clark, Robert Krajcik, Jeff Thompson, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
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diff --git a/LICENSE.html b/LICENSE.html
index d260ed97..5b2d2be1 100644
--- a/LICENSE.html
+++ b/LICENSE.html
@@ -70,7 +70,7 @@ <h6 class="dropdown-header" data-toc-skip>User Guides</h6>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Aaron Clark, Jeff Thompson, Robert Krajcik, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
+  <p></p><p>Developed by Aaron Clark, Robert Krajcik, Jeff Thompson, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
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diff --git a/articles/Administrative_Tools_and_Options_V0.1.1.html b/articles/Administrative_Tools_and_Options_V0.1.1.html
index 84b803fa..6b7fffb4 100644
--- a/articles/Administrative_Tools_and_Options_V0.1.1.html
+++ b/articles/Administrative_Tools_and_Options_V0.1.1.html
@@ -582,7 +582,7 @@ <h2 id="decision-automation">Decision Automation<a class="anchor" aria-label="an
 
     <footer><div class="pkgdown-footer-left">
   <p></p>
-<p>Developed by Aaron Clark, Jeff Thompson, Robert Krajcik, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
+<p>Developed by Aaron Clark, Robert Krajcik, Jeff Thompson, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
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diff --git a/articles/Credential_Manager.html b/articles/Credential_Manager.html
index 1459c44a..a0906c8f 100644
--- a/articles/Credential_Manager.html
+++ b/articles/Credential_Manager.html
@@ -407,7 +407,7 @@ <h4 id="additional-columns-in-passwords-table">Additional columns in Passwords t
 
     <footer><div class="pkgdown-footer-left">
   <p></p>
-<p>Developed by Aaron Clark, Jeff Thompson, Robert Krajcik, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
+<p>Developed by Aaron Clark, Robert Krajcik, Jeff Thompson, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
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diff --git a/articles/Deployment.html b/articles/Deployment.html
index ecb40c94..e9627070 100644
--- a/articles/Deployment.html
+++ b/articles/Deployment.html
@@ -560,7 +560,7 @@ <h3 id="shinyproxy">ShinyProxy<a class="anchor" aria-label="anchor" href="#shiny
 
     <footer><div class="pkgdown-footer-left">
   <p></p>
-<p>Developed by Aaron Clark, Jeff Thompson, Robert Krajcik, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
+<p>Developed by Aaron Clark, Robert Krajcik, Jeff Thompson, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
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diff --git a/articles/Deployment_V0.1.1.html b/articles/Deployment_V0.1.1.html
index d18eab4b..dfd533ff 100644
--- a/articles/Deployment_V0.1.1.html
+++ b/articles/Deployment_V0.1.1.html
@@ -314,7 +314,7 @@ <h3 id="shinyproxy">ShinyProxy<a class="anchor" aria-label="anchor" href="#shiny
 
     <footer><div class="pkgdown-footer-left">
   <p></p>
-<p>Developed by Aaron Clark, Jeff Thompson, Robert Krajcik, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
+<p>Developed by Aaron Clark, Robert Krajcik, Jeff Thompson, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
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diff --git a/articles/User_Roles_and_Privileges.html b/articles/User_Roles_and_Privileges.html
index e6cbda4e..cd615586 100644
--- a/articles/User_Roles_and_Privileges.html
+++ b/articles/User_Roles_and_Privileges.html
@@ -520,7 +520,7 @@ <h2 id="roles">Roles<a class="anchor" aria-label="anchor" href="#roles"></a>
 
     <footer><div class="pkgdown-footer-left">
   <p></p>
-<p>Developed by Aaron Clark, Jeff Thompson, Robert Krajcik, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
+<p>Developed by Aaron Clark, Robert Krajcik, Jeff Thompson, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
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diff --git a/articles/dev_Using_SQLite_Command_Line.html b/articles/dev_Using_SQLite_Command_Line.html
index f130f452..72487dae 100644
--- a/articles/dev_Using_SQLite_Command_Line.html
+++ b/articles/dev_Using_SQLite_Command_Line.html
@@ -251,7 +251,7 @@ <h3 id="sqlitestudio">SQLiteStudio<a class="anchor" aria-label="anchor" href="#s
 
     <footer><div class="pkgdown-footer-left">
   <p></p>
-<p>Developed by Aaron Clark, Jeff Thompson, Robert Krajcik, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
+<p>Developed by Aaron Clark, Robert Krajcik, Jeff Thompson, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
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diff --git a/articles/dev_renv.html b/articles/dev_renv.html
index de6d7174..1c698d91 100644
--- a/articles/dev_renv.html
+++ b/articles/dev_renv.html
@@ -198,7 +198,7 @@ <h2 id="references">References<a class="anchor" aria-label="anchor" href="#refer
 
     <footer><div class="pkgdown-footer-left">
   <p></p>
-<p>Developed by Aaron Clark, Jeff Thompson, Robert Krajcik, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
+<p>Developed by Aaron Clark, Robert Krajcik, Jeff Thompson, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
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diff --git a/articles/index.html b/articles/index.html
index 75f55024..7634b104 100644
--- a/articles/index.html
+++ b/articles/index.html
@@ -98,7 +98,7 @@ <h3>Old User Guides</h3>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Aaron Clark, Jeff Thompson, Robert Krajcik, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
+  <p></p><p>Developed by Aaron Clark, Robert Krajcik, Jeff Thompson, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
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diff --git a/articles/riskassessment.html b/articles/riskassessment.html
index 52d0351c..44b5942c 100644
--- a/articles/riskassessment.html
+++ b/articles/riskassessment.html
@@ -93,11 +93,10 @@ <h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#i
 </h2>
 <p>Welcome! This guide will help users get started with the
 <code>riskassessment</code> application for the first time. For more
-information about how to deploy the application, please reference the <a href="./Deployment.html"><code>Deployment</code></a> guide. And note:
-this guide assumes you have already downloaded the
-<code>riskassessment</code> package &amp; all of it’s dependencies
-following the <a href="../index.html#installation">installation
-instructions</a>.</p>
+information about how to deploy the application, please reference the
+<code>Deployments</code> [INSERT LINK] guide. And note: this guide
+assumes you have already downloaded the <code>riskassessment</code>
+package &amp; all of it’s dependencies following the <a href="../index.html#installation">installation instructions</a>.</p>
 <p><br></p>
 </div>
 <div class="section level2">
@@ -593,7 +592,7 @@ <h2 id="where-to-go-from-here">Where to go from here?<a class="anchor" aria-labe
 
     <footer><div class="pkgdown-footer-left">
   <p></p>
-<p>Developed by Aaron Clark, Jeff Thompson, Robert Krajcik, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
+<p>Developed by Aaron Clark, Robert Krajcik, Jeff Thompson, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
 </div>
 
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diff --git a/authors.html b/authors.html
index 1e9b2823..21580512 100644
--- a/authors.html
+++ b/authors.html
@@ -65,11 +65,11 @@ <h2>Authors</h2>
           </p>
         </li>
         <li>
-          <p><strong>Jeff Thompson</strong>. Author. 
-          <br><small>Co-Lead</small></p>
+          <p><strong>Robert Krajcik</strong>. Author. 
+          </p>
         </li>
         <li>
-          <p><strong>Robert Krajcik</strong>. Author. 
+          <p><strong>Jeff Thompson</strong>. Author. 
           </p>
         </li>
         <li>
@@ -134,13 +134,13 @@ <h2>Authors</h2>
       <h2 id="citation">Citation</h2>
       <p><small class="dont-index">Source: <a href="https://github.com/pharmaR/riskassessment/blob/HEAD/DESCRIPTION" class="external-link"><code>DESCRIPTION</code></a></small></p>
 
-      <p>Clark A, Thompson J, Krajcik R, Andersen L, Borgman A, Gotti M, Gans M, Kallem A, Fission Labs India Pvt Ltd (2024).
+      <p>Clark A, Krajcik R, Thompson J, Andersen L, Borgman A, Gotti M, Gans M, Kallem A, Fission Labs India Pvt Ltd (2024).
 <em>riskassessment: A web app designed to interface with the 'riskmetric' package</em>.
 R package version 3.1.0, https://pharmar.github.io/riskassessment/, <a href="https://github.com/pharmaR/riskassessment" class="external-link">https://github.com/pharmaR/riskassessment</a>. 
 </p>
       <pre>@Manual{,
   title = {riskassessment: A web app designed to interface with the `riskmetric` package},
-  author = {Aaron Clark and Jeff Thompson and Robert Krajcik and Lars Andersen and Andrew Borgman and Marly Gotti and Maya Gans and Aravind Reddy Kallem and {Fission Labs India Pvt Ltd}},
+  author = {Aaron Clark and Robert Krajcik and Jeff Thompson and Lars Andersen and Andrew Borgman and Marly Gotti and Maya Gans and Aravind Reddy Kallem and {Fission Labs India Pvt Ltd}},
   year = {2024},
   note = {R package version 3.1.0, https://pharmar.github.io/riskassessment/},
   url = {https://github.com/pharmaR/riskassessment},
@@ -151,7 +151,7 @@ <h2 id="citation">Citation</h2>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Aaron Clark, Jeff Thompson, Robert Krajcik, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
+  <p></p><p>Developed by Aaron Clark, Robert Krajcik, Jeff Thompson, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/index.html b/index.html
index 838930d8..12847ae1 100644
--- a/index.html
+++ b/index.html
@@ -123,7 +123,7 @@ <h3 id="echo-ing-riskmetrics-approach-to-validation-">Echo-ing <code>{riskmetric
 <a class="anchor" aria-label="anchor" href="#echo-ing-riskmetrics-approach-to-validation-"></a>
 </h3>
 <p>Validation can serve as an umbrella for various terms, and admittedly, companies will diverge on what may be the “correct approach”. The <code>riskassessment</code> app is built on a <code>rismetric</code>-foundation, whose developers follow the validation philosophy proposed in <a href="https://www.pharmar.org/white-paper/" class="external-link">this white paper</a> published by the R Validation Hub. As such, the scope of <code>riskassessment</code> and <code>riskmetric</code> are only designed to support decision making from that view point. The full robustness and reliability of any software may (and likely will) require deeper inspection by the reviewing party.</p>
-<p><em>Note:</em> Development of both <code>riskassessment</code> and <code>riskmetric</code> were made possible thanks to the <a href="https://www.pharmar.org" class="external-link">R Validation Hub</a>, a collaboration to support the adoption of R within a biopharmaceutical regulatory setting.</p>
+<p><em>Note:</em> Development of both <code>riskassessment</code> and <code>riskmetric</code> were made possible thanks to the <a href="https://www.pharmar.org/about/" class="external-link">R Validation Hub</a>, a collaboration to support the adoption of R within a biopharmaceutical regulatory setting.</p>
 </div>
 <div class="section level3">
 <h3 id="usage">Usage<a class="anchor" aria-label="anchor" href="#usage"></a>
@@ -215,8 +215,8 @@ <h2 data-toc-skip>Citation</h2>
 <h2 data-toc-skip>Developers</h2>
 <ul class="list-unstyled">
 <li>Aaron Clark <br><small class="roles"> Author, maintainer </small>  </li>
-<li>Jeff Thompson <br><small class="roles"> Author </small>  </li>
 <li>Robert Krajcik <br><small class="roles"> Author </small>  </li>
+<li>Jeff Thompson <br><small class="roles"> Author </small>  </li>
 <li>Lars Andersen <br><small class="roles"> Author </small>  </li>
 <li>Andrew Borgman <br><small class="roles"> Author </small>  </li>
 <li>Marly Gotti <br><small class="roles"> Author </small>  </li>
@@ -246,7 +246,7 @@ <h2 data-toc-skip>Dev status</h2>
 
     <footer><div class="pkgdown-footer-left">
   <p></p>
-<p>Developed by Aaron Clark, Jeff Thompson, Robert Krajcik, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
+<p>Developed by Aaron Clark, Robert Krajcik, Jeff Thompson, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
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diff --git a/news/index.html b/news/index.html
index f6608f25..901a0839 100644
--- a/news/index.html
+++ b/news/index.html
@@ -319,7 +319,7 @@ <h2 class="pkg-version" data-toc-text="0.0.0.9000" id="riskassessment-0009000">r
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Aaron Clark, Jeff Thompson, Robert Krajcik, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
+  <p></p><p>Developed by Aaron Clark, Robert Krajcik, Jeff Thompson, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/pkgdown.yml b/pkgdown.yml
index 2ee3b547..77ac26f4 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -10,7 +10,7 @@ articles:
   dev_Using_SQLite_Command_Line: dev_Using_SQLite_Command_Line.html
   dev_renv: dev_renv.html
   riskassessment: riskassessment.html
-last_built: 2024-07-02T12:34Z
+last_built: 2024-07-02T12:40Z
 urls:
   reference: https://pharmar.github.io/riskassessment/reference
   article: https://pharmar.github.io/riskassessment/articles
diff --git a/reference/aboutInfoServer.html b/reference/aboutInfoServer.html
index f303107a..779f6eee 100644
--- a/reference/aboutInfoServer.html
+++ b/reference/aboutInfoServer.html
@@ -84,7 +84,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Aaron Clark, Jeff Thompson, Robert Krajcik, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
+  <p></p><p>Developed by Aaron Clark, Robert Krajcik, Jeff Thompson, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
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index 70975ab6..64593328 100644
--- a/reference/aboutInfoUI.html
+++ b/reference/aboutInfoUI.html
@@ -80,7 +80,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Aaron Clark, Jeff Thompson, Robert Krajcik, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
+  <p></p><p>Developed by Aaron Clark, Robert Krajcik, Jeff Thompson, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
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index aa8a3469..5ef2f9b8 100644
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+++ b/reference/addCommentServer.html
@@ -96,7 +96,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Aaron Clark, Jeff Thompson, Robert Krajcik, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
+  <p></p><p>Developed by Aaron Clark, Robert Krajcik, Jeff Thompson, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
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index bdcb522f..ea1bdf38 100644
--- a/reference/addCommentUI.html
+++ b/reference/addCommentUI.html
@@ -83,7 +83,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Aaron Clark, Jeff Thompson, Robert Krajcik, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
+  <p></p><p>Developed by Aaron Clark, Robert Krajcik, Jeff Thompson, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
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diff --git a/reference/add_shinymanager_auth.html b/reference/add_shinymanager_auth.html
index f36834b7..e4792d4c 100644
--- a/reference/add_shinymanager_auth.html
+++ b/reference/add_shinymanager_auth.html
@@ -88,7 +88,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Aaron Clark, Jeff Thompson, Robert Krajcik, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
+  <p></p><p>Developed by Aaron Clark, Robert Krajcik, Jeff Thompson, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
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index ef29bee8..f093445a 100644
--- a/reference/add_tags.html
+++ b/reference/add_tags.html
@@ -84,7 +84,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Aaron Clark, Jeff Thompson, Robert Krajcik, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
+  <p></p><p>Developed by Aaron Clark, Robert Krajcik, Jeff Thompson, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
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index 82e820f7..67fb70d6 100644
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@@ -86,7 +86,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
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+  <p></p><p>Developed by Aaron Clark, Robert Krajcik, Jeff Thompson, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
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diff --git a/reference/assessmentInfoServer.html b/reference/assessmentInfoServer.html
index 31a96d92..fb460b05 100644
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@@ -84,7 +84,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
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-  <p></p><p>Developed by Aaron Clark, Jeff Thompson, Robert Krajcik, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
+  <p></p><p>Developed by Aaron Clark, Robert Krajcik, Jeff Thompson, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
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diff --git a/reference/assessmentInfoUI.html b/reference/assessmentInfoUI.html
index 5069cf64..e5f67833 100644
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@@ -80,7 +80,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
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-  <p></p><p>Developed by Aaron Clark, Jeff Thompson, Robert Krajcik, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
+  <p></p><p>Developed by Aaron Clark, Robert Krajcik, Jeff Thompson, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
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diff --git a/reference/auto_font.html b/reference/auto_font.html
index 1d49807f..cbe3be4b 100644
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+  <p></p><p>Developed by Aaron Clark, Robert Krajcik, Jeff Thompson, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
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diff --git a/reference/build_comm_cards.html b/reference/build_comm_cards.html
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+  <p></p><p>Developed by Aaron Clark, Robert Krajcik, Jeff Thompson, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
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diff --git a/reference/build_comm_plotly.html b/reference/build_comm_plotly.html
index cbb68baf..1b679671 100644
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+  <p></p><p>Developed by Aaron Clark, Robert Krajcik, Jeff Thompson, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
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diff --git a/reference/build_db_cards.html b/reference/build_db_cards.html
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+  <p></p><p>Developed by Aaron Clark, Robert Krajcik, Jeff Thompson, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
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diff --git a/reference/build_dep_cards.html b/reference/build_dep_cards.html
index f5b750c7..e76c58d5 100644
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+  <p></p><p>Developed by Aaron Clark, Robert Krajcik, Jeff Thompson, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
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diff --git a/reference/communityMetricsServer.html b/reference/communityMetricsServer.html
index b149841a..cfe56e61 100644
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@@ -92,7 +92,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
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+  <p></p><p>Developed by Aaron Clark, Robert Krajcik, Jeff Thompson, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
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diff --git a/reference/communityMetricsUI.html b/reference/communityMetricsUI.html
index f89db25f..8540551a 100644
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+  <p></p><p>Developed by Aaron Clark, Robert Krajcik, Jeff Thompson, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
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diff --git a/reference/create_credentials_db.html b/reference/create_credentials_db.html
index 3efeb7d8..a8800fc6 100644
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+  <p></p><p>Developed by Aaron Clark, Robert Krajcik, Jeff Thompson, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
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diff --git a/reference/create_credentials_dev_db.html b/reference/create_credentials_dev_db.html
index fe4ffdd0..11eea0d1 100644
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+  <p></p><p>Developed by Aaron Clark, Robert Krajcik, Jeff Thompson, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
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diff --git a/reference/create_db.html b/reference/create_db.html
index e16bc725..0097230b 100644
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@@ -80,7 +80,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
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+  <p></p><p>Developed by Aaron Clark, Robert Krajcik, Jeff Thompson, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
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index a9f70b19..0826f3c4 100644
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+  <p></p><p>Developed by Aaron Clark, Robert Krajcik, Jeff Thompson, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
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index 56bd4945..cf43cfba 100644
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-  <p></p><p>Developed by Aaron Clark, Jeff Thompson, Robert Krajcik, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
+  <p></p><p>Developed by Aaron Clark, Robert Krajcik, Jeff Thompson, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
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index 8dc03ac3..ce599b6f 100644
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+  <p></p><p>Developed by Aaron Clark, Robert Krajcik, Jeff Thompson, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
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index 66e2d795..6831b833 100644
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-  <p></p><p>Developed by Aaron Clark, Jeff Thompson, Robert Krajcik, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
+  <p></p><p>Developed by Aaron Clark, Robert Krajcik, Jeff Thompson, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
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index 23570b1f..19066913 100644
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+  <p></p><p>Developed by Aaron Clark, Robert Krajcik, Jeff Thompson, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
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+  <p></p><p>Developed by Aaron Clark, Robert Krajcik, Jeff Thompson, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
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index f6f55296..a00fbdfb 100644
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+  <p></p><p>Developed by Aaron Clark, Robert Krajcik, Jeff Thompson, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
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index 80e04be6..baba05bb 100644
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+  <p></p><p>Developed by Aaron Clark, Robert Krajcik, Jeff Thompson, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
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+  <p></p><p>Developed by Aaron Clark, Robert Krajcik, Jeff Thompson, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
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+  <p></p><p>Developed by Aaron Clark, Robert Krajcik, Jeff Thompson, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
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+  <p></p><p>Developed by Aaron Clark, Robert Krajcik, Jeff Thompson, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
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+  <p></p><p>Developed by Aaron Clark, Robert Krajcik, Jeff Thompson, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
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+  <p></p><p>Developed by Aaron Clark, Robert Krajcik, Jeff Thompson, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
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+  <p></p><p>Developed by Aaron Clark, Robert Krajcik, Jeff Thompson, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
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     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Aaron Clark, Jeff Thompson, Robert Krajcik, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
+  <p></p><p>Developed by Aaron Clark, Robert Krajcik, Jeff Thompson, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
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diff --git a/reference/metricGridUI.html b/reference/metricGridUI.html
index 68b816c6..f39ae818 100644
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@@ -80,7 +80,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Aaron Clark, Jeff Thompson, Robert Krajcik, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
+  <p></p><p>Developed by Aaron Clark, Robert Krajcik, Jeff Thompson, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
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diff --git a/reference/metric_gauge.html b/reference/metric_gauge.html
index 33ff4f84..25e9f0cd 100644
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@@ -86,7 +86,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Aaron Clark, Jeff Thompson, Robert Krajcik, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
+  <p></p><p>Developed by Aaron Clark, Robert Krajcik, Jeff Thompson, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
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diff --git a/reference/packageDependenciesServer.html b/reference/packageDependenciesServer.html
index 8e7477ed..5f8da8a7 100644
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@@ -92,7 +92,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Aaron Clark, Jeff Thompson, Robert Krajcik, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
+  <p></p><p>Developed by Aaron Clark, Robert Krajcik, Jeff Thompson, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
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diff --git a/reference/packageDependenciesUI.html b/reference/packageDependenciesUI.html
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@@ -80,7 +80,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
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-  <p></p><p>Developed by Aaron Clark, Jeff Thompson, Robert Krajcik, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
+  <p></p><p>Developed by Aaron Clark, Robert Krajcik, Jeff Thompson, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
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diff --git a/reference/reportPreviewServer.html b/reference/reportPreviewServer.html
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@@ -134,7 +134,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Aaron Clark, Jeff Thompson, Robert Krajcik, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
+  <p></p><p>Developed by Aaron Clark, Robert Krajcik, Jeff Thompson, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
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diff --git a/reference/reportPreviewUI.html b/reference/reportPreviewUI.html
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@@ -80,7 +80,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Aaron Clark, Jeff Thompson, Robert Krajcik, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
+  <p></p><p>Developed by Aaron Clark, Robert Krajcik, Jeff Thompson, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
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diff --git a/reference/reweightViewServer.html b/reference/reweightViewServer.html
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@@ -88,7 +88,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
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-  <p></p><p>Developed by Aaron Clark, Jeff Thompson, Robert Krajcik, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
+  <p></p><p>Developed by Aaron Clark, Robert Krajcik, Jeff Thompson, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
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@@ -80,7 +80,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
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-  <p></p><p>Developed by Aaron Clark, Jeff Thompson, Robert Krajcik, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
+  <p></p><p>Developed by Aaron Clark, Robert Krajcik, Jeff Thompson, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
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diff --git a/reference/riskassessment-package.html b/reference/riskassessment-package.html
index 67e4ef4a..aa34f582 100644
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     <div class="section level2">
     <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2>
     <p><strong>Maintainer</strong>: Aaron Clark <a href="mailto:clark.aaronchris@gmail.com">clark.aaronchris@gmail.com</a></p>
-<p>Authors:</p><ul><li><p>Jeff Thompson <a href="mailto:jeff.thompson51317@gmail.com">jeff.thompson51317@gmail.com</a> (Co-Lead)</p></li>
-<li><p>Robert Krajcik <a href="mailto:robert.krajcik@biogen.com">robert.krajcik@biogen.com</a></p></li>
+<p>Authors:</p><ul><li><p>Robert Krajcik <a href="mailto:robert.krajcik@biogen.com">robert.krajcik@biogen.com</a></p></li>
+<li><p>Jeff Thompson <a href="mailto:jeff.thompson51317@gmail.com">jeff.thompson51317@gmail.com</a></p></li>
 <li><p>Lars Andersen <a href="mailto:lars.andersen@boehringer-ingelheim.com">lars.andersen@boehringer-ingelheim.com</a></p></li>
 <li><p>Andrew Borgman <a href="mailto:andrew.borgman@biogen.com">andrew.borgman@biogen.com</a></p></li>
 <li><p>Marly Gotti <a href="mailto:marly.cormar@biogen.com">marly.cormar@biogen.com</a></p></li>
@@ -112,7 +112,7 @@ <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a><
 
 
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-  <p></p><p>Developed by Aaron Clark, Jeff Thompson, Robert Krajcik, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
+  <p></p><p>Developed by Aaron Clark, Robert Krajcik, Jeff Thompson, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
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index 145188af..9f446965 100644
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-  <p></p><p>Developed by Aaron Clark, Jeff Thompson, Robert Krajcik, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
+  <p></p><p>Developed by Aaron Clark, Robert Krajcik, Jeff Thompson, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
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index 8532ef50..a59b4b1f 100644
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@@ -95,7 +95,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
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-  <p></p><p>Developed by Aaron Clark, Jeff Thompson, Robert Krajcik, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
+  <p></p><p>Developed by Aaron Clark, Robert Krajcik, Jeff Thompson, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
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index 71ebb039..eb61546a 100644
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@@ -83,7 +83,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
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-  <p></p><p>Developed by Aaron Clark, Jeff Thompson, Robert Krajcik, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
+  <p></p><p>Developed by Aaron Clark, Robert Krajcik, Jeff Thompson, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
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index 3336aa41..3bf6ff74 100644
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@@ -91,7 +91,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
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-  <p></p><p>Developed by Aaron Clark, Jeff Thompson, Robert Krajcik, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
+  <p></p><p>Developed by Aaron Clark, Robert Krajcik, Jeff Thompson, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
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@@ -83,7 +83,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
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-  <p></p><p>Developed by Aaron Clark, Jeff Thompson, Robert Krajcik, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
+  <p></p><p>Developed by Aaron Clark, Robert Krajcik, Jeff Thompson, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
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diff --git a/reference/uploadPackageServer.html b/reference/uploadPackageServer.html
index c23d9ee7..167a2f97 100644
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@@ -92,7 +92,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
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-  <p></p><p>Developed by Aaron Clark, Jeff Thompson, Robert Krajcik, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
+  <p></p><p>Developed by Aaron Clark, Robert Krajcik, Jeff Thompson, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
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index 82365df2..881d7a9b 100644
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@@ -80,7 +80,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Aaron Clark, Jeff Thompson, Robert Krajcik, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
+  <p></p><p>Developed by Aaron Clark, Robert Krajcik, Jeff Thompson, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
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diff --git a/reference/upload_pkg_lst.html b/reference/upload_pkg_lst.html
index 38eb564f..40fb9a8d 100644
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@@ -118,7 +118,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Aaron Clark, Jeff Thompson, Robert Krajcik, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
+  <p></p><p>Developed by Aaron Clark, Robert Krajcik, Jeff Thompson, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
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index 14ba918b..fc2407f8 100644
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@@ -98,7 +98,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Aaron Clark, Jeff Thompson, Robert Krajcik, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
+  <p></p><p>Developed by Aaron Clark, Robert Krajcik, Jeff Thompson, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
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index ebacd55b..1cf8b42d 100644
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@@ -83,7 +83,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Aaron Clark, Jeff Thompson, Robert Krajcik, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
+  <p></p><p>Developed by Aaron Clark, Robert Krajcik, Jeff Thompson, Lars Andersen, Andrew Borgman, Marly Gotti, Maya Gans, Aravind Reddy Kallem, Fission Labs India Pvt Ltd, PSI special interest group Application and Implementation of Methodologies in Statistics, R Validation Hub.</p>
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diff --git a/search.json b/search.json
index 13b7d7e2..f6b9695d 100644
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+++ b/search.json
@@ -1 +1 @@
-[{"path":"https://pharmar.github.io/riskassessment/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2022 2020 Fission Labs R Validation Hub contributors Permission hereby granted, free charge, person obtaining copy software associated documentation files (“Software”), deal Software without restriction, including without limitation rights use, copy, modify, merge, publish, distribute, sublicense, /sell copies Software, permit persons Software furnished , subject following conditions: copyright notice permission notice shall included copies substantial portions Software. SOFTWARE PROVIDED “”, WITHOUT WARRANTY KIND, EXPRESS IMPLIED, INCLUDING LIMITED WARRANTIES MERCHANTABILITY, FITNESS PARTICULAR PURPOSE NONINFRINGEMENT. EVENT SHALL AUTHORS COPYRIGHT HOLDERS LIABLE CLAIM, DAMAGES LIABILITY, WHETHER ACTION CONTRACT, TORT OTHERWISE, ARISING , CONNECTION SOFTWARE USE DEALINGS SOFTWARE.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/Administrative_Tools_and_Options_V0.1.1.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"Administrative Tools and Options V0.1.1","text":"’s secret users administrator privileges access certain features application. guide assists ADMIN users manage privileges, (minimum) include: govern user credentials re-weight metrics determine risk scores calculated define automated decision rules based risk scores verify ADMIN access, first check can see navigation tabs within app, especially rightmost Administrative Tools tab. see tab, granted access! gain access, ’ll request access known ADMIN user within organization.    can also hover cursor  symbol bottom-right corner page. Upon hovering, two additional buttons appear. middle one log  button, Administrator mode  button appear top, shown. button appear non-ADMIN users.  selected Administrative Tools tab, currently two areas available review: first Credential Manager second Assessment Reweighting, seen .","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/Administrative_Tools_and_Options_V0.1.1.html","id":"credential-manager","dir":"Articles","previous_headings":"","what":"Credential Manager","title":"Administrative Tools and Options V0.1.1","text":"Credential Manager tab shown default contains two tables: first one, indicated  Users icon, used manage users. second one, indicated  key icon, used manage passwords. also button bottom download copy current sqlite database.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/Administrative_Tools_and_Options_V0.1.1.html","id":"managing-users","dir":"Articles","previous_headings":"Credential Manager","what":"Managing Users","title":"Administrative Tools and Options V0.1.1","text":"first table provides tools managing users: adding, editing, deleting.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/Administrative_Tools_and_Options_V0.1.1.html","id":"add-a-user","dir":"Articles","previous_headings":"Credential Manager > Managing Users","what":"Add a User","title":"Administrative Tools and Options V0.1.1","text":"add new user, click button labelled: “Add user”.   prompt appear can specify user name, well optional start & expire date new member. default set today’s date (later).  , ’ll type “PeterParker” User Name field.  Notice  checkbox grant new user administrator privileges also checked default. unique password generated user prompted change first time /logs , long “Ask change password” box remains checked.     Upon clicking CONFIRM NEW USER, confirmation modal appear. Now good time notify user sending userid temporary password.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/Administrative_Tools_and_Options_V0.1.1.html","id":"user-start-and-expire-dates","dir":"Articles","previous_headings":"Credential Manager > Managing Users","what":"User start and expire dates","title":"Administrative Tools and Options V0.1.1","text":"either start date set future date expire date set today’s date, account expired message appear, log-attempt fail.  Feel free set either dates needed, just leave blank ignore/avoid time-based access particular user.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/Administrative_Tools_and_Options_V0.1.1.html","id":"edit-a-user","dir":"Articles","previous_headings":"Credential Manager > Managing Users","what":"Edit a user","title":"Administrative Tools and Options V0.1.1","text":"Edit user information clicking EDIT button, found right-hand side table. Edit User window appear:   Make changes, click CONFIRM CHANGE.   small modal dialog box appear (briefly) indicating user successfully updated.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/Administrative_Tools_and_Options_V0.1.1.html","id":"more-edit-options","dir":"Articles","previous_headings":"Credential Manager > Managing Users","what":"More Edit options","title":"Administrative Tools and Options V0.1.1","text":"bottom table bar three buttons:   first one  checkbox select multiple users followed EDIT SELECTED USERS REMOVE SELECTED USERS button. buttons enabled select two users.  Note “Edit Selected Users” button allows modify start expire dates selected group users.  ’ve made changes, click CONFIRM CHANGE.    , small modal dialog box briefly appear indicating users updated.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/Administrative_Tools_and_Options_V0.1.1.html","id":"delete-a-user","dir":"Articles","previous_headings":"Credential Manager > Managing Users","what":"Delete a user","title":"Administrative Tools and Options V0.1.1","text":"Delete user clicking REMOVE button right-hand side table. see confirmatory modal dialog box. Click “Delete User(s).”   can also delete multiple users like editing multiple users. Just click REMOVE SELECTED USERS button bottom table.   confirmatory modal dialog box appear. Click DELETE USER(S).","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/Administrative_Tools_and_Options_V0.1.1.html","id":"replace-initial-admin-user","dir":"Articles","previous_headings":"Credential Manager > Managing Users","what":"Replace initial Admin user","title":"Administrative Tools and Options V0.1.1","text":"administrator, ’s recommended replace initial ADMIN user ID created first time app launched. Note must always least one admin user, delete ! want delete initial admin user first need create another user ID administrative privileges, described .  Just , click “Add user” button make sure check Admin box. temporary password can overridden un-checking “ask change password” box setting password whatever want.  completing form, sign using new credentials delete original ADMIN user clicking REMOVE button row table.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/Administrative_Tools_and_Options_V0.1.1.html","id":"managing-passwords","dir":"Articles","previous_headings":"Credential Manager","what":"Managing Passwords","title":"Administrative Tools and Options V0.1.1","text":"second table allows password management.    Click CHANGE PASSWORD button force corresponding user change /password next log-. confirmatory modal dialog box appear, like :   click RESET PASSWORD button generate temporary password. , confirmatory modal dialog box appear, like :   Click CONFIRM see another modal dialog box new temporary password .   responsible delivering new temporary password user. bottom User table, also  checkbox select multiple users followed FORCE SELECTED USERS CHANGE PASSWORD button. button enabled select two users.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/Administrative_Tools_and_Options_V0.1.1.html","id":"additional-columns-in-passwords-table","dir":"Articles","previous_headings":"Credential Manager > Managing Passwords","what":"Additional columns in Passwords table","title":"Administrative Tools and Options V0.1.1","text":"Must change column: Indicates whether user change /password next log-. changed column: Indicates user already changed /password. Date Last changed column: Indicates date password updated.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/Administrative_Tools_and_Options_V0.1.1.html","id":"assessment-reweighting","dir":"Articles","previous_headings":"","what":"Assessment Reweighting","title":"Administrative Tools and Options V0.1.1","text":"Head tab available ADMIN users called Assessment Reweighting. high level view:  three buttons page: UPDATE WEIGHT top right, DOWNLOAD middle left, RE-CALCULATE bottom left.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/Administrative_Tools_and_Options_V0.1.1.html","id":"download-database","dir":"Articles","previous_headings":"Assessment Reweighting","what":"Download Database","title":"Administrative Tools and Options V0.1.1","text":"First, simplest: DOWNLOAD database button.   clicked, button download copy current database (default, called “database.sqlite”). app developers recommend anytime plan make integral changes database (like changing metric weights), anything else.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/Administrative_Tools_and_Options_V0.1.1.html","id":"updating-weights","dir":"Articles","previous_headings":"Assessment Reweighting","what":"Updating Weights","title":"Administrative Tools and Options V0.1.1","text":"name suggests, modules allows us view existing change metric weights used calculate risk score using riskmemtric.   can either select metric Select metric dropdown box select row “CURRENT RISK SCORE WEIGHTS METRIC” table. metric selected, enter new (numeric) weight “Choose new weight” box select UPDATE WEIGHT button. ’ll notice row change appear highlighted, showing old weight value new weight value:   updated least one metric weight, RE-CALCULATE button enabled, allowing apply new weights re-calculated risk package. ’ve made final re-weighting changes, can click “Re-calculate” button pictured . Note weight changes take effect packages database, updating risk score .   click RE-CALCULATE get confirmation modal, reminding “updating risk metrics reverted”, strongly recommending download copy current database first clicking SUBMIT. modal also details actions take effect app submit changes.   click SUBMIT modal dialog box appear indicating applying weights updating risk scores package uploaded. followed brief “updates completed” message.   Now go database overview tab confirm risk scores updated. can also view new weights, including standardized weight Assessment Criteria tab.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/Administrative_Tools_and_Options_V0.1.1.html","id":"decision-automation","dir":"Articles","previous_headings":"","what":"Decision Automation","title":"Administrative Tools and Options V0.1.1","text":"organization black white rules package risk decisions based solely riskmetric scores, decision automation . leveraged, help automatically classify packages “Low”, “Medium”, “High” risk decision categories upon upload. current automation rules always displayed ‘Upload Package’ tab. Please note ADMIN users necessary privileges edit. get started, click small  (gear) button upper right hand corner section.   decision rules applied, ’ll see following risk decision categories next empty check boxes. setting rules organization, can choose much little automation needed.   example, want set automatic decision “High” risk scores, need select check box make risk score designation / cut value. Every time package uploaded risk score > 0.66, automatically receive decision label: “High” saves review team time mental capacity reviewing large groups packages.   Similarly, package risk thresholds mapped decision category, apply ! user interface won’t allow slider ranges overlap, allow gaps range. example , adopt automatic decisions packages risk scores less 0.33 greater .66. fictitious example, let’s say organization policy package whose risk score falls 0.33 0.66 need reviewed manually.   apply changes, ADMIN need select APPLY DECISION RULES. pop-ask user review confirm selected automation rules:   Upon clicking submit, automation rules stored users see ‘Upload Package’ tab. uploading new CSV packages, can see ‘Summary Uploaded Package(s)’ now includes summary decisions made, category. example , can see 10 packages uploaded, 5 automatic decisions made: four received “low” designation one labeled “high” risk. summary table, risk score decision right-hand side. can also observe packages weren’t found don’t exist CRAN.   Consulting ‘PACKAGE CONTROL PANEL’, select one packages decision made, can see ‘Status’ changed “Reviewed” risk decision slider adjusted accordingly disabled. addition, ‘Overall Comment’ submitted, stating decision made driven via automation rules.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/Credential_Manager.html","id":"the-admin-privilege","dir":"Articles","previous_headings":"","what":"The admin Privilege","title":"Credential Manager","text":"Starting Version 1.0.0, major overhaul privileges function within application. Privileges now tied user roles! allows additional flexibility manage user’s access. However, one privilege whose assignment mandatory app deployment: admin privilege. admin privilege important (required least one user) person manage credentials roles users. Though can changed, default app configuration gives admins access privileges. learn privileges, details provided “User Roles Privileges” guide. ’ll use vignette discuss admin-specific privilege: credentials management. verify admin access, first check can see navigation tabs within app, especially rightmost Administrative Tools tab. see tab, granted access! gain access, ’ll request access known admin user within organization.    can also hover cursor  symbol bottom-right corner page. Upon hovering, two additional buttons appear. middle one log  button, Administrator mode  button appear top, shown. button appear non-admin users.  selected Administrative Tools tab, currently two areas available review: first Credential Manager second Roles & Privileges, seen . Note: may also see tab labelled Assessment Reweighting, connected different privilege may included role.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/Credential_Manager.html","id":"the-credential-manager","dir":"Articles","previous_headings":"","what":"The Credential Manager","title":"Credential Manager","text":"Credential Manager tab shown default contains two tables: first one, indicated  Users icon, used manage users. second one, indicated  key icon, used manage passwords. also button bottom download copy current sqlite database.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/Credential_Manager.html","id":"managing-users","dir":"Articles","previous_headings":"The Credential Manager","what":"Managing Users","title":"Credential Manager","text":"first table provides tools managing users: adding, editing, deleting.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/Credential_Manager.html","id":"add-a-user","dir":"Articles","previous_headings":"The Credential Manager > Managing Users","what":"Add a User","title":"Credential Manager","text":"add new user, click button labelled: “Add user”.   prompt appear can specify user name, well optional start & expire date new member. default set today’s date (later).  , ’ll type “PeterParker” User Name field.  Notice  checkbox grant new user administrator privileges also checked default. unique password generated user prompted change first time /logs , long “Ask change password” box remains checked.     Upon clicking CONFIRM NEW USER, confirmation modal appear. Now good time notify user sending userid temporary password.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/Credential_Manager.html","id":"user-start-and-expire-dates","dir":"Articles","previous_headings":"The Credential Manager > Managing Users","what":"User start and expire dates","title":"Credential Manager","text":"either start date set future date expire date set today’s date, account expired message appear, log-attempt fail.  Feel free set either dates needed, just leave blank ignore/avoid time-based access particular user.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/Credential_Manager.html","id":"edit-a-user","dir":"Articles","previous_headings":"The Credential Manager > Managing Users","what":"Edit a user","title":"Credential Manager","text":"Edit user information clicking EDIT button, found right-hand side table. Edit User window appear:   Make changes, click CONFIRM CHANGE.   small modal dialog box appear (briefly) indicating user successfully updated.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/Credential_Manager.html","id":"more-edit-options","dir":"Articles","previous_headings":"The Credential Manager > Managing Users","what":"More Edit options","title":"Credential Manager","text":"bottom table bar three buttons:   first one  checkbox select multiple users followed EDIT SELECTED USERS REMOVE SELECTED USERS button. buttons enabled select two users.  Note “Edit Selected Users” button allows modify start expire dates selected group users.  ’ve made changes, click CONFIRM CHANGE.    , small modal dialog box briefly appear indicating users updated.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/Credential_Manager.html","id":"delete-a-user","dir":"Articles","previous_headings":"The Credential Manager > Managing Users","what":"Delete a user","title":"Credential Manager","text":"Delete user clicking REMOVE button right-hand side table. see confirmatory modal dialog box. Click “Delete User(s).”   can also delete multiple users like editing multiple users. Just click REMOVE SELECTED USERS button bottom table.   confirmatory modal dialog box appear. Click DELETE USER(S).","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/Credential_Manager.html","id":"replace-initial-admin-user","dir":"Articles","previous_headings":"The Credential Manager > Managing Users","what":"Replace initial admin user","title":"Credential Manager","text":"administrator, ’s recommended replace initial admin user ID created first time app launched. Note must always least one admin user, delete ! want delete initial admin user first need create another user ID administrative privileges, described .  Just , click “Add user” button make sure check Admin box. temporary password can overridden un-checking “ask change password” box setting password whatever want.  completing form, sign using new credentials delete original admin user clicking REMOVE button row table.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/Credential_Manager.html","id":"managing-passwords","dir":"Articles","previous_headings":"The Credential Manager","what":"Managing Passwords","title":"Credential Manager","text":"second table allows password management.    Click CHANGE PASSWORD button force corresponding user change /password next log-. confirmatory modal dialog box appear, like :   click RESET PASSWORD button generate temporary password. , confirmatory modal dialog box appear, like :   Click CONFIRM see another modal dialog box new temporary password .   responsible delivering new temporary password user. bottom User table, also  checkbox select multiple users followed FORCE SELECTED USERS CHANGE PASSWORD button. button enabled select two users.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/Credential_Manager.html","id":"additional-columns-in-passwords-table","dir":"Articles","previous_headings":"The Credential Manager > Managing Passwords","what":"Additional columns in Passwords table","title":"Credential Manager","text":"Must change column: Indicates whether user change /password next log-. changed column: Indicates user already changed /password. Date Last changed column: Indicates date password updated.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/Deployment.html","id":"installing-vs-forking","dir":"Articles","previous_headings":"","what":"Installing vs Forking","title":"Deployment","text":"discuss deployment methods, note riskassessment application developed using renv form source control. helps maintain stability code base. can install riskassessment Github, strongly recommended use fork riskassessment repository deployment. serve handful purposes organization: can utilize renv deployment help ensure share environment app developers, ensuring consistent behavior. easier access configuration file allowing streamlined deployment several projects.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/Deployment.html","id":"the-db-config-yml-file","dir":"Articles","previous_headings":"","what":"The db-config.yml file","title":"Deployment","text":"Starting {riskassessment} v1.0.0, configuration file can found inst/db-config.yml used initialize application deployment. configuration contains elements vital app initialization grow development continues. Many elements file also editable within application (provided user role privileges ). Currently, db-config.yml contains following major elements: assessment_db: string designating file path assessment SQLite database (created upon initialization). default value database.sqlite. credential_db: string designating file path credentials SQLite database (created upon initialization). default value credentials.sqlite. loggit_json: string designating file path logging JSON file (created upon initialization). default value loggit.json. credentials: list defining user roles privileges assigned roles credentials database. decisions: list defining decision categories, automated decision rules (optional), custom decision category colors (also optional). metric_weights: list containing riskmetric weights use upon initialization. weights used increase decrease priority one metric. look current default configuration fork riskassessment code today:","code":"default:   assessment_db: database.sqlite   loggit_json: loggit.json   credential_db: credentials.sqlite   credentials:     roles:       - admin       - lead       - reviewer     privileges:       admin: [admin, weight_adjust, auto_decision_adjust, final_decision, revert_decision, add_package, delete_package]       lead: [weight_adjust, auto_decision_adjust, final_decision, revert_decision, add_package, delete_package]       reviewer: add_package   decisions:     categories:       - Low Risk       - Medium Risk       - High Risk   metric_weights:     covr_coverage: 0"},{"path":"https://pharmar.github.io/riskassessment/articles/Deployment.html","id":"configuring-the-assessment-database","dir":"Articles","previous_headings":"The db-config.yml file","what":"Configuring the assessment database","title":"Deployment","text":"riskassessment::run_app() function ran, code base check assessment sqlite file exists name give (default database.sqlite) doesn’t, several tables initiated create database just app launches. Note user authority name database file whatever like using inst/db-config.yml file. , can include file path preceding file name wish move location database away root directory. example, following code create database called “database.sqlite” dev/ folder: time vignette authored, database initialize following tables NULL values: comments: stores user comments, including user names associated comment entry, comment type, timestamp community_usage_metrics: stores CRAN package downloads per month metric: stores metric info, including riskmetric name, label, short description, type, weight package_metrics: stores package-specific rismetric metrics package: Contains package information, like name, version, maintainer, etc. also contains riskmetric score, weighted score, decision, timestamp. Note: changes/ updates occur tables new release riskassessment, may need delete database file re-running app. changes announced ‘breaking changes’ app. , remember save copy current database file another directory backup purposes.","code":"default:   assessment_db: ./dev/database.sqlite"},{"path":"https://pharmar.github.io/riskassessment/articles/Deployment.html","id":"database-log-file-config","dir":"Articles","previous_headings":"The db-config.yml file","what":"Database log file config","title":"Deployment","text":"mentioned previously, loggit.json file initiated track general actions performed application, especially reflect change assessment db (database.sqlite file). time vignette authored, ’s summary actions logged: App start User log-ins Enabling/ Disabling changing automated decision rules Decisions initiated users decision automation rules, including pkgs added removed database, issues process, like absence data support certain metrics Re-weighting pkg metrics database issues conflicts may arise loggit “transaction” recorded contains lot info, notably, contain time stamp, record type (“info”, “warn”, “error”), message. database transactions, message usually include query executed. log entries always printed R console convenience. example: Feel free use information see fit! Similar assessment_db parameter inst/db-config, can name file whatever like, save directory ’d like. , save dev/ folder name “loggit.json”:","code":"riskassessment::run_app() > [1] \"Log file set to loggit.json\" > Listening on http://127.0.0.1:4097 > {\"timestamp\": \"2023-03-20T11:46:23-0400\", \"log_lvl\": \"INFO\", \"log_msg\": \"User admin signed on as admin\"} > {\"timestamp\": \"2023-03-20T11:46:33-0400\", \"log_lvl\": \"INFO\", \"log_msg\": \"The following decision rules were implemented by admin (admin): Medium = (0.33__COMMA__ 0.66]; Low = (0__COMMA__ 0.33]; High = (0.66__COMMA__ 1].\"} default:   assessment_db: ./dev/database.sqlite   loggit_json: ./dev/loggit.json"},{"path":"https://pharmar.github.io/riskassessment/articles/Deployment.html","id":"credentials-configuration","dir":"Articles","previous_headings":"The db-config.yml file","what":"Credentials configuration","title":"Deployment","text":"Similar assessment database, riskassessment::run_app() function executes, code base check credentials sqlite file exists name give (default credentials.sqlite) doesn’t, riskassessment initiate new database app launches. Note user authority name database sqlite file whatever desire using inst/db-config.yml. , can include file path preceding file name wish move location database away root directory. example, following code create database called “credentials.sqlite” dev/ folder: Right credentials_db element used, credentials element (two sub-elements: roles privileges) must populated. guide, snippet default values elements, encourage design configuration works (organization). Note “User Roles Privileges” guide entirely dedicated config. full details, please visit & read article!","code":"default:   assessment_db: ./dev/database.sqlite   loggit_json: ./dev/loggit.json   credential_db: ./dev/credentials.sqlite credentials:   roles:     - admin     - lead     - reviewer   privileges:     admin: [admin, weight_adjust, auto_decision_adjust, final_decision, revert_decision, add_package, delete_package]     lead: [weight_adjust, auto_decision_adjust, final_decision, revert_decision, add_package, delete_package]     reviewer: add_package"},{"path":"https://pharmar.github.io/riskassessment/articles/Deployment.html","id":"decisions-configuration","dir":"Articles","previous_headings":"The db-config.yml file","what":"Decisions configuration","title":"Deployment","text":"decisions element contains three sub-elements: categories (mandatory), rules, colors. example configuration ’ll walk together:","code":"decisions:   categories:       - Insignificant Risk       - Minor Risk       - Needs Review       - Moderate Risk       - Major Risk       - Severe Risk     rules:       rule_1:         metric: bugs_status         condition: ~ metric_score(.x) <= .25         decision: Severe Risk       rule_2:         metric: dependencies         condition: ~ length(.x) >= 30         decision: Major Risk       rule_3:         metric: has_vignettes         condition: ~ .x == 0         decision: Moderate Risk       Severe Risk:         - .7         - 1       Insignificant Risk:         - 0         - .1       rule_else:         decision: Needs Review   colors:     Moderate Risk: !expr grDevices::rgb(52, 235, 229, maxColorValue = 255)"},{"path":"https://pharmar.github.io/riskassessment/articles/Deployment.html","id":"categories","dir":"Articles","previous_headings":"The db-config.yml file > Decisions configuration","what":"Categories","title":"Deployment","text":"Notice can set many decision categories wish, must specify least two! ’s suggested category names define ordinal way, first category lowest risk designation last category highest risk. example configuration , can see categories defined low risk category “Insignificant Risk” high risk category “Severe Risk”. non-ordinal category ’d like use, like “Needs Review” example, ’s possible - just don’t list first last.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/Deployment.html","id":"rules","dir":"Articles","previous_headings":"The db-config.yml file > Decisions configuration","what":"Rules","title":"Deployment","text":"Using rules element, may set automated decision rules prior launching app. , package uploaded, automatically get labelled appropriate decision rules condition met. rules executed order, top--bottom, ’s important place rules greatest priority top list. implement decision based risk score, list category name mutually exclusive range values directly beneath label packages whose risk score falls two values. , ’ve defined rules dictate risk scores 0.7 1 automatically categorized “Severe Risk”. Similarly, packages scoring 0 0.1 get labelled “Insignificant Risk”. addition, configuration file can evaluate expressions define rules. , rule needs three elements: metric, condition, decision seen . metric element simply name riskmetric assessment ’d like evaluate. Next, provide R code (including riskmetric code) help define rules using formula syntax. Note: .x translated selected metric’s assessment value. wish convert metric score, use riskmetric::metric_score(.x) shown . Last, provide decision category apply condition met. , specified hypothetical rules 1 - 3 apply decisions manner; , spell expressions sentence format, taking account previous condition isn’t met: packages bug closure rate less 25% considered “Severe Risk” packages 30 dependencies (>25% bug close rate) “Major Risk” packages vignettes (<30 dependencies >25% bug close rate) ”Moderate Risk” Categories addressed rules banner receive automated decisions. However, can provide optional rule_else element define decision category apply packages don’t meet rules . Also, keep mind users privileges edit decision rules may change configuration app later time.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/Deployment.html","id":"colors","dir":"Articles","previous_headings":"The db-config.yml file > Decisions configuration","what":"Colors","title":"Deployment","text":"Last, using colors element can detail specific colors assigned certain categories. Notice element accept expression evaluate launching application. don’t care color used category, color-blind friendly color palette used fill categories specified.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/Deployment.html","id":"metric-weights-configuration","dir":"Articles","previous_headings":"The db-config.yml file","what":"Metric weights configuration","title":"Deployment","text":"metric_weights element contains named list weights. weight supplied, default 1. current list weights can included following: has_vignettes, has_news, news_current, has_bug_reports_url, has_website, has_maintainer, has_source_control, export_help, bugs_status, license, covr_coverage, downloads_1yr. seen , default configuration sets weight covr_coverage 0. want ignore certain metric little value organization, give value zero. metrics explicitly given , app uses default weight 1 , unless course already exists assessment database previously initialized metric weights manually changed. wanted toggle current metrics, harm stating metric weight, set config file look like , example: riskmetric use weights score package according org’s needs!","code":"metric_weights:   has_vignettes: 2   has_news: 0.5   news_current: 2   has_bug_reports_url: 1   has_website: 1   has_maintainer: 1   has_source_control: 1   export_help: 2   bugs_status: 5   license: 1   downloads_1yr.: 3   covr_coverage: 0"},{"path":[]},{"path":"https://pharmar.github.io/riskassessment/articles/Deployment.html","id":"shinyapps-io","dir":"Articles","previous_headings":"Deployment options","what":"shinyapps.io","title":"Deployment","text":"Beware: shinyapps.io offer persistent storage riskassessment’s SQLite database logs. Thus, likely viable deployment option organization group. example, demo application (hosted shinyapps.io) contains pre-prepared database packages can’t permanently altered. CAN altered within session, changes persist outside session.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/Deployment.html","id":"posit-connect-shiny-server","dir":"Articles","previous_headings":"Deployment options","what":"Posit Connect & Shiny Server","title":"Deployment","text":"server, want save files disk, ’ll need set write permissions accordingly folder want save database, logs, auto-decision json file. Posit Connect, need use absolute path specify directory save files. can find information : Persistent Storage Posit Connect.  Beyond , ’s important note strongly encourage deploying app take advantage renv.lock file used maintain package version dependencies. information use renv.lock general dev philosophy pertains package management, please read “Using renv” article. Highly related, encourage use git-backed deployment possible. , immediately update/sync package dependencies using renv, may want run rsconnect::writeManifest() deploying dedicated branch. convenience, maintain current manifest.json follow renv.lock file GitHub repo. , ’ve forked application, able deploy latest version app -, directly master branch. information git-backed deployment & manifest files, please read Posit article git-backed content.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/Deployment.html","id":"shinyproxy","dir":"Articles","previous_headings":"Deployment options","what":"ShinyProxy","title":"Deployment","text":"ShinyProxy, can use Docker volume write files outside application container. application.yml, use can something like specs describing application: container-volumes: [ “/var/log/shinylogs:/root/logs” ] /var/log/shinylogs directory server deploy applications ShinyProxy. /root/logs directory inside Docker image.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/Deployment_V0.1.1.html","id":"the-database-sqlite-file","dir":"Articles","previous_headings":"","what":"The database.sqlite file","title":"Deployment V0.1.1","text":"riskassessment::run_app() function ran, code base check database.sqlite file exists, doesn’t, several tables initiated create database just app launches. Note user authority name database file whatever like using assessment_db_name argument run_app(). addition, can include file path preceding file name wish move location database away root directory. example, following code create database called “test_database.sqlite” dev/ folder: time vignette authored, database initialize following tables NULL values: comments: stores user comments, including user names associated comment entry, comment type, timestamp community_usage_metrics: stores CRAN package downloads per month metric: stores metric info, including riskmetric name, label, short description, type, weight package_metrics: stores package-specific rismetric metrics package: Contains package information, like name, version, maintainer, etc. also contains riskmetric score, weighted score, decision, timestamp. one exception : metric table populated data via initialize_metric_table.sql file. user deploying app wants enter certain weights prior launching application, good place . example, org wants place heavier weight “has_vignettes”, can increase weight value accordingly. course, can still application, require manual change app launched. Similarly, want ignore certain metric little value organization, give value zero . Note: changes/ updates occur tables new release riskassessment, may need delete database file re-running app. changes announced ‘breaking changes’ app. , remember save copy current database file another directory backup purposes.","code":"run_app(assessment_db_name = './dev/test_database.sqlite')"},{"path":"https://pharmar.github.io/riskassessment/articles/Deployment_V0.1.1.html","id":"the-loggit-json-file","dir":"Articles","previous_headings":"","what":"The loggit.json file","title":"Deployment V0.1.1","text":"mentioned previously, loggit.json file initiated track general actions performed application, especially impact change database.sqlite file. time vignette authored, ’s summary actions logged: App start User log-ins Enabling/ Disabling changing automated decision rules Decisions initiated users decision automation rules, including pkgs added removed database, issues process, like absence data support certain metrics Re-weighting pkg metrics database issues conflicts may arise loggit “transaction” recorded contains lot info, notably, contain timestamp, record type (“info”, “warn”, “error”), message. database transactions, message usually include query executed. log entries always printed R console convenience. example: Feel free use information see fit!","code":"riskassessment::run_app() > [1] \"Log file set to loggit.json\" > Listening on http://127.0.0.1:4097 > {\"timestamp\": \"2023-03-20T11:46:23-0400\", \"log_lvl\": \"INFO\", \"log_msg\": \"User admin signed on as admin\"} > {\"timestamp\": \"2023-03-20T11:46:33-0400\", \"log_lvl\": \"INFO\", \"log_msg\": \"The following decision rules were implemented by admin (admin): Medium = (0.33__COMMA__ 0.66]; Low = (0__COMMA__ 0.33]; High = (0.66__COMMA__ 1].\"}"},{"path":"https://pharmar.github.io/riskassessment/articles/Deployment_V0.1.1.html","id":"the-auto_decisions-json-file","dir":"Articles","previous_headings":"","what":"The auto_decisions.json file","title":"Deployment V0.1.1","text":"riskassessment::run_app() executed, search performed see exists auto_decisions.json file root directory. Without file, empty one automatically created. file used keep track decision automation rules. add & edit rules app, json file update accordingly, keeping track categories risk score range. example, following json file coordinates ranges displayed app:","code":"{\"Medium\":[0.33,0.66],\"Low\":[0,0.33],\"High\":[0.66,1]}"},{"path":[]},{"path":"https://pharmar.github.io/riskassessment/articles/Deployment_V0.1.1.html","id":"shinyapps-io","dir":"Articles","previous_headings":"Deployment options","what":"shinyapps.io","title":"Deployment V0.1.1","text":"Beware: shinyapps.io offer persistent storage riskassessment’s SQLite database logs. Thus, likely viable deployment option organization group. example, demo application (hosted shinyapps.io) contains pre-prepared database packages can’t permanently altered. CAN altered within session, changes persist outside session.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/Deployment_V0.1.1.html","id":"posit-connect-shiny-server","dir":"Articles","previous_headings":"Deployment options","what":"Posit Connect & Shiny Server","title":"Deployment V0.1.1","text":"server, want save files disk, ’ll need set write permissions accordingly folder want save database, logs, auto-decision json file. Posit Connect, need use absolute path specify directory save files. can find information : Persistent Storage Posit Connect.  Beyond , ’s important note strongly encourage deploying app take advantage renv.lock file used maintain package version dependencies. information use renv.lock general dev philosophy pertains package management, please read “Using renv” article. Highly related, encourage use git-backed deployment possible. , immediately update/sync package dependencies using renv, may want run rsconnect::writeManifest() deploying dedicated branch. information git-backed deployment & manifest files, please read Posit article git-backed content.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/Deployment_V0.1.1.html","id":"shinyproxy","dir":"Articles","previous_headings":"Deployment options","what":"ShinyProxy","title":"Deployment V0.1.1","text":"ShinyProxy, can use Docker volume write files outside application container. application.yml, use can something like specs describing application: container-volumes: [ “/var/log/shinylogs:/root/logs” ] /var/log/shinylogs directory server deploy applications ShinyProxy. /root/logs directory inside Docker image.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/User_Roles_and_Privileges.html","id":"privileges","dir":"Articles","previous_headings":"","what":"Privileges","title":"User Roles and Privileges","text":"time vignette authored, eight different privileges can assigned role: Administrator (admin): manages users application Weight Adjustment (weight_adjust): manages weights applied riskmetric risk calculation Automated Decision Adjustment (auto_decision_adjust): manages decision automation rules decision category display colors Final Decision (final_decision): makes final decisions regarding packages Revert Decision (revert_decision): can undo final decisions made regarding packages Add Packages (add_package): adds packages consideration Delete Packages (delete_package): can remove packages consideration Overall Commentator (overall_comment): can add/edit overall comment summary package General Commentator (general_comment): can add maintenance community metric comments","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/User_Roles_and_Privileges.html","id":"administrator","dir":"Articles","previous_headings":"Privileges","what":"Administrator","title":"User Roles and Privileges","text":"Basically, admin privilege allows user manage credentials privileges users. credential-heavy features admin privilege discussed length “Credential Manager” guide. Please reference vignette information. return top","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/User_Roles_and_Privileges.html","id":"weight-adjustment","dir":"Articles","previous_headings":"Privileges","what":"Weight Adjustment","title":"User Roles and Privileges","text":"weight_adjust privilege allows user change weights applied riskmetric risk calculation. options can found Assessment Reweighting Administrative Tools tab. high level view:  three buttons page: CONFIRM top right, DOWNLOAD middle left, UPDATE bottom left.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/User_Roles_and_Privileges.html","id":"download-database","dir":"Articles","previous_headings":"Privileges > Weight Adjustment","what":"Download Database","title":"User Roles and Privileges","text":"First, simplest: DOWNLOAD database button.   clicked, button download copy current database (default, called “database.sqlite”). app developers recommend anytime plan make integral changes database (like changing metric weights), anything else.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/User_Roles_and_Privileges.html","id":"updating-weights","dir":"Articles","previous_headings":"Privileges > Weight Adjustment","what":"Updating Weights","title":"User Roles and Privileges","text":"CONFIRM button allows view existing change metric weights used calculate risk score using riskmemtric.   can either select metric Select metric dropdown box select row “CURRENT RISK SCORE WEIGHTS METRIC” table. metric selected, enter new (numeric) weight “Choose new weight” box click CONFIRM button. ’ll notice row change appear highlighted, showing old weight value new weight value:   updated least one metric weight, UPDATE button enabled, allowing apply new weights re-calculated risk package. ’ve made final re-weighting changes, can click “Update” button pictured . Note weight changes take effect packages database, updating risk score .   click UPDATE get confirmation modal, reminding “updating risk metrics reverted”, strongly recommending download copy current database first clicking SUBMIT. modal also details actions take effect app submit changes. Note starting Version 1.0.0, re-calculation stored riskmetric assessments, re-assessment.   click SUBMIT modal dialog box appear indicating applying weights updating risk scores package uploaded. followed brief “updates completed” message.   Now go database overview tab confirm risk scores updated. can also view new weights, including standardized weight Assessment Criteria tab. return top","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/User_Roles_and_Privileges.html","id":"automated-decision-adjustment","dir":"Articles","previous_headings":"Privileges","what":"Automated Decision Adjustment","title":"User Roles and Privileges","text":"Users auto_decision_adjust privilege can edit decision automation rules decision category colors. organization black white rules package risk decisions based solely riskmetric scores, decision automation . leveraged, help automatically classify packages “Low Risk”, “Medium Risk”, “High Risk” decision categories upon upload (default configuration). current automation rules accessible two locations: ‘Upload Package’ Risk Assessment tab & ‘Decision Categories’ Database tab. get started, click small  (gear) button upper right hand corner either section.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/User_Roles_and_Privileges.html","id":"select-category-colors","dir":"Articles","previous_headings":"Privileges > Automated Decision Adjustment","what":"Select Category Colors","title":"User Roles and Privileges","text":"change color one decision categories, select new color either typing desired hexidecimal code use color input.  apply changes, click APPLY COLORS. pop-ask user review confirm selection: modal contains summary decision categories respective new colors. happy selections, simply click SUBMIT database application updated selections.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/User_Roles_and_Privileges.html","id":"automate-decision-by-risk-score","dir":"Articles","previous_headings":"Privileges > Automated Decision Adjustment","what":"Automate Decision by Risk Score","title":"User Roles and Privileges","text":"decision rules applied, ’ll see following decision categories adjacent empty check boxes. setting rules organization, can choose much little automation desired.   example, want set automatic decision “High Risk” scores, need select check box make risk score designation / cut value. , every time package uploaded risk score > 0.67, automatically receive decision label: “High Risk” saves review team time mental capacity reviewing large groups packages.   Similarly, package risk thresholds mapped decision category, apply ! user interface won’t allow slider ranges overlap, allow gaps range. example , adopt automatic decisions packages risk scores less 0.33 greater .67. fictitious example, let’s say organization policy package whose risk score falls 0.33 0.67 need reviewed manually.   apply changes, click APPLY DECISION RULES. pop-ask user review confirm selected automation rules:   Upon clicking submit, automation rules stored users see ‘Upload Package’ tab. uploading new set packages, can see ‘Summary Uploaded Package(s)’ now includes summary decisions made category automatically assigned. example , can see 10 packages uploaded, 7 automatic decisions made: six received “low risk” designation one labeled “high risk”. summary table, can note risk score decision right-hand side. can also observe packages weren’t found don’t exist CRAN.   ‘PACKAGE CONTROL PANEL’, select one packages decision made, see ‘Status’ changed “Reviewed” risk decision slider adjusted accordingly disabled. addition, ‘Overall Comment’ submitted, stating decision made driven via automation rules.  return top","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/User_Roles_and_Privileges.html","id":"final-decision","dir":"Articles","previous_headings":"Privileges","what":"Final Decision","title":"User Roles and Privileges","text":"name suggests, user final_decision privilege can make final decisions category package assigned. Overall comments regarding package also tied privilege.   return top","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/User_Roles_and_Privileges.html","id":"revert-decision","dir":"Articles","previous_headings":"Privileges","what":"Revert Decision","title":"User Roles and Privileges","text":"user revert_decision privilege can undo final decision made. set package’s status “review” re-enable “overall comments” regarding decision.   return top","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/User_Roles_and_Privileges.html","id":"add-packages","dir":"Articles","previous_headings":"Privileges","what":"Add Packages","title":"User Roles and Privileges","text":"user add_package privilege can upload packages database consideration.   return top","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/User_Roles_and_Privileges.html","id":"delete-packages","dir":"Articles","previous_headings":"Privileges","what":"Delete Packages","title":"User Roles and Privileges","text":"user delete_package privilege can remove packages consideration (database).   return top","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/User_Roles_and_Privileges.html","id":"overall-commentator","dir":"Articles","previous_headings":"Privileges","what":"Overall Commentator","title":"User Roles and Privileges","text":"user overall_comment privilege can add/edit two optional high-level summaries package: First, “Overall Comment”, located sidebar, outlet users specify quick synopsis related package decision, Package Summary, located “Build Report” tab, allows user compose long-form, open-ended summary evaluation / review process package interest Unlike maintenance community usage metrics, package can one entry “Overall Comment” “Package Summary”.   return top","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/User_Roles_and_Privileges.html","id":"general-commentator","dir":"Articles","previous_headings":"Privileges","what":"General Commentator","title":"User Roles and Privileges","text":"user general_comment privilege can add comments regarding maintenance community metrics package. meant provide suggestions justifications decision making.   return top","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/User_Roles_and_Privileges.html","id":"roles","dir":"Articles","previous_headings":"","what":"Roles","title":"User Roles and Privileges","text":"User roles group select privileges together providing users different, necessarily mutually exclusive, access application. default configuration contains four user roles: admin, lead, reviewer, viewer. snippet inst/db-config.yml file roles defined:   configuration, admin user access entire application, lead user access privileges except administrative ones (e.g. managing user credentials), reviewer privilege add packages consideration adding comments/descriptions, viewer can view current state assessment. organization can customize user roles support needs. information please reference “Deployment” guide. return top","code":"privileges:   admin: [admin, weight_adjust, auto_decision_adjust, final_decision, revert_decision, add_package, delete_package, overall_comment, general_comment]   lead: [weight_adjust, auto_decision_adjust, final_decision, revert_decision, add_package, delete_package, overall_comment, general_comment]   reviewer: [add_package, general_comment]   viewer:"},{"path":"https://pharmar.github.io/riskassessment/articles/dev_Using_SQLite_Command_Line.html","id":"about-sqlite","dir":"Articles","previous_headings":"","what":"About SQLite","title":"Using SQLite Command Line","text":"SQLite software library provides relational database management system. lite SQLite means lightweight terms setup, database administration, required resources. SQLite following noticeable features: self-contained, serverless, zero-configuration, transactional. information, see SQLite","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/dev_Using_SQLite_Command_Line.html","id":"why-sqlite","dir":"Articles","previous_headings":"","what":"Why SQLite?","title":"Using SQLite Command Line","text":"one obvious reason – riskassessment App data stored SQLite database. Also, one SQLite’s advantages can run nearly anywhere. vignette provide means accessing database outside riskassessment App.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/dev_Using_SQLite_Command_Line.html","id":"download-sqlite-tools","dir":"Articles","previous_headings":"","what":"Download SQLite tools","title":"Using SQLite Command Line","text":"Open download page SQLite Download Page work SQLite Windows, download command-line shell program shown screenshot . using Mac, need download one:   either case, downloaded file ZIP format size quite small.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/dev_Using_SQLite_Command_Line.html","id":"run-sqlite-tools","dir":"Articles","previous_headings":"","what":"Run SQLite tools","title":"Using SQLite Command Line","text":"Installing SQLite simple straightforward. Create new folder e.g., C:\\sqlite. Extract content .zip file downloaded previous section C:\\sqlite folder. see three programs shown :","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/dev_Using_SQLite_Command_Line.html","id":"open-the-command-line-window-","dir":"Articles","previous_headings":"","what":"Open the command line window.","title":"Using SQLite Command Line","text":"Windows, type “cmd” search bar.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/dev_Using_SQLite_Command_Line.html","id":"navigate-to-the-csqlite-folder-","dir":"Articles","previous_headings":"","what":"Navigate to the C:\\sqlite folder.","title":"Using SQLite Command Line","text":"Next, type sqlite3 press enter, see following output: Navigate directory containing riskassessment database. Note: app’s default behavior call database “database.sqlite”, unless ’ve specified otherwise using assessment_db_name arg run_app(). Next, use .open FILENAME command open . example: .open database.sqlite; show tables, type .tables show structure table, type .schema TABLE can also type .help sqlite> prompt see available commands. exit, type .quitor .exit","code":"C:\\cd c:\\sqlite C:\\sqlite> C:\\sqlite>sqlite3  SQLite version 3.33.0 2020-08-14 13:23:32  Enter \".help\" for usage hints.  Connected to a transient in-memory database.  Use \".open FILENAME\" to reopen on a persistent database.  sqlite> sqlite> .tables comments                 metric                   package_metrics community_usage_metrics  package sqlite> sqlite> .schema package_metrics CREATE TABLE package_metrics (   id           INTEGER PRIMARY KEY AUTOINCREMENT,   package_id   INT,    metric_id    INT,   value        CHAR,   /* value == 'pkg_metric_error' indicates an error. */   /* value == NA indicates metric is not applicable for this package. */   weight       REAL,   FOREIGN KEY (package_id) REFERENCES package(id),   FOREIGN KEY (metric_id) REFERENCES metric(id)); sqlite> sqlite> .help .archive ...             Manage SQL archives .auth ON|OFF             Show authorizer callbacks .backup ?DB? FILE        Backup DB (default \"main\") to FILE .bail on|off             Stop after hitting an error.  Default OFF .binary on|off           Turn binary output on or off.  Default OFF .cd DIRECTORY            Change the working directory to DIRECTORY .changes on|off          Show number of rows changed by SQL .check GLOB              Fail if output since .testcase does not match .clone NEWDB             Clone data into NEWDB from the existing database .databases               List names and files of attached databases .dbconfig ?op? ?val?     List or change sqlite3_db_config() options .dbinfo ?DB?             Show status information about the database .dump ?TABLE?            Render database content as SQL .echo on|off             Turn command echo on or off .eqp on|off|full|...     Enable or disable automatic EXPLAIN QUERY PLAN .excel                   Display the output of next command in spreadsheet ... additional output not displayed"},{"path":"https://pharmar.github.io/riskassessment/articles/dev_Using_SQLite_Command_Line.html","id":"command-line-shell","dir":"Articles","previous_headings":"","what":"Command Line Shell","title":"Using SQLite Command Line","text":"can also temporarily add C:\\sqlite Windows path. set PATH=%PATH%;C:\\sqlite Verify typing echo %PATH% riskassessment directory, can just enter following command line: sqlite3 database.sqlite see can also use system2 command execute SQLite commands RStudio command line. can build queries commands SQLite execute . info, see Command Line Shell SQLite","code":"SQLite version 3.33.0 2020-08-14 13:23:32 Enter \".help\" for usage hints. sqlite> > system2(\"C:/sqlite/sqlite3\", args =c(\"database.sqlite\", \".tables\", \".quit\")) comments                 metric                   package_metrics         community_usage_metrics  package > table_name <- \"package\" > query <- glue::glue(\"select * from { table_name } limit 1;\") > frst_row <- system2(\"C:/sqlite/sqlite3\", args =\"database.sqlite\", input = query, stdout = TRUE) >  > frst_row [1] \"1|glue|1.6.2|glue: Interpreted String Literals|An implementation of interpreted string literals, inspired by   Pythons Literal String Interpolation   <https://www.python.org/dev/peps/pep-0498/> and Docstrings   <https://www.python.org/dev/peps/pep-0257/> and Julias Triple-Quoted   String Literals   <https://docs.julialang.org/en/v1.3/manual/strings/#Triple-Quoted-String-Literals-1>.|Jennifer Bryan  <jenny at rstudio.com>|Jim Hester  [aut], Jennifer Bryan    [aut, cre], RStudio [cph, fnd]|MIT + file LICENSE|2022-02-24|0.11|||2022-02-24\""},{"path":"https://pharmar.github.io/riskassessment/articles/dev_Using_SQLite_Command_Line.html","id":"sqlitestudio","dir":"Articles","previous_headings":"","what":"SQLiteStudio","title":"Using SQLite Command Line","text":"SQLiteStudio tool free GUI tool managing SQLite databases. free, portable, intuitive, cross-platform. SQLite tool also provides important features work SQLite databases importing, exporting data various formats including CSV, XML, JSON. Visit SQLite Studio can download SQLiteStudio installer portable version visiting download page. , can extract (install) download file folder e.g., C: launch . following picture illustrates launch SQLiteStudio:","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/dev_renv.html","id":"overview","dir":"Articles","previous_headings":"","what":"Overview","title":"Developer onboarding - using renv","text":"renv package provides project-local R dependency management projects. helps manage library paths (project-specific state) help isolate project’s R dependencies. renv package helps create reproducible environments R projects. make R packages isolated, portable reproducible.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/dev_renv.html","id":"actions-performed-only-once-in-the-repo","dir":"Articles","previous_headings":"","what":"Actions performed only once in the repo","title":"Developer onboarding - using renv","text":"First someone initialized new project-local environment private R library - can done via renv::init(). action result creation lockfile - named renv.lock root directory. lock file contains ton environment metadata, including developers installed packages & versions, plus repository source packages installed (.e. CRAN, GitHub, RSPM, etc). ’s important note dev team use repo source point production CRAN, want stable (aka unchanging) source pkgs. addition, lockfile () upgraded need important new feature relies latest version new existing pkg lock file. developer working within repo first time need sync packages stored renv.lock file. first time , ’ll need run renv::activate() ask confirm decision. Note new pkg installations impact R project, R system library stored elsewhere.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/dev_renv.html","id":"if-new-packages-installations-are-needed","dir":"Articles","previous_headings":"","what":"If new packages installations are needed","title":"Developer onboarding - using renv","text":"new dependencies needed, can save current state project library renv::snapshot(). However, pkg changes must expressly documented justified PR’s comments section considered ready review. Without , reviewer reject & request changes PR immediately. dev team’s philosophy renv.lock file () upgraded need important new feature/functionality relies different version new existing pkg. Even updating pkg, R sometimes ask want upgrade packages, seen . always say “3: None” possible.    just want test new package committing lockfile, can . Go ahead install package interest want revert back pkg line stored lock file anytime, just run renv::restore(). Similarly, anytime fellow developer(s) submit PR change lock file, ’ll need run renv::restore() sync development rest team. time sync renv.lock file, can run renv::status() see packages ahead behind lock file.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/dev_renv.html","id":"how-to-ignore-files-pkgs-in-the-lock-file","dir":"Articles","previous_headings":"","what":"How to ignore files & pkgs in the lock file","title":"Developer onboarding - using renv","text":"default renv ignores files stated .gitignore file. want extend , can use .renvignore file - specified similar .gitignore file. addition, can ignore package renv thinks need add lock file using following command: renv::settings$ignored.packages(\"<<package name>>\")","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/dev_renv.html","id":"cache-location-on-different-operating-systems","dir":"Articles","previous_headings":"","what":"Cache Location on different Operating Systems","title":"Developer onboarding - using renv","text":"Linux ~/.local/share/renv macOS ~/Library/Application Support/renv Windows %LOCALAPPDATA%/renv","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/dev_renv.html","id":"references","dir":"Articles","previous_headings":"","what":"References","title":"Developer onboarding - using renv","text":"github.io/renv/ Introduction renv","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/riskassessment.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"Get Started with {riskassessment}","text":"Welcome! guide help users get started riskassessment application first time. information deploy application, please reference Deployment guide. note: guide assumes already downloaded riskassessment package & ’s dependencies following installation instructions.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/riskassessment.html","id":"run-deploy-app-r","dir":"Articles","previous_headings":"","what":"Run / Deploy app.R","title":"Get Started with {riskassessment}","text":"application already deployed, can skip step! installed riskassessment package, now able run app locally using provided app.R file. applicable, can specify application options file, using either options() arguments run_app() function (run ?riskassessment::run_app learn ). However, purposes guide, ’ll run function -, accepting defaults: Running code launch application doesn’t already exist, create initial database authentication.","code":"# launch the application riskassessment::run_app()"},{"path":"https://pharmar.github.io/riskassessment/articles/riskassessment.html","id":"first-time-log-in","dir":"Articles","previous_headings":"","what":"First time log in","title":"Get Started with {riskassessment}","text":"first page ’ll see authentication screen default note bottom:  NOTE: LOG FIRST TIME, USE ADMIN USER: ADMIN PASSWORD QWERTY1. recall, application acts central hub organization review assess risk R packages, thus establishing users specific roles vital. start, application needs admin user.   admin user asked change password immediately. supplying new secure password, click “UPDATE NEW PASSWORD”. password successfully updated, ’ll prompted “LOGIN” new credentials.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/riskassessment.html","id":"subsequent-logins","dir":"Articles","previous_headings":"","what":"Subsequent logins","title":"Get Started with {riskassessment}","text":"designated admin user(s) special privileges duties application, including limited creating new users, admin non-admin roles. admins, please see article titled “Credential Manager” create new users. non-admin roles, receive temporary password initial log , ’ll prompted change immediately upon first visit app. subsequent visits, won’t worry first-time log procedures!","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/riskassessment.html","id":"welcome-to-the-app","dir":"Articles","previous_headings":"","what":"Welcome to the app!","title":"Get Started with {riskassessment}","text":"Upon successful log , ’ll notice many tabs panels.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/riskassessment.html","id":"self-guided-tours","dir":"Articles","previous_headings":"Welcome to the app!","what":"Self-guided tours","title":"Get Started with {riskassessment}","text":"Throughout app, small help buttons strategically placed upper right-hand corners page. clicked, empower users walk UI elements visible -screen desired pace. Consider personal tour guide need quick reminder “?”.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/riskassessment.html","id":"upload-a-package","dir":"Articles","previous_headings":"","what":"Upload a package","title":"Get Started with {riskassessment}","text":"Now main event - let’s upload packages review & assess organization. ’s first time using app, empty database initialized app launch populated packages, riskmetric outputs, organization’s assessment preferences. begin filling database package info, ’ll need start upload list packages want review. Risk Assessment tab, main panel titled, R PACKAGE RISK ASSESSMENT APP four tabs . default, ’ll directed Upload Package tab. Uploading packages can done manually typing one () package names prompt , long list packages asses, may convenient upload CSV file package names. CSV file requires two columns: “package” “version.” However, right now riskmetric can tackle current version, version column ignored. meantime, can make life easier setting version “0.0.0” packages CSV. Additionally, third column “decision” can included. can helpful organization already list packages approved use. simplified example acceptable CSV file: Alternatively, may prefer test app typing package, “glue” prompt. Notice text input pre-populate CRAN packages upon click, thus forget spelling case package, auto-complete feature can assist . ready, select red “>” button progress modal like one appear indicating process generating package info various sources begun app start inserting information database. Upon completion, “Summary Uploaded Packages” section display. lists total packages uploaded, number packages new database, number undiscovered (probably misspelled) packages, number duplicate packages, .e. packages already existed database.","code":"package,version stringr,0.0.0 tidyr,0.0.0"},{"path":"https://pharmar.github.io/riskassessment/articles/riskassessment.html","id":"decision-automation","dir":"Articles","previous_headings":"","what":"Decision Automation","title":"Get Started with {riskassessment}","text":"organization black white rules package risk decisions based solely riskmetric scores, decision automation . leveraged, help automatically classify packages “Low”, “Medium”, “High” risk decision categories upon upload. automation saves review team time mental capacity reviewing large groups packages. current automation rules always displayed ‘Upload Package’ tab. Please note admin users necessary privileges edit. get started, click small gear button upper left hand corner   fictitious example , let’s say admin user adopts automated decision rules packages risk scores less 0.33 greater .66. Perhaps organization policy mandates package whose risk score falls 0.33 0.66 need reviewed manually. uploading new CSV packages, can see ‘Summary Uploaded Package(s)’ displays number decisions made overall risk category. , can see 10 packages uploaded, 5 automatic decisions made: four received “low” designation one labeled “high” risk. summary table, decisions displayed respective risk scores right-hand side. can also observe packages weren’t found don’t exist CRAN.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/riskassessment.html","id":"sidebar","dir":"Articles","previous_headings":"","what":"Sidebar","title":"Get Started with {riskassessment}","text":"Now database populated package data, direct attention PACKAGE CONTROL PANEL left select package (glue) list. package selected, VERSION, STATUS RISK boxes populated information. now, latest version package displayed. Since decision endorse reject package hasn’t made yet, STATUS “Review”. Third, RISK box contains riskmetric score, represented number 0 (low risk) 1 (high risk). also two submission buttons : SUBMIT DECISION SUBMIT OVERALL COMMENT. goal thorough review info contain application, user well informed enough categorize package’s risk either “low”, “medium”, “high” risk using slider. Clicking submit completes review package organization can undone admin user. ’re looking submit something less formal, submitting decision, consider submitting “overall comment” summarizing high level thoughts package. Though ’s required, ’s recommended always submit “overall comment” submitting final decision.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/riskassessment.html","id":"package-metrics-review-tabs","dir":"Articles","previous_headings":"","what":"‘Package Metrics’ Review Tabs","title":"Get Started with {riskassessment}","text":"Package Metrics tab contains riskmetric derived assessments one place, consolidates different like-kind groups convenience-sake. , metrics sorted either “Maintenance” “Community Usage” categories. latest version app, 3rd category added better support analysis “Dependencies”, can selected via drop top tab: ’s tabs bulk automated review occurs metric provides context determines final riskmetric score. highly encourage users become familiar metrics decide important organization. available riskmetric, riskassessment allows admin users set organization-wide metric weights risk score based meaningful metrics, reduces influence less important metrics. Thus, metric un-important org, highly recommend weighting 0. learn options, please read “Metric weights configuration” guide.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/riskassessment.html","id":"maintenance-metrics","dir":"Articles","previous_headings":"‘Package Metrics’ Review Tabs","what":"Maintenance Metrics","title":"Get Started with {riskassessment}","text":"look Maintenance Metrics output “glue” package: metric tab measures something related package maintenance best practices, whether storing code public URL, providing vignettes guide users, package authors sufficiently giving attention bugs. Note metrics report assessment “Found”. ’s application uses “pkg_cran_remote” source compiling metrics, capability gather info possible metrics. -going effort build information remote metrics. learn , please explore package assessment topics riskmetric documentation. Note can add replace comments Maintenance Metrics package, review paste comments made users. great platform form opinions, write others organization read consider evaluation.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/riskassessment.html","id":"community-usage-metrics","dir":"Articles","previous_headings":"‘Package Metrics’ Review Tabs","what":"Community Usage Metrics","title":"Get Started with {riskassessment}","text":"first look Community Usage Metrics “glue” package:   metric tab measures something related package’s usage community. user community plays important role open source software development. words, exposure package community, ad-hoc testing exposed . time “better packages” tend rise top, leading downloads increased exposure. Note riskmetric considers metric called Number download last year Reverse Dependencies risk score calculation. data presented tab accessories help user explore idea community usage. Notably, tab includes highly interactive visual, shows number downloads month since package first released. information metrics, explore package assessments riskmetric documentation. , can add replace comments Community Usage metrics package.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/riskassessment.html","id":"the-source-explorer-tab","dir":"Articles","previous_headings":"","what":"The ‘Source Explorer’ Tab","title":"Get Started with {riskassessment}","text":"Introduced v2.0.0 riskassessment, Source Explorer tab offers users manual, hands-approach assessing packages exploring source contents package. Just developer forking repository explore code, can now page files bundled stored CRAN. exceptions, however: certain file types don’t display well file browser, like RDS example, aren’t compatible. ; example, viewing DESCRIPTION file (doesn’t extension) glue package. possibilities truly endless access source code: can browse R scripts containing exported (non-exported) functions, read contents LICENSE file, even explore tests/ folder inspect robustness ’s unit tests. Just expand file tree left hand side reveal contents folders.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/riskassessment.html","id":"the-build-report-tab","dir":"Articles","previous_headings":"","what":"The ‘Build Report’ Tab","title":"Get Started with {riskassessment}","text":"top portion Build Report tab. tab pulls information viewed previous tabs consolidates easy browse report, downloaded HTML, DOCX, PDF. However, first gives user ample control care see report using check boxes, pre-checked default. Optionally, “Package Summary” section allows reviewers log information explicit acknowledged metrics, plots, risk-based decision, comments. field allow organizations satisfy custom documentation needs app privy . Note one summary can logged per package, submitted, add another, must edit existing summary acceptable.   Directly beneath configurations “report preview” can see first-hand configs & review efforts impact report download.  addition metric info, can see contains vital metadata assessment performed app. quick view metadata referenced . ’s vital understand context report & score calculated. Users encouraged send information rich reports choose, especially savvy riskassessment app… yet.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/riskassessment.html","id":"make-a-decision","dir":"Articles","previous_headings":"","what":"Make a decision","title":"Get Started with {riskassessment}","text":", ’ve uploaded package, reviewed ’s metrics, package score, double-checked metric weights, even read co-workers comments. ’s really nothing left make final decision. waiting ! Let’s ! Head Package Control Panel. First ’ll start “Overall Comment”. Write words ’ve learned evaluation recommend brief succinct .   clicking submit, ’ll receive prompt just confirms wrote. Click dismiss now turn attention decision slider, options “Low”, “Medium”, “High”. Consider organization may treat category? example, “Low” might mean ’s permitted use regulatory environments, “Medium” may mean package isn’t fully endorsed yet, needs stay holding patter. “High” course means rejection.   purposes guide, submitted decision selection “Low” received following dialogue box asking us confirm decision:   clicking ‘Submit’, ’ll notice STATUS updated “REVIEWED” decision slider now disabled & grayed . logged admin user, button now displays “RESET DECISION” non-admin users option.   Congratulations! ’ve reviewed first package! goal, accomplished . Now keep going, waiting ? time guide authored, 19,038 packages CRAN organization may want use !","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/riskassessment.html","id":"other-tabs","dir":"Articles","previous_headings":"","what":"Other Tabs","title":"Get Started with {riskassessment}","text":"may noticed navigation tabs top app contain following four tabs.   work performed first tab: Risk Assessment. ’ll painfully brief touch tabs , just know -depth guides exist .","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/riskassessment.html","id":"database","dir":"Articles","previous_headings":"Other Tabs","what":"Database","title":"Get Started with {riskassessment}","text":"second tab, Database shows, package loaded, package name version, ’s riskmetric score, whether decision made, decision, timestamp last comment provided. Reports (either .html, .docx, .pdf format) can downloaded selected package(s). multiple packages selected, really helpful","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/riskassessment.html","id":"assessment-criteria","dir":"Articles","previous_headings":"Other Tabs","what":"Assessment Criteria","title":"Get Started with {riskassessment}","text":"third tab, Assessment Criteria provides detailed description assessment criteria used Risk Calculation, Maintenance Metrics, Community Usage Metrics, Testing metrics. metric even short description included riskmetric. Risk Calculation tab shown . Browse tab information.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/riskassessment.html","id":"administrative-tools","dir":"Articles","previous_headings":"Other Tabs","what":"Administrative Tools","title":"Get Started with {riskassessment}","text":"fourth tab, Administrative tools, contains two sub-tabs: Credential Manager Assessment Reweighting. former allows admin users add delete users well change passwords others. details provided “Credential Manager” guide   Assessment Reweighting tab admin users fine tune package risk score generated riskmetric manipulating value placed metrics assessed app. Changes made apply packages database, plus packages uploaded future. details provided “User Roles Privileges” guide.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/riskassessment.html","id":"where-to-go-from-here","dir":"Articles","previous_headings":"","what":"Where to go from here?","title":"Get Started with {riskassessment}","text":"Check riskmetric riskassessment presentations www.pharmar.org/present/. read prepared guides boost knowledge become power user!","code":""},{"path":"https://pharmar.github.io/riskassessment/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Aaron Clark. Author, maintainer. Jeff Thompson. Author.            Co-Lead Robert Krajcik. Author. Lars Andersen. Author. Andrew Borgman. Author. Munshi Imran Hossain. Contributor. Scott Schumacker. Contributor. Marly Gotti. Author. Maya Gans. Author. Aravind Reddy Kallem. Author. Eduardo Almeida. Contributor. Narayanan Iyer. Contributor. Fission Labs India Pvt Ltd. Author. PSI special interest group Application Implementation Methodologies Statistics. Copyright holder, funder. R Validation Hub. Copyright holder, funder. GSK contributors. Contributor.            Author 'pharmaR/pkg_explorer' repo Appsilon. Contributor.","code":""},{"path":"https://pharmar.github.io/riskassessment/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Clark , Thompson J, Krajcik R, Andersen L, Borgman , Gotti M, Gans M, Kallem , Fission Labs India Pvt Ltd (2024). riskassessment: web app designed interface 'riskmetric' package. R package version 3.1.0, https://pharmar.github.io/riskassessment/, https://github.com/pharmaR/riskassessment.","code":"@Manual{,   title = {riskassessment: A web app designed to interface with the `riskmetric` package},   author = {Aaron Clark and Jeff Thompson and Robert Krajcik and Lars Andersen and Andrew Borgman and Marly Gotti and Maya Gans and Aravind Reddy Kallem and {Fission Labs India Pvt Ltd}},   year = {2024},   note = {R package version 3.1.0, https://pharmar.github.io/riskassessment/},   url = {https://github.com/pharmaR/riskassessment}, }"},{"path":"https://pharmar.github.io/riskassessment/index.html","id":"the-riskassessment-application-","dir":"","previous_headings":"","what":"A web app designed to interface with the `riskmetric` package","title":"A web app designed to interface with the `riskmetric` package","text":"riskassessment R package containing shiny front-end augment utility riskmetric package within organizational context. ’re honored announce app recently awarded title “Best App” Shiny Conf 2023 (see Recognition section ).   riskmetric framework quantify R package’s “risk use” assessing number meaningful metrics designed evaluate package development best practices, code documentation, community engagement, development sustainability. Together, riskassessment app riskmetric package aim provide context validation within regulated industries. app extends functionality riskmetric allowing reviewer : analyze riskmetric output without need write code R contribute personalized comments value individual metrics categorize package overall assessment (.e., low, medium, high risk) based subjective opinions tabulating user(s) consensus evaluating metric output download static reports package risk, metrics outputs, reviewer summary & comments, plus store assessments database future viewing historical backup user authentication privileges & admin-defined roles manage users tasks performed app","code":""},{"path":"https://pharmar.github.io/riskassessment/index.html","id":"echo-ing-riskmetrics-approach-to-validation-","dir":"","previous_headings":"","what":"Echo-ing {riskmetric}’s Approach to Validation","title":"A web app designed to interface with the `riskmetric` package","text":"Validation can serve umbrella various terms, admittedly, companies diverge may “correct approach”. riskassessment app built rismetric-foundation, whose developers follow validation philosophy proposed white paper published R Validation Hub. , scope riskassessment riskmetric designed support decision making view point. full robustness reliability software may (likely ) require deeper inspection reviewing party. Note: Development riskassessment riskmetric made possible thanks R Validation Hub, collaboration support adoption R within biopharmaceutical regulatory setting.","code":""},{"path":"https://pharmar.github.io/riskassessment/index.html","id":"usage","dir":"","previous_headings":"","what":"Usage","title":"A web app designed to interface with the `riskmetric` package","text":"new using riskassessment app, welcome! ’d highly encourage start exploring demo version app currently deployed shinyapps.io. , ’ll find number pre-loaded packages just waiting assessed. Hands experience help become familiar general layout app poke around explore. said, immediately recognize app requires authentication, since ’s intended use within organization. several pre-defined roles, important admin user. default, admin can add/delete users, download entire copy database, modify metric weights used calculation risk scores, define custom decision categories, automation rules base risk scores. demo version app tells prompts log initially. However, launch app.R file locally, admin user leverage password QWERTY1 initially. log credential, app immediately prompt change password repeat process new credentials. want quick overview project demo application, highly recommend watching following video walk Shiny Conf 2023. conference, riskassessment voted “best application” conference attendees! app also featured Rstudio::Global 2021.","code":""},{"path":"https://pharmar.github.io/riskassessment/index.html","id":"installation","dir":"","previous_headings":"Usage","what":"Installation","title":"A web app designed to interface with the `riskmetric` package","text":"recommend run/deploy application controlled development environment. course, can install latest version GitHub using code , doesn’t take consideration environment dependencies… example, using different version riskmetric dev team? Thus, development team can’t guarantee ’s stability, recommend clone repo’s R project locally instead. cloned/ forked, run following code order take advantage renv.lock file set’s project dependencies: step complete, can simply run contents app.R launch /deploy application default settings! information dev philosophy pertains package management, please read “Using renv” article. , learn manipulate app’s configuration away defaults reading guide “Deployment” covers use app’s configuration file tailor app needs.","code":"# DON'T RUN THIS CODE! There's a better way! remotes::install_github(\"pharmaR/riskmetric\") remotes::install_github(\"pharmaR/riskassessment\")  # Run the application  riskassessment::run_app() # First, clone the repo from GitHub, then... # Get dependcies synced using {renv} renv::activate() renv::restore()"},{"path":"https://pharmar.github.io/riskassessment/index.html","id":"user-guides-and-user-feedback","dir":"","previous_headings":"","what":"User Guides and User Feedback","title":"A web app designed to interface with the `riskmetric` package","text":"’re constantly improving app ’s documentation. Please explore user guides developed date, available riskassessment documentation site. sure read ‘Get Started’ tab perhaps another article two! course, ever specific feedback developers, encounter problem / bug within app, recommend opening new issue GitHub ’ll address promptly.  also want align users big picture, strategic topics. Specifically, want hear groups ’ve built (currently building) R-package validation process, whether use riskmetric / riskassessment ! Ideally, goal form consensus companies regarding validation approach can make riskmetric riskassessment better. example, ’d love understand users currently weighting metrics used calculate package’s risk score. ’d also love learn companies leverage certain risk score thresholds make GxP environment inclusion (exclusion) decisions package. facilitate gathering information, ’ve created incredibly brief questionnaire let us know ’re .","code":""},{"path":"https://pharmar.github.io/riskassessment/index.html","id":"deployment","dir":"","previous_headings":"User Guides and User Feedback","what":"Deployment","title":"A web app designed to interface with the `riskmetric` package","text":"might expect, certain deployment environments offer persistent storage others . example, shinyapps.io . means even demo app ’s hosted shinyapps.io contains package database can’t permanently altered. ’s advantageous since organization needs continually add new packages, publish comments, make decisions packages. Thus, ’d recommend exploring deployment options (allow persistent storage): Shiny Server Posit Connect ShinyProxy information , highly recommend reading ‘Deployment’ article.","code":""},{"path":"https://pharmar.github.io/riskassessment/index.html","id":"recognition","dir":"","previous_headings":"User Guides and User Feedback","what":"Recognition","title":"A web app designed to interface with the `riskmetric` package","text":"March 2023, Appsilon hosted 2nd annual Shiny Conf fully virtual, boasting approximately 4k registrants. Aaron Clark, package maintainer R Validation Hub Executive member, presented riskassessment app work “Shiny Showcase” among 20+ app submissions. end conference, riskassessment awarded title “Best App” popular vote.","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/aboutInfoServer.html","id":null,"dir":"Reference","previous_headings":"","what":"Server Logic for 'About' Module — aboutInfoServer","title":"Server Logic for 'About' Module — aboutInfoServer","text":"Server Logic '' Module","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/aboutInfoServer.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Server Logic for 'About' Module — aboutInfoServer","text":"","code":"aboutInfoServer(id, metric_weights)"},{"path":"https://pharmar.github.io/riskassessment/reference/aboutInfoServer.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Server Logic for 'About' Module — aboutInfoServer","text":"id module id name metric_weights object outputted reweightViewServer()","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/aboutInfoUI.html","id":null,"dir":"Reference","previous_headings":"","what":"UI for 'About' Module — aboutInfoUI","title":"UI for 'About' Module — aboutInfoUI","text":"UI '' Module","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/aboutInfoUI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"UI for 'About' Module — aboutInfoUI","text":"","code":"aboutInfoUI(id)"},{"path":"https://pharmar.github.io/riskassessment/reference/aboutInfoUI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"UI for 'About' Module — aboutInfoUI","text":"id module id name","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/addCommentServer.html","id":null,"dir":"Reference","previous_headings":"","what":"addComment module's server logic — addCommentServer","title":"addComment module's server logic — addCommentServer","text":"addComment module's server logic","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/addCommentServer.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"addComment module's server logic — addCommentServer","text":"","code":"addCommentServer(id, metric_abrv, user, credentials, pkg_name)"},{"path":"https://pharmar.github.io/riskassessment/reference/addCommentServer.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"addComment module's server logic — addCommentServer","text":"id module id name metric_abrv placeholder pkg_name string name package user_name placeholder user_role placeholder","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/addCommentUI.html","id":null,"dir":"Reference","previous_headings":"","what":"The UI for the 'addComment' module — addCommentUI","title":"The UI for the 'addComment' module — addCommentUI","text":"Module display comments specified metric. comments update user inserts comments.","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/addCommentUI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The UI for the 'addComment' module — addCommentUI","text":"","code":"addCommentUI(id)"},{"path":"https://pharmar.github.io/riskassessment/reference/addCommentUI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The UI for the 'addComment' module — addCommentUI","text":"id module id name","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/add_shinymanager_auth.html","id":null,"dir":"Reference","previous_headings":"","what":"Add an Authentication Screen — add_shinymanager_auth","title":"Add an Authentication Screen — add_shinymanager_auth","text":"Adds authentication screen via shinymanager::secure_app().","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/add_shinymanager_auth.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add an Authentication Screen — add_shinymanager_auth","text":"","code":"add_shinymanager_auth(app_ui, app_ver, login_note)"},{"path":"https://pharmar.github.io/riskassessment/reference/add_shinymanager_auth.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add an Authentication Screen — add_shinymanager_auth","text":"app_ui app_ui function application. app_ver See identical param run_app(). login_note See identical param run_app().","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/add_tags.html","id":null,"dir":"Reference","previous_headings":"","what":"The 'Add tags' function — add_tags","title":"The 'Add tags' function — add_tags","text":"'Add tags' function","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/add_tags.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The 'Add tags' function — add_tags","text":"","code":"add_tags(ui, ...)"},{"path":"https://pharmar.github.io/riskassessment/reference/add_tags.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The 'Add tags' function — add_tags","text":"ui placeholder ... placeholder","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/app_theme.html","id":null,"dir":"Reference","previous_headings":"","what":"Application Theme — app_theme","title":"Application Theme — app_theme","text":"sets riskassessment Application theme object using bslib's bs_theme() function. app_theme object gets used run_app.R, addition app_ui.R","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/app_theme.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Application Theme — app_theme","text":"","code":"app_theme()"},{"path":"https://pharmar.github.io/riskassessment/reference/app_theme.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Application Theme — app_theme","text":"bs_theme object several classes","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/assessmentInfoServer.html","id":null,"dir":"Reference","previous_headings":"","what":"Server Logic for 'Assessment Info' Module — assessmentInfoServer","title":"Server Logic for 'Assessment Info' Module — assessmentInfoServer","text":"Server Logic 'Assessment Info' Module","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/assessmentInfoServer.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Server Logic for 'Assessment Info' Module — assessmentInfoServer","text":"","code":"assessmentInfoServer(id, metric_weights)"},{"path":"https://pharmar.github.io/riskassessment/reference/assessmentInfoServer.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Server Logic for 'Assessment Info' Module — assessmentInfoServer","text":"id module id name metric_weights placeholder","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/assessmentInfoUI.html","id":null,"dir":"Reference","previous_headings":"","what":"UI for 'Assessment Info' Module — assessmentInfoUI","title":"UI for 'Assessment Info' Module — assessmentInfoUI","text":"UI 'Assessment Info' Module","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/assessmentInfoUI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"UI for 'Assessment Info' Module — assessmentInfoUI","text":"","code":"assessmentInfoUI(id)"},{"path":"https://pharmar.github.io/riskassessment/reference/assessmentInfoUI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"UI for 'Assessment Info' Module — assessmentInfoUI","text":"id module id name","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/auto_font.html","id":null,"dir":"Reference","previous_headings":"","what":"Automatic font re-sizer — auto_font","title":"Automatic font re-sizer — auto_font","text":"function adjusts number (used font size) proportional length text string. longer text string, smaller font. Used MetricBox.R.","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/auto_font.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Automatic font re-sizer — auto_font","text":"","code":"auto_font(txt, txt_max = 45, size_min = 0.75, size_max = 1.5, num_bins = NULL)"},{"path":"https://pharmar.github.io/riskassessment/reference/auto_font.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Automatic font re-sizer — auto_font","text":"txt string txt_max integer specify length text considered \"long\" continue toggle font size size_min integer specifying smallest font size like see output size_max integer specifying largest font size like see output num_bins NULL (default), accepts integer bins continuous font size categorical one.","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/build_comm_cards.html","id":null,"dir":"Reference","previous_headings":"","what":"The 'Build Community Cards' function — build_comm_cards","title":"The 'Build Community Cards' function — build_comm_cards","text":"'Build Community Cards' function","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/build_comm_cards.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The 'Build Community Cards' function — build_comm_cards","text":"","code":"build_comm_cards(   data,   db_name = golem::get_golem_options(\"assessment_db_name\") )"},{"path":"https://pharmar.github.io/riskassessment/reference/build_comm_cards.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The 'Build Community Cards' function — build_comm_cards","text":"data data.frame","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/build_comm_plotly.html","id":null,"dir":"Reference","previous_headings":"","what":"Build a plotly of community usage metrics — build_comm_plotly","title":"Build a plotly of community usage metrics — build_comm_plotly","text":"Responsible building interactive {plotly} graphic containing trend line number CRAN pkg downloads month.","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/build_comm_plotly.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Build a plotly of community usage metrics — build_comm_plotly","text":"","code":"build_comm_plotly(data = NULL, pkg_name = NULL)"},{"path":"https://pharmar.github.io/riskassessment/reference/build_comm_plotly.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Build a plotly of community usage metrics — build_comm_plotly","text":"data data.frame containing monthly download data, built using generate_comm_data(). argument optional, NULL, pkg_name must provided. pkg_name string package name. parameter optional. pkg_name provided, data argument NULL.","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/build_comm_plotly.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Build a plotly of community usage metrics — build_comm_plotly","text":"plotly object interactive plotly object","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/build_comm_plotly.html","id":"example","dir":"Reference","previous_headings":"","what":"Example","title":"Build a plotly of community usage metrics — build_comm_plotly","text":"","code":"build_comm_plotly(pkg_name = \"ggplot2\")"},{"path":[]},{"path":"https://pharmar.github.io/riskassessment/reference/build_db_cards.html","id":null,"dir":"Reference","previous_headings":"","what":"The 'Build Database Cards' function — build_db_cards","title":"The 'Build Database Cards' function — build_db_cards","text":"'Build Database Cards' function","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/build_db_cards.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The 'Build Database Cards' function — build_db_cards","text":"","code":"build_db_cards(data)"},{"path":"https://pharmar.github.io/riskassessment/reference/build_db_cards.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The 'Build Database Cards' function — build_db_cards","text":"data data.frame","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/build_dep_cards.html","id":null,"dir":"Reference","previous_headings":"","what":"The 'Build Dependency Cards' function — build_dep_cards","title":"The 'Build Dependency Cards' function — build_dep_cards","text":"'Build Dependency Cards' function","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/build_dep_cards.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The 'Build Dependency Cards' function — build_dep_cards","text":"","code":"build_dep_cards(data, loaded, toggled)"},{"path":"https://pharmar.github.io/riskassessment/reference/build_dep_cards.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The 'Build Dependency Cards' function — build_dep_cards","text":"data data.frame loaded vector package names loaded db","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/communityMetricsServer.html","id":null,"dir":"Reference","previous_headings":"","what":"Community Usage Metrics server logic — communityMetricsServer","title":"Community Usage Metrics server logic — communityMetricsServer","text":"Community Usage Metrics server logic","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/communityMetricsServer.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Community Usage Metrics server logic — communityMetricsServer","text":"","code":"communityMetricsServer(id, selected_pkg, community_metrics, user, credentials)"},{"path":"https://pharmar.github.io/riskassessment/reference/communityMetricsServer.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Community Usage Metrics server logic — communityMetricsServer","text":"id module id name selected_pkg placeholder community_metrics placeholder user placeholder","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/communityMetricsUI.html","id":null,"dir":"Reference","previous_headings":"","what":"Community Usage Metrics UI function — communityMetricsUI","title":"Community Usage Metrics UI function — communityMetricsUI","text":"Community Usage Metrics UI function","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/communityMetricsUI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Community Usage Metrics UI function — communityMetricsUI","text":"","code":"communityMetricsUI(id)"},{"path":"https://pharmar.github.io/riskassessment/reference/communityMetricsUI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Community Usage Metrics UI function — communityMetricsUI","text":"id module id name","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/create_credentials_db.html","id":null,"dir":"Reference","previous_headings":"","what":"Create credentials database — create_credentials_db","title":"Create credentials database — create_credentials_db","text":"Note: credentials_db_name object assigned deployment user R/run_app.R","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/create_credentials_db.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create credentials database — create_credentials_db","text":"","code":"create_credentials_db(db_name, admin_role = \"\")"},{"path":"https://pharmar.github.io/riskassessment/reference/create_credentials_db.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create credentials database — create_credentials_db","text":"db_name string denoting name database admin_role string denoting initialized privileges admin","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/create_credentials_dev_db.html","id":null,"dir":"Reference","previous_headings":"","what":"Create credentials dev database — create_credentials_dev_db","title":"Create credentials dev database — create_credentials_dev_db","text":"Create credentials dev database","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/create_credentials_dev_db.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create credentials dev database — create_credentials_dev_db","text":"","code":"create_credentials_dev_db(db_name)"},{"path":"https://pharmar.github.io/riskassessment/reference/create_credentials_dev_db.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create credentials dev database — create_credentials_dev_db","text":"db_name string denoting name database","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/create_db.html","id":null,"dir":"Reference","previous_headings":"","what":"Create package database — create_db","title":"Create package database — create_db","text":"Note: database_name object assigned deployment users R/run_app.R","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/create_db.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create package database — create_db","text":"","code":"create_db(db_name)"},{"path":"https://pharmar.github.io/riskassessment/reference/create_db.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create package database — create_db","text":"db_name string denoting name database","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/databaseViewServer.html","id":null,"dir":"Reference","previous_headings":"","what":"Server logic for 'Database View' module — databaseViewServer","title":"Server logic for 'Database View' module — databaseViewServer","text":"Server logic 'Database View' module","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/databaseViewServer.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Server logic for 'Database View' module — databaseViewServer","text":"","code":"databaseViewServer(id, user, uploaded_pkgs, metric_weights, changes, parent)"},{"path":"https://pharmar.github.io/riskassessment/reference/databaseViewServer.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Server logic for 'Database View' module — databaseViewServer","text":"id module id name user user name uploaded_pkgs vector uploaded package names metric_weights reactive data.frame holding metric weights changes reactive value integer count parent parent (calling module) session information","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/databaseViewUI.html","id":null,"dir":"Reference","previous_headings":"","what":"UI for 'Database View' module — databaseViewUI","title":"UI for 'Database View' module — databaseViewUI","text":"UI 'Database View' module","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/databaseViewUI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"UI for 'Database View' module — databaseViewUI","text":"","code":"databaseViewUI(id)"},{"path":"https://pharmar.github.io/riskassessment/reference/databaseViewUI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"UI for 'Database View' module — databaseViewUI","text":"id module id name","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/generate_comm_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate Community Usage Data — generate_comm_data","title":"Generate Community Usage Data — generate_comm_data","text":"Extracts community usage metrics given package.","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/generate_comm_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate Community Usage Data — generate_comm_data","text":"","code":"generate_comm_data(pkg_name)"},{"path":"https://pharmar.github.io/riskassessment/reference/generate_comm_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate Community Usage Data — generate_comm_data","text":"pkg_name string containing name package.","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/generate_comm_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate Community Usage Data — generate_comm_data","text":"tibble community usage metrics data.frame includes downloads per month given pkg","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/generate_comm_data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Generate Community Usage Data — generate_comm_data","text":"","code":"if( interactive()) { ggplot_comm_df <- generate_comm_data(\"ggplot2\") head(ggplot_comm_df) }"},{"path":"https://pharmar.github.io/riskassessment/reference/getTimeStamp.html","id":null,"dir":"Reference","previous_headings":"","what":"getTimeStamp — getTimeStamp","title":"getTimeStamp — getTimeStamp","text":"Retrieves Sys.time(), transforms slightly","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/getTimeStamp.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"getTimeStamp — getTimeStamp","text":"","code":"getTimeStamp()"},{"path":"https://pharmar.github.io/riskassessment/reference/get_date_span.html","id":null,"dir":"Reference","previous_headings":"","what":"The 'Get Date Span' function — get_date_span","title":"The 'Get Date Span' function — get_date_span","text":"Function accepts start date optional end date ","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/get_date_span.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The 'Get Date Span' function — get_date_span","text":"","code":"get_date_span(start, end = get_Date())"},{"path":"https://pharmar.github.io/riskassessment/reference/get_date_span.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The 'Get Date Span' function — get_date_span","text":"start starting date end ending date","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/get_latest_pkg_info.html","id":null,"dir":"Reference","previous_headings":"","what":"Get the package general information from CRAN/local — get_latest_pkg_info","title":"Get the package general information from CRAN/local — get_latest_pkg_info","text":"Get package general information CRAN/local","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/get_latest_pkg_info.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get the package general information from CRAN/local — get_latest_pkg_info","text":"","code":"get_latest_pkg_info(pkg_name)"},{"path":"https://pharmar.github.io/riskassessment/reference/get_latest_pkg_info.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get the package general information from CRAN/local — get_latest_pkg_info","text":"pkg_name string name package","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/initialize_raa.html","id":null,"dir":"Reference","previous_headings":"","what":"Initialize riskassessment Application Settings — initialize_raa","title":"Initialize riskassessment Application Settings — initialize_raa","text":"sets environment running riskassessment Application. sets log file, initializes package database missing, initializes credentials database missing.","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/initialize_raa.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Initialize riskassessment Application Settings — initialize_raa","text":"","code":"initialize_raa(assess_db, cred_db, configuration)"},{"path":"https://pharmar.github.io/riskassessment/reference/initialize_raa.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Initialize riskassessment Application Settings — initialize_raa","text":"assess_db string denoting name assessment database. cred_db string denoting name credentials database. configuration list dictating configuration databases","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/initialize_raa.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Initialize riskassessment Application Settings — initialize_raa","text":"return value. function run side effects.","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/introJSServer.html","id":null,"dir":"Reference","previous_headings":"","what":"Server logic for introJS module — introJSServer","title":"Server logic for introJS module — introJSServer","text":"Server logic introJS module","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/introJSServer.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Server logic for introJS module — introJSServer","text":"","code":"introJSServer(id, text, user, credentials)"},{"path":"https://pharmar.github.io/riskassessment/reference/introJSServer.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Server logic for introJS module — introJSServer","text":"id module id text data.frame containing info step: element names, text strings guiding users, position place text relationship element. Please see R/introJSText.R data.frames populate argument app user placeholder","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/introJSUI.html","id":null,"dir":"Reference","previous_headings":"","what":"UI for Module to display introJS button and functionality. — introJSUI","title":"UI for Module to display introJS button and functionality. — introJSUI","text":"UI Module display introJS button functionality.","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/introJSUI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"UI for Module to display introJS button and functionality. — introJSUI","text":"","code":"introJSUI(id)"},{"path":"https://pharmar.github.io/riskassessment/reference/introJSUI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"UI for Module to display introJS button and functionality. — introJSUI","text":"id module id","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/maintenanceMetricsServer.html","id":null,"dir":"Reference","previous_headings":"","what":"Maintenance Metrics module's server logic — maintenanceMetricsServer","title":"Maintenance Metrics module's server logic — maintenanceMetricsServer","text":"Maintenance Metrics module's server logic","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/maintenanceMetricsServer.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Maintenance Metrics module's server logic — maintenanceMetricsServer","text":"","code":"maintenanceMetricsServer(   id,   selected_pkg,   maint_metrics,   user,   credentials,   parent )"},{"path":"https://pharmar.github.io/riskassessment/reference/maintenanceMetricsServer.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Maintenance Metrics module's server logic — maintenanceMetricsServer","text":"id module id name selected_pkg placeholder maint_metrics placeholder user placeholder parent parent (calling module) session information","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/maintenanceMetricsUI.html","id":null,"dir":"Reference","previous_headings":"","what":"Maintenance Metrics module's UI. — maintenanceMetricsUI","title":"Maintenance Metrics module's UI. — maintenanceMetricsUI","text":"Maintenance Metrics module's UI.","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/maintenanceMetricsUI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Maintenance Metrics module's UI. — maintenanceMetricsUI","text":"","code":"maintenanceMetricsUI(id)"},{"path":"https://pharmar.github.io/riskassessment/reference/maintenanceMetricsUI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Maintenance Metrics module's UI. — maintenanceMetricsUI","text":"id module id name","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/metricBoxServer.html","id":null,"dir":"Reference","previous_headings":"","what":"Server logic for the 'Metric Box' module — metricBoxServer","title":"Server logic for the 'Metric Box' module — metricBoxServer","text":"Server logic 'Metric Box' module","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/metricBoxServer.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Server logic for the 'Metric Box' module — metricBoxServer","text":"","code":"metricBoxServer(   id,   title,   desc,   value,   score = \"NULL\",   is_perc = FALSE,   is_url = FALSE,   succ_icon = \"check\",   unsucc_icon = \"triangle-exclamation\",   icon_class = \"text-success\",   type = \"information\" )"},{"path":"https://pharmar.github.io/riskassessment/reference/metricBoxServer.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Server logic for the 'Metric Box' module — metricBoxServer","text":"id module id name title title. desc description. value metric value. score metric score, character value is_perc logical value percentage? is_url logical value url succ_icon icon used is_true. unsucc_icon icon used is_true. icon_class string type icon type string color icon (\"information\" \"danger\")","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/metricBoxUI.html","id":null,"dir":"Reference","previous_headings":"","what":"The UI for the 'Metric Box' module — metricBoxUI","title":"The UI for the 'Metric Box' module — metricBoxUI","text":"UI 'Metric Box' module","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/metricBoxUI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The UI for the 'Metric Box' module — metricBoxUI","text":"","code":"metricBoxUI(id)"},{"path":"https://pharmar.github.io/riskassessment/reference/metricBoxUI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The UI for the 'Metric Box' module — metricBoxUI","text":"id module id name","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/metricGridServer.html","id":null,"dir":"Reference","previous_headings":"","what":"Metric Grid module's server logic — metricGridServer","title":"Metric Grid module's server logic — metricGridServer","text":"Metric Grid module's server logic","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/metricGridServer.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Metric Grid module's server logic — metricGridServer","text":"","code":"metricGridServer(id, metrics)"},{"path":"https://pharmar.github.io/riskassessment/reference/metricGridServer.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Metric Grid module's server logic — metricGridServer","text":"id module id name metrics placeholder","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/metricGridUI.html","id":null,"dir":"Reference","previous_headings":"","what":"Metric Grid module's UI. — metricGridUI","title":"Metric Grid module's UI. — metricGridUI","text":"Metric Grid module's UI.","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/metricGridUI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Metric Grid module's UI. — metricGridUI","text":"","code":"metricGridUI(id)"},{"path":"https://pharmar.github.io/riskassessment/reference/metricGridUI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Metric Grid module's UI. — metricGridUI","text":"id module id name","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/metric_gauge.html","id":null,"dir":"Reference","previous_headings":"","what":"Metric Gauge — metric_gauge","title":"Metric Gauge — metric_gauge","text":"HTML meter element, used displaying metric scores app","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/metric_gauge.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Metric Gauge — metric_gauge","text":"","code":"metric_gauge(score)"},{"path":"https://pharmar.github.io/riskassessment/reference/metric_gauge.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Metric Gauge — metric_gauge","text":"score whole number 0 100","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/metric_gauge.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Metric Gauge — metric_gauge","text":"tagList object","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/packageDependenciesServer.html","id":null,"dir":"Reference","previous_headings":"","what":"Package Dependencies module's server logic — packageDependenciesServer","title":"Package Dependencies module's server logic — packageDependenciesServer","text":"Package Dependencies module's server logic","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/packageDependenciesServer.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Package Dependencies module's server logic — packageDependenciesServer","text":"","code":"packageDependenciesServer(id, selected_pkg, user, credentials, parent)"},{"path":"https://pharmar.github.io/riskassessment/reference/packageDependenciesServer.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Package Dependencies module's server logic — packageDependenciesServer","text":"id module id name selected_pkg placeholder user placeholder parent parent (calling module) session information","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/packageDependenciesUI.html","id":null,"dir":"Reference","previous_headings":"","what":"Package Dependencies module's UI. — packageDependenciesUI","title":"Package Dependencies module's UI. — packageDependenciesUI","text":"Package Dependencies module's UI.","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/packageDependenciesUI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Package Dependencies module's UI. — packageDependenciesUI","text":"","code":"packageDependenciesUI(id)"},{"path":"https://pharmar.github.io/riskassessment/reference/packageDependenciesUI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Package Dependencies module's UI. — packageDependenciesUI","text":"id module id name","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/reportPreviewServer.html","id":null,"dir":"Reference","previous_headings":"","what":"Server logic for 'Report Preview' module — reportPreviewServer","title":"Server logic for 'Report Preview' module — reportPreviewServer","text":"Server logic 'Report Preview' module","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/reportPreviewServer.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Server logic for 'Report Preview' module — reportPreviewServer","text":"","code":"reportPreviewServer(   id,   selected_pkg,   maint_metrics,   com_metrics,   com_metrics_raw,   mm_comments,   cm_comments,   dep_comments,   downloads_plot_data,   user,   credentials,   app_version,   metric_weights )"},{"path":"https://pharmar.github.io/riskassessment/reference/reportPreviewServer.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Server logic for 'Report Preview' module — reportPreviewServer","text":"id module id name selected_pkg placeholder maint_metrics placeholder com_metrics placeholder com_metrics_raw placeholder mm_comments placeholder cm_comments placeholder downloads_plot_data placeholder user placeholder app_version placeholder metric_weights placeholder","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/reportPreviewUI.html","id":null,"dir":"Reference","previous_headings":"","what":"UI for 'Report Preview' module — reportPreviewUI","title":"UI for 'Report Preview' module — reportPreviewUI","text":"UI 'Report Preview' module","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/reportPreviewUI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"UI for 'Report Preview' module — reportPreviewUI","text":"","code":"reportPreviewUI(id)"},{"path":"https://pharmar.github.io/riskassessment/reference/reportPreviewUI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"UI for 'Report Preview' module — reportPreviewUI","text":"id module id name","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/reweightViewServer.html","id":null,"dir":"Reference","previous_headings":"","what":"Server logic for the 'Re-weight View' module — reweightViewServer","title":"Server logic for the 'Re-weight View' module — reweightViewServer","text":"Server logic 'Re-weight View' module","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/reweightViewServer.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Server logic for the 'Re-weight View' module — reweightViewServer","text":"","code":"reweightViewServer(id, user, decision_list, credentials)"},{"path":"https://pharmar.github.io/riskassessment/reference/reweightViewServer.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Server logic for the 'Re-weight View' module — reweightViewServer","text":"id module id user user name decision_list list containing decision automation criteria","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/reweightViewUI.html","id":null,"dir":"Reference","previous_headings":"","what":"UI for the 'Re-weight View' module — reweightViewUI","title":"UI for the 'Re-weight View' module — reweightViewUI","text":"UI 'Re-weight View' module","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/reweightViewUI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"UI for the 'Re-weight View' module — reweightViewUI","text":"","code":"reweightViewUI(id)"},{"path":"https://pharmar.github.io/riskassessment/reference/reweightViewUI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"UI for the 'Re-weight View' module — reweightViewUI","text":"id module id","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/riskassessment-package.html","id":null,"dir":"Reference","previous_headings":"","what":"The riskassessment package — riskassessment-package","title":"The riskassessment package — riskassessment-package","text":"riskassessment App interactive web application serving front end application riskmetric R package. riskmetric framework quantify risk assessing number metrics meant evaluate development best practices, code documentation, community engagement, development sustainability. app riskmetric aim provide context validation within regulated industries.","code":""},{"path":[]},{"path":"https://pharmar.github.io/riskassessment/reference/riskassessment-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"The riskassessment package — riskassessment-package","text":"Maintainer: Aaron Clark clark.aaronchris@gmail.com Authors: Jeff Thompson jeff.thompson51317@gmail.com (Co-Lead) Robert Krajcik robert.krajcik@biogen.com Lars Andersen lars.andersen@boehringer-ingelheim.com Andrew Borgman andrew.borgman@biogen.com Marly Gotti marly.cormar@biogen.com Maya Gans maya.gans@biogen.com Aravind Reddy Kallem Fission Labs India Pvt Ltd contributors: Munshi Imran Hossain [contributor] Scott Schumacker scottschu97@gmail.com [contributor] Eduardo Almeida eduardoalmeida7393@gmail.com [contributor] Narayanan Iyer NarayananSeshan.Iyer@pfizer.com [contributor] PSI special interest group Application Implementation Methodologies Statistics [copyright holder, funder] R Validation Hub [copyright holder, funder] GSK contributors (Author 'pharmaR/pkg_explorer' repo) [contributor] Appsilon [contributor]","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/run_app.html","id":null,"dir":"Reference","previous_headings":"","what":"Run the Shiny Application — run_app","title":"Run the Shiny Application — run_app","text":"Run Shiny Application","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/run_app.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Run the Shiny Application — run_app","text":"","code":"run_app(   onStart = initialize_raa,   options = list(),   enableBookmarking = NULL,   uiPattern = \"/\",   app_ver = NULL,   login_note = NULL,   ... )"},{"path":"https://pharmar.github.io/riskassessment/reference/run_app.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Run the Shiny Application — run_app","text":"onStart function called app actually run. needed shinyAppObj, since shinyAppDir case, global.R file can used purpose. options Named options passed runApp call (can following: \"port\", \"launch.browser\", \"host\", \"quiet\", \"display.mode\" \"test.mode\"). can also specify width height parameters provide hint embedding environment ideal height/width app. enableBookmarking Can one \"url\", \"server\", \"disable\". default value, NULL, respect setting previous calls  enableBookmarking(). See enableBookmarking() information bookmarking app. uiPattern regular expression applied GET request determine whether ui used handle request. Note entire request path must match regular expression order match considered successful. app_ver \"global\" variable passed several modules & reports details installed package version specified. can overwritten include specific version name text string. login_note text string display underneath auth screen's login button, provided guide users ... arguments pass golem_opts. See ?golem::get_golem_options details.","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/run_app.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Run the Shiny Application — run_app","text":"shiny app object","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/showComments.html","id":null,"dir":"Reference","previous_headings":"","what":"showComments — showComments","title":"showComments — showComments","text":"Displays formatted comments","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/showComments.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"showComments — showComments","text":"","code":"showComments(pkg_name, comments, none_txt = \"No comments\")"},{"path":"https://pharmar.github.io/riskassessment/reference/showComments.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"showComments — showComments","text":"pkg_name string name package comments data.frame comments table entry none_txt text show comments object, display text string. Default: \"comments\"","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/showComments.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"showComments — showComments","text":"formatted string comments","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/showHelperMessage.html","id":null,"dir":"Reference","previous_headings":"","what":"showHelperMessage — showHelperMessage","title":"showHelperMessage — showHelperMessage","text":"Displays helper message. default, informs user select package.","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/showHelperMessage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"showHelperMessage — showHelperMessage","text":"","code":"showHelperMessage(message = \"Please select a package\")"},{"path":"https://pharmar.github.io/riskassessment/reference/showHelperMessage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"showHelperMessage — showHelperMessage","text":"message string","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/sidebarServer.html","id":null,"dir":"Reference","previous_headings":"","what":"Sidebar Server Logic — sidebarServer","title":"Sidebar Server Logic — sidebarServer","text":"Also known 'Control Panel', rightfully , controls components app, central function","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/sidebarServer.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sidebar Server Logic — sidebarServer","text":"","code":"sidebarServer(id, user, uploaded_pkgs, credentials)"},{"path":"https://pharmar.github.io/riskassessment/reference/sidebarServer.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sidebar Server Logic — sidebarServer","text":"id module id user username uploaded_pkgs vector packages","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/sidebarUI.html","id":null,"dir":"Reference","previous_headings":"","what":"Sidebar UI — sidebarUI","title":"Sidebar UI — sidebarUI","text":"Also known 'Control Panel', rightfully , controls components app, central function","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/sidebarUI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sidebar UI — sidebarUI","text":"","code":"sidebarUI(id)"},{"path":"https://pharmar.github.io/riskassessment/reference/sidebarUI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sidebar UI — sidebarUI","text":"id module id","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/uploadPackageServer.html","id":null,"dir":"Reference","previous_headings":"","what":"Server logic for the 'Upload Package' module — uploadPackageServer","title":"Server logic for the 'Upload Package' module — uploadPackageServer","text":"Server logic 'Upload Package' module","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/uploadPackageServer.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Server logic for the 'Upload Package' module — uploadPackageServer","text":"","code":"uploadPackageServer(id, user, auto_list, credentials, parent)"},{"path":"https://pharmar.github.io/riskassessment/reference/uploadPackageServer.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Server logic for the 'Upload Package' module — uploadPackageServer","text":"id module id user username auto_list list decision automation rules parent parent (calling module) session information","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/uploadPackageUI.html","id":null,"dir":"Reference","previous_headings":"","what":"'Upload Package' UI — uploadPackageUI","title":"'Upload Package' UI — uploadPackageUI","text":"'Upload Package' UI","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/uploadPackageUI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"'Upload Package' UI — uploadPackageUI","text":"","code":"uploadPackageUI(id)"},{"path":"https://pharmar.github.io/riskassessment/reference/uploadPackageUI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"'Upload Package' UI — uploadPackageUI","text":"id module id","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/upload_pkg_lst.html","id":null,"dir":"Reference","previous_headings":"","what":"Upload a Package List — upload_pkg_lst","title":"Upload a Package List — upload_pkg_lst","text":"Uploads list packages database. Designed used set assessment database deployment application.","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/upload_pkg_lst.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Upload a Package List — upload_pkg_lst","text":"","code":"upload_pkg_lst(   pkg_lst,   assess_db,   repos,   repo_pkgs,   user_name = \"system\",   updateProgress = NULL )"},{"path":"https://pharmar.github.io/riskassessment/reference/upload_pkg_lst.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Upload a Package List — upload_pkg_lst","text":"pkg_lst character vector packages upload assess_db character name (file path) database repos character vector, base URL(s) repositories use repo_pkgs internal use , allows function available.packages() run user_name character name user updateProgress internal use , provides function update progress meter application","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/upload_pkg_lst.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Upload a Package List — upload_pkg_lst","text":"data frame object containing summary upload process","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/viewCommentsServer.html","id":null,"dir":"Reference","previous_headings":"","what":"viewComment module's server logic — viewCommentsServer","title":"viewComment module's server logic — viewCommentsServer","text":"viewComment module's server logic","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/viewCommentsServer.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"viewComment module's server logic — viewCommentsServer","text":"","code":"viewCommentsServer(   id,   pkg_name,   comments,   none_txt = \"No comments\",   label = \"Current Comments\" )"},{"path":"https://pharmar.github.io/riskassessment/reference/viewCommentsServer.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"viewComment module's server logic — viewCommentsServer","text":"id module id name pkg_name string name package comments data.frame comments table entry label string default: Current Comments","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/viewCommentsUI.html","id":null,"dir":"Reference","previous_headings":"","what":"The UI for the 'viewComment' module — viewCommentsUI","title":"The UI for the 'viewComment' module — viewCommentsUI","text":"Module display comments specified metric. comments update user inserts comments.","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/viewCommentsUI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The UI for the 'viewComment' module — viewCommentsUI","text":"","code":"viewCommentsUI(id)"},{"path":"https://pharmar.github.io/riskassessment/reference/viewCommentsUI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The UI for the 'viewComment' module — viewCommentsUI","text":"id module id name","code":""},{"path":[]},{"path":"https://pharmar.github.io/riskassessment/news/index.html","id":"user-enhancements-3-1-0","dir":"Changelog","previous_headings":"","what":"User Enhancements","title":"riskassessment 3.1.0","text":"Allow users specify decisions within CSV file used upload pkgs (#663) Drastically shortened waiting time Code explorer/ Package explorer reading tarballs memory (#707) Added Package Dependencies content Reports (#721) Added option include Suggests pkgs downloadable Reports (#721) Added Decision column Package Dependencies tab’s table output (#774) Added Decision Summary card Package Dependencies tab (#774) Added hyperlink dependencies/reverse dependencies cards, directing users Package Dependencies page detail (#597) Added new table display reverse dependencies highlights pkgs already exist database","code":""},{"path":"https://pharmar.github.io/riskassessment/news/index.html","id":"squashed-bugs-3-1-0","dir":"Changelog","previous_headings":"","what":"Squashed Bugs","title":"riskassessment 3.1.0","text":"Fixed bug causing application crash trying delete zero packages (#781) Fixed bug app doesn’t reset decision decision date fields re-scoring/re-weighting packages (#680) Fixed bug user privileges table aligned available privileges application (#697) Fixed typo privileges table (#719) Fixed bug HTML reports displayed darker green cards’ meters Updated logo reports lighter version match application UI Updated Dependency Cards slightly informative","code":""},{"path":"https://pharmar.github.io/riskassessment/news/index.html","id":"docs-3-1-0","dir":"Changelog","previous_headings":"","what":"Docs","title":"riskassessment 3.1.0","text":"Added page introduce audience project little better, providing useful resources attribution highlights individual contributors Added context metric score card visuals inserting tool tips & creating legend modal describes & interprets possible visuals (#652) Added introjs file browser & function explorer( #581) Added riskmetric assessment documentation URLs tab, Risk Assessment Criteria page.","code":""},{"path":"https://pharmar.github.io/riskassessment/news/index.html","id":"for-devs-3-1-0","dir":"Changelog","previous_headings":"","what":"For Devs","title":"riskassessment 3.1.0","text":"Added non-shinymanager deployment option users may use Posit Credentials instead (#700) Moved package upload process function, allowing devs populate database outside application Added tests Code Explorer Function explorer modules Added repo specification configuration file (#701) Ensured configuration checkers run configuring database Utilized archive parse DESCRIPTION file, increasing speed package upload process Updated manifest file deployments article Updated version riskmetric used v0.2.4.9000 Updated version R v4.3.3 & Posit Package Manager snapshot dates 2024-04-08","code":""},{"path":[]},{"path":"https://pharmar.github.io/riskassessment/news/index.html","id":"enhancements-3-0-0","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"riskassessment 3.0.0","text":"Added “Suggests” pkgs Dependencies tab (#624) Summarized Package Dependencies (#618) Integrated ‘Function Explorer’ offer users function-level browsing source code, unit testing, automatic rendering help documentation (#498) Started showing metric_scores assessment’s card, using html meter (#634) Added default DT based filter Database Overview tab (#586) Allowed users create decision automation rules individual metrics (#483) Added checkbox databaseView select packages reportDownload handler (#649) Allowed users identify store preferred elements include downloaded reports (#526) Add “Explore Metrics” button Uploaded Pkgs Summary tab Upload Packages tab (#653) Added comment module Function Explorer (#643) Made color palette used app even colorblind-friendly created lighter “User Guide” logo (#654)","code":""},{"path":"https://pharmar.github.io/riskassessment/news/index.html","id":"squashed-bugs-3-0-0","dir":"Changelog","previous_headings":"","what":"Squashed Bugs","title":"riskassessment 3.0.0","text":"Fixed app’s logo hyperlink docs functioning expected “zone” (#633) Fixed tests showing “Package Downloads” community usage card non-metric (#621) Removed “Suggests” Riskassessment Criteria weights table (#646) Forced formation new lines cards (#671) Ensured users couldn’t create & select packages CRAN don’t exist Upload Packages tab","code":""},{"path":"https://pharmar.github.io/riskassessment/news/index.html","id":"for-devs-3-0-0","dir":"Changelog","previous_headings":"","what":"For Devs","title":"riskassessment 3.0.0","text":"Migrated jsTreeR {shinyTree} (#585) Removed unneeded/unused dependencies Updated shinytest2 chromote recent versions testing Added correct remotes reference DESCRIPTION file pharmar/riskmetric & rstudio/chromote Stopped using CRAN repo snapshot date renv (#677)","code":""},{"path":[]},{"path":"https://pharmar.github.io/riskassessment/news/index.html","id":"enhancements-2-0-0","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"riskassessment 2.0.0","text":"Expand privileges include commenting metrics packages (#564) Allow admin users edit roles privileges (#541) Download source tarball uploading package database users can explore source contents package (#574) Added card Download Trend linear trend plot community usage metrics (#438) Introduced cards Database tab, reviewing contents db (#587) Prominently display date package added (#486) Fix issue repository used gather information inconsistent Added Package Dependencies page “Package Metrics” tab, two new cards Maintenance Metrics page (#261) Identify non-riskmetric cards (#573)","code":""},{"path":"https://pharmar.github.io/riskassessment/news/index.html","id":"squashed-bugs-2-0-0","dir":"Changelog","previous_headings":"","what":"Squashed Bugs","title":"riskassessment 2.0.0","text":"Fixed busted button introduced #547 (#592)","code":""},{"path":"https://pharmar.github.io/riskassessment/news/index.html","id":"docs-2-0-0","dir":"Changelog","previous_headings":"","what":"Docs","title":"riskassessment 2.0.0","text":"Updated riskassessment vignette reflect new tab structure","code":""},{"path":"https://pharmar.github.io/riskassessment/news/index.html","id":"for-devs-2-0-0","dir":"Changelog","previous_headings":"","what":"For Devs","title":"riskassessment 2.0.0","text":"Disable using Microsoft R Application Network (MRAN) restoring packages Removed legacy code set covr_coverage assessment’s metric weight 0 assessmentInfo mod metric table initialization sql file.","code":""},{"path":[]},{"path":"https://pharmar.github.io/riskassessment/news/index.html","id":"enhancements-1-0-0","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"riskassessment 1.0.0","text":"Updated version riskmetric used V0.2.2 Added decision categories (#459) Added decision automation rules (#459) Added log file designation (#463) Implemented user roles/privileges allow granular access actions application (#527) Allow metric weights initialized (#482) package upload, inserting community metrics database (#516) metric weights changed, re-score instead re-assess, saving huge amounts time (#537) Added Decision-related columns like decision time stamp & decision source Introduced decision category table holistic Report Builder. allows users define content shows report (#348). Users can now compose long form “Package Summary” keep track pertinent items (perhaps items less central {riskmetric} output) rounded package review (#348). Allowed certain users set custom color decision categories (#465) Added code coverage (covr_coverage) card add optimized card layout logic (#533)","code":""},{"path":"https://pharmar.github.io/riskassessment/news/index.html","id":"squashed-bugs-1-0-0","dir":"Changelog","previous_headings":"","what":"Squashed Bugs","title":"riskassessment 1.0.0","text":"Fixed Chromote error (#477) Fixed bug preventing icons displaying admin tab (#427) Fixed button alignment issues (#514) Re-positioned footer bottom visible page (#518) Added new check conditionally delivers message differing pkg versions CSV file loaded (#515) Fixed broken links docs","code":""},{"path":"https://pharmar.github.io/riskassessment/news/index.html","id":"docs-1-0-0","dir":"Changelog","previous_headings":"","what":"Docs","title":"riskassessment 1.0.0","text":"Updated help files build_comm_plotly() include example output (#409). Created new (updated ) user guides explain precisely control app deployment using configuration file. Retired pertinent “old”” user guides case users still running old versions riskassessment","code":""},{"path":"https://pharmar.github.io/riskassessment/news/index.html","id":"for-devs-1-0-0","dir":"Changelog","previous_headings":"","what":"For Devs","title":"riskassessment 1.0.0","text":"Utilized glue::glue_sql() inside update select functions (#520) Improved speed inserting community metrics database (#516) Re-score instead re-assess metric weights changed, meaning now storing pkg assessment (#537) Pass warning instead error default privilege config gets combined another config (#547)","code":""},{"path":[]},{"path":"https://pharmar.github.io/riskassessment/news/index.html","id":"enhancements-0-1-1","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"riskassessment 0.1.1","text":"Upgraded leverage {riskmetric} v0.2.0 impacts risk score calculations Add button redirects pkg metrics Added ‘search’ capability database view tab Added Excel & CSV export options Database View tab Added hyperlink documentation site / user guide within application Added check URLs needed upload packages reachable, just case! Added riskassessment logo docx pdf reports general aesthetic improvements, example: made sure tab headers consistent size","code":""},{"path":"https://pharmar.github.io/riskassessment/news/index.html","id":"squashed-bugs-0-1-1","dir":"Changelog","previous_headings":"","what":"Squashed Bugs","title":"riskassessment 0.1.1","text":"Fixed bug card displaying “Number downloads last 12 months” faulty, summing months previous year none current year. Report headings changed “asis” sentence case avoid altering case package names reports Fix failing tests: prefix AppDriver$new ‘shinytest2::’ Fix Chromote error provided Winston Chang","code":""},{"path":"https://pharmar.github.io/riskassessment/news/index.html","id":"docs-0-1-1","dir":"Changelog","previous_headings":"","what":"Docs","title":"riskassessment 0.1.1","text":"Added User Feedback survey README (#411) Fixed broken R-CMD-CHECK badge README Updated vignettes describe new ‘Decision Automation’ feature","code":""},{"path":"https://pharmar.github.io/riskassessment/news/index.html","id":"for-devs-0-1-1","dir":"Changelog","previous_headings":"","what":"For Devs","title":"riskassessment 0.1.1","text":"Removed {golem} testing option pre_auth_user arguments run_app() Improved stability ease--use testing introJS module Preload information select list packages improve tests utilizing shinytest2 Upgraded R Version v4.2.2","code":""},{"path":[]},{"path":"https://pharmar.github.io/riskassessment/news/index.html","id":"all-new-features-0-1-0","dir":"Changelog","previous_headings":"","what":"All New Features","title":"riskassessment 0.1.0","text":"Allowed users type package names assessed app, instead uploading CSV file. Also allow point--click deletion packages. Added decision automation capabilities user can set decision rules uploaded packages auto-assigned.","code":""},{"path":"https://pharmar.github.io/riskassessment/news/index.html","id":"enhancements-0-1-0","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"riskassessment 0.1.0","text":"Added “PDF report” download option (#280) Added risk score Report Preview tab downloaded reports (#264). Exported generate_comm_data() help users build community usage data needed run build_comm_plotly() (also exported) produce “downloads month”” plot seen Community Usage tab application. (#266).","code":""},{"path":"https://pharmar.github.io/riskassessment/news/index.html","id":"for-deployment-0-1-0","dir":"Changelog","previous_headings":"","what":"For deployment","title":"riskassessment 0.1.0","text":"Created argument run_app() called login_note allows users deploying app add custom log-notes authentication screen. default, displays note use default usernames passwords gain entry first time. Engineered new argument run_app() called app_version allows users deploying application publish custom text string app’s authentication screen downloaded reports. default, display installed version.","code":""},{"path":"https://pharmar.github.io/riskassessment/news/index.html","id":"docs-0-1-0","dir":"Changelog","previous_headings":"","what":"Docs","title":"riskassessment 0.1.0","text":"Updated README include description, ‘Usage’ info, including install & run app first time. Last, included links demo app & short video walk-. brief notes included regarding deployment environments. “Get started riskassessment” vignette “Administrative Tools Options” vignette Designed hex logo updated documentation reflect new repo name ‘riskassessment’ without ’_’ separate two words. suggest installation riskmetric GitHub, CRAN (now)","code":""},{"path":"https://pharmar.github.io/riskassessment/news/index.html","id":"squashed-bugs-0-1-0","dir":"Changelog","previous_headings":"","what":"Squashed Bugs","title":"riskassessment 0.1.0","text":"Fixed bug causing Community Usage metrics fail Mac computers Fixed bug causing report fail Community Metrics available package. Add founders/copyright holders DESCRIPTION file Fixed bug Assessment Criteria tables failing render. Improved metric ‘card’ aesthetics order remove scroll bars (#198). Added console warnings, log-note, modals warn user bug {fontawesome} v0.4.0. info, bug status can tracked . Fixed summary community usage data one package version released month Fixed bug logging file set Fixed package delete button shadow; fix introjs admin/non-admin roles Fixed display ‘Report Bugs’ metric align current riskmetric presentation 0 1","code":""},{"path":"https://pharmar.github.io/riskassessment/news/index.html","id":"for-devs-0-1-0","dir":"Changelog","previous_headings":"","what":"For Devs","title":"riskassessment 0.1.0","text":"general re-organizing package’s infrastructure make testing development easier. Added unit tests attain test coverage >85% (#295). Added renv renv.lock file well corresponding vignette developers/contributors align . Reduce number package dependencies 33 26 Changed risk-based color gradient use colorblind-friendly color palette (#324). Adopt (temporary) CRAN-first data collection method pkg info via riskmetric::pkg_ref()","code":""},{"path":"https://pharmar.github.io/riskassessment/news/index.html","id":"riskassessment-001","dir":"Changelog","previous_headings":"","what":"riskassessment 0.0.1","title":"riskassessment 0.0.1","text":"Initiated simple app.R easier deployment using runURL(\"https://github.com/pharmaR/riskassessment/archive/master.zip\") shiny::runGitHub('riskassessment', 'pharmaR')","code":""},{"path":"https://pharmar.github.io/riskassessment/news/index.html","id":"riskassessment-0009000","dir":"Changelog","previous_headings":"","what":"riskassessment 0.0.0.9000","title":"riskassessment 0.0.0.9000","text":"Added NEWS.md file track changes package. Used golem complete “packagization” riskassessment","code":""}]
+[{"path":"https://pharmar.github.io/riskassessment/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2022 2020 Fission Labs R Validation Hub contributors Permission hereby granted, free charge, person obtaining copy software associated documentation files (“Software”), deal Software without restriction, including without limitation rights use, copy, modify, merge, publish, distribute, sublicense, /sell copies Software, permit persons Software furnished , subject following conditions: copyright notice permission notice shall included copies substantial portions Software. SOFTWARE PROVIDED “”, WITHOUT WARRANTY KIND, EXPRESS IMPLIED, INCLUDING LIMITED WARRANTIES MERCHANTABILITY, FITNESS PARTICULAR PURPOSE NONINFRINGEMENT. EVENT SHALL AUTHORS COPYRIGHT HOLDERS LIABLE CLAIM, DAMAGES LIABILITY, WHETHER ACTION CONTRACT, TORT OTHERWISE, ARISING , CONNECTION SOFTWARE USE DEALINGS SOFTWARE.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/Administrative_Tools_and_Options_V0.1.1.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"Administrative Tools and Options V0.1.1","text":"’s secret users administrator privileges access certain features application. guide assists ADMIN users manage privileges, (minimum) include: govern user credentials re-weight metrics determine risk scores calculated define automated decision rules based risk scores verify ADMIN access, first check can see navigation tabs within app, especially rightmost Administrative Tools tab. see tab, granted access! gain access, ’ll request access known ADMIN user within organization.    can also hover cursor  symbol bottom-right corner page. Upon hovering, two additional buttons appear. middle one log  button, Administrator mode  button appear top, shown. button appear non-ADMIN users.  selected Administrative Tools tab, currently two areas available review: first Credential Manager second Assessment Reweighting, seen .","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/Administrative_Tools_and_Options_V0.1.1.html","id":"credential-manager","dir":"Articles","previous_headings":"","what":"Credential Manager","title":"Administrative Tools and Options V0.1.1","text":"Credential Manager tab shown default contains two tables: first one, indicated  Users icon, used manage users. second one, indicated  key icon, used manage passwords. also button bottom download copy current sqlite database.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/Administrative_Tools_and_Options_V0.1.1.html","id":"managing-users","dir":"Articles","previous_headings":"Credential Manager","what":"Managing Users","title":"Administrative Tools and Options V0.1.1","text":"first table provides tools managing users: adding, editing, deleting.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/Administrative_Tools_and_Options_V0.1.1.html","id":"add-a-user","dir":"Articles","previous_headings":"Credential Manager > Managing Users","what":"Add a User","title":"Administrative Tools and Options V0.1.1","text":"add new user, click button labelled: “Add user”.   prompt appear can specify user name, well optional start & expire date new member. default set today’s date (later).  , ’ll type “PeterParker” User Name field.  Notice  checkbox grant new user administrator privileges also checked default. unique password generated user prompted change first time /logs , long “Ask change password” box remains checked.     Upon clicking CONFIRM NEW USER, confirmation modal appear. Now good time notify user sending userid temporary password.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/Administrative_Tools_and_Options_V0.1.1.html","id":"user-start-and-expire-dates","dir":"Articles","previous_headings":"Credential Manager > Managing Users","what":"User start and expire dates","title":"Administrative Tools and Options V0.1.1","text":"either start date set future date expire date set today’s date, account expired message appear, log-attempt fail.  Feel free set either dates needed, just leave blank ignore/avoid time-based access particular user.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/Administrative_Tools_and_Options_V0.1.1.html","id":"edit-a-user","dir":"Articles","previous_headings":"Credential Manager > Managing Users","what":"Edit a user","title":"Administrative Tools and Options V0.1.1","text":"Edit user information clicking EDIT button, found right-hand side table. Edit User window appear:   Make changes, click CONFIRM CHANGE.   small modal dialog box appear (briefly) indicating user successfully updated.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/Administrative_Tools_and_Options_V0.1.1.html","id":"more-edit-options","dir":"Articles","previous_headings":"Credential Manager > Managing Users","what":"More Edit options","title":"Administrative Tools and Options V0.1.1","text":"bottom table bar three buttons:   first one  checkbox select multiple users followed EDIT SELECTED USERS REMOVE SELECTED USERS button. buttons enabled select two users.  Note “Edit Selected Users” button allows modify start expire dates selected group users.  ’ve made changes, click CONFIRM CHANGE.    , small modal dialog box briefly appear indicating users updated.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/Administrative_Tools_and_Options_V0.1.1.html","id":"delete-a-user","dir":"Articles","previous_headings":"Credential Manager > Managing Users","what":"Delete a user","title":"Administrative Tools and Options V0.1.1","text":"Delete user clicking REMOVE button right-hand side table. see confirmatory modal dialog box. Click “Delete User(s).”   can also delete multiple users like editing multiple users. Just click REMOVE SELECTED USERS button bottom table.   confirmatory modal dialog box appear. Click DELETE USER(S).","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/Administrative_Tools_and_Options_V0.1.1.html","id":"replace-initial-admin-user","dir":"Articles","previous_headings":"Credential Manager > Managing Users","what":"Replace initial Admin user","title":"Administrative Tools and Options V0.1.1","text":"administrator, ’s recommended replace initial ADMIN user ID created first time app launched. Note must always least one admin user, delete ! want delete initial admin user first need create another user ID administrative privileges, described .  Just , click “Add user” button make sure check Admin box. temporary password can overridden un-checking “ask change password” box setting password whatever want.  completing form, sign using new credentials delete original ADMIN user clicking REMOVE button row table.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/Administrative_Tools_and_Options_V0.1.1.html","id":"managing-passwords","dir":"Articles","previous_headings":"Credential Manager","what":"Managing Passwords","title":"Administrative Tools and Options V0.1.1","text":"second table allows password management.    Click CHANGE PASSWORD button force corresponding user change /password next log-. confirmatory modal dialog box appear, like :   click RESET PASSWORD button generate temporary password. , confirmatory modal dialog box appear, like :   Click CONFIRM see another modal dialog box new temporary password .   responsible delivering new temporary password user. bottom User table, also  checkbox select multiple users followed FORCE SELECTED USERS CHANGE PASSWORD button. button enabled select two users.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/Administrative_Tools_and_Options_V0.1.1.html","id":"additional-columns-in-passwords-table","dir":"Articles","previous_headings":"Credential Manager > Managing Passwords","what":"Additional columns in Passwords table","title":"Administrative Tools and Options V0.1.1","text":"Must change column: Indicates whether user change /password next log-. changed column: Indicates user already changed /password. Date Last changed column: Indicates date password updated.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/Administrative_Tools_and_Options_V0.1.1.html","id":"assessment-reweighting","dir":"Articles","previous_headings":"","what":"Assessment Reweighting","title":"Administrative Tools and Options V0.1.1","text":"Head tab available ADMIN users called Assessment Reweighting. high level view:  three buttons page: UPDATE WEIGHT top right, DOWNLOAD middle left, RE-CALCULATE bottom left.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/Administrative_Tools_and_Options_V0.1.1.html","id":"download-database","dir":"Articles","previous_headings":"Assessment Reweighting","what":"Download Database","title":"Administrative Tools and Options V0.1.1","text":"First, simplest: DOWNLOAD database button.   clicked, button download copy current database (default, called “database.sqlite”). app developers recommend anytime plan make integral changes database (like changing metric weights), anything else.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/Administrative_Tools_and_Options_V0.1.1.html","id":"updating-weights","dir":"Articles","previous_headings":"Assessment Reweighting","what":"Updating Weights","title":"Administrative Tools and Options V0.1.1","text":"name suggests, modules allows us view existing change metric weights used calculate risk score using riskmemtric.   can either select metric Select metric dropdown box select row “CURRENT RISK SCORE WEIGHTS METRIC” table. metric selected, enter new (numeric) weight “Choose new weight” box select UPDATE WEIGHT button. ’ll notice row change appear highlighted, showing old weight value new weight value:   updated least one metric weight, RE-CALCULATE button enabled, allowing apply new weights re-calculated risk package. ’ve made final re-weighting changes, can click “Re-calculate” button pictured . Note weight changes take effect packages database, updating risk score .   click RE-CALCULATE get confirmation modal, reminding “updating risk metrics reverted”, strongly recommending download copy current database first clicking SUBMIT. modal also details actions take effect app submit changes.   click SUBMIT modal dialog box appear indicating applying weights updating risk scores package uploaded. followed brief “updates completed” message.   Now go database overview tab confirm risk scores updated. can also view new weights, including standardized weight Assessment Criteria tab.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/Administrative_Tools_and_Options_V0.1.1.html","id":"decision-automation","dir":"Articles","previous_headings":"","what":"Decision Automation","title":"Administrative Tools and Options V0.1.1","text":"organization black white rules package risk decisions based solely riskmetric scores, decision automation . leveraged, help automatically classify packages “Low”, “Medium”, “High” risk decision categories upon upload. current automation rules always displayed ‘Upload Package’ tab. Please note ADMIN users necessary privileges edit. get started, click small  (gear) button upper right hand corner section.   decision rules applied, ’ll see following risk decision categories next empty check boxes. setting rules organization, can choose much little automation needed.   example, want set automatic decision “High” risk scores, need select check box make risk score designation / cut value. Every time package uploaded risk score > 0.66, automatically receive decision label: “High” saves review team time mental capacity reviewing large groups packages.   Similarly, package risk thresholds mapped decision category, apply ! user interface won’t allow slider ranges overlap, allow gaps range. example , adopt automatic decisions packages risk scores less 0.33 greater .66. fictitious example, let’s say organization policy package whose risk score falls 0.33 0.66 need reviewed manually.   apply changes, ADMIN need select APPLY DECISION RULES. pop-ask user review confirm selected automation rules:   Upon clicking submit, automation rules stored users see ‘Upload Package’ tab. uploading new CSV packages, can see ‘Summary Uploaded Package(s)’ now includes summary decisions made, category. example , can see 10 packages uploaded, 5 automatic decisions made: four received “low” designation one labeled “high” risk. summary table, risk score decision right-hand side. can also observe packages weren’t found don’t exist CRAN.   Consulting ‘PACKAGE CONTROL PANEL’, select one packages decision made, can see ‘Status’ changed “Reviewed” risk decision slider adjusted accordingly disabled. addition, ‘Overall Comment’ submitted, stating decision made driven via automation rules.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/Credential_Manager.html","id":"the-admin-privilege","dir":"Articles","previous_headings":"","what":"The admin Privilege","title":"Credential Manager","text":"Starting Version 1.0.0, major overhaul privileges function within application. Privileges now tied user roles! allows additional flexibility manage user’s access. However, one privilege whose assignment mandatory app deployment: admin privilege. admin privilege important (required least one user) person manage credentials roles users. Though can changed, default app configuration gives admins access privileges. learn privileges, details provided “User Roles Privileges” guide. ’ll use vignette discuss admin-specific privilege: credentials management. verify admin access, first check can see navigation tabs within app, especially rightmost Administrative Tools tab. see tab, granted access! gain access, ’ll request access known admin user within organization.    can also hover cursor  symbol bottom-right corner page. Upon hovering, two additional buttons appear. middle one log  button, Administrator mode  button appear top, shown. button appear non-admin users.  selected Administrative Tools tab, currently two areas available review: first Credential Manager second Roles & Privileges, seen . Note: may also see tab labelled Assessment Reweighting, connected different privilege may included role.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/Credential_Manager.html","id":"the-credential-manager","dir":"Articles","previous_headings":"","what":"The Credential Manager","title":"Credential Manager","text":"Credential Manager tab shown default contains two tables: first one, indicated  Users icon, used manage users. second one, indicated  key icon, used manage passwords. also button bottom download copy current sqlite database.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/Credential_Manager.html","id":"managing-users","dir":"Articles","previous_headings":"The Credential Manager","what":"Managing Users","title":"Credential Manager","text":"first table provides tools managing users: adding, editing, deleting.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/Credential_Manager.html","id":"add-a-user","dir":"Articles","previous_headings":"The Credential Manager > Managing Users","what":"Add a User","title":"Credential Manager","text":"add new user, click button labelled: “Add user”.   prompt appear can specify user name, well optional start & expire date new member. default set today’s date (later).  , ’ll type “PeterParker” User Name field.  Notice  checkbox grant new user administrator privileges also checked default. unique password generated user prompted change first time /logs , long “Ask change password” box remains checked.     Upon clicking CONFIRM NEW USER, confirmation modal appear. Now good time notify user sending userid temporary password.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/Credential_Manager.html","id":"user-start-and-expire-dates","dir":"Articles","previous_headings":"The Credential Manager > Managing Users","what":"User start and expire dates","title":"Credential Manager","text":"either start date set future date expire date set today’s date, account expired message appear, log-attempt fail.  Feel free set either dates needed, just leave blank ignore/avoid time-based access particular user.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/Credential_Manager.html","id":"edit-a-user","dir":"Articles","previous_headings":"The Credential Manager > Managing Users","what":"Edit a user","title":"Credential Manager","text":"Edit user information clicking EDIT button, found right-hand side table. Edit User window appear:   Make changes, click CONFIRM CHANGE.   small modal dialog box appear (briefly) indicating user successfully updated.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/Credential_Manager.html","id":"more-edit-options","dir":"Articles","previous_headings":"The Credential Manager > Managing Users","what":"More Edit options","title":"Credential Manager","text":"bottom table bar three buttons:   first one  checkbox select multiple users followed EDIT SELECTED USERS REMOVE SELECTED USERS button. buttons enabled select two users.  Note “Edit Selected Users” button allows modify start expire dates selected group users.  ’ve made changes, click CONFIRM CHANGE.    , small modal dialog box briefly appear indicating users updated.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/Credential_Manager.html","id":"delete-a-user","dir":"Articles","previous_headings":"The Credential Manager > Managing Users","what":"Delete a user","title":"Credential Manager","text":"Delete user clicking REMOVE button right-hand side table. see confirmatory modal dialog box. Click “Delete User(s).”   can also delete multiple users like editing multiple users. Just click REMOVE SELECTED USERS button bottom table.   confirmatory modal dialog box appear. Click DELETE USER(S).","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/Credential_Manager.html","id":"replace-initial-admin-user","dir":"Articles","previous_headings":"The Credential Manager > Managing Users","what":"Replace initial admin user","title":"Credential Manager","text":"administrator, ’s recommended replace initial admin user ID created first time app launched. Note must always least one admin user, delete ! want delete initial admin user first need create another user ID administrative privileges, described .  Just , click “Add user” button make sure check Admin box. temporary password can overridden un-checking “ask change password” box setting password whatever want.  completing form, sign using new credentials delete original admin user clicking REMOVE button row table.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/Credential_Manager.html","id":"managing-passwords","dir":"Articles","previous_headings":"The Credential Manager","what":"Managing Passwords","title":"Credential Manager","text":"second table allows password management.    Click CHANGE PASSWORD button force corresponding user change /password next log-. confirmatory modal dialog box appear, like :   click RESET PASSWORD button generate temporary password. , confirmatory modal dialog box appear, like :   Click CONFIRM see another modal dialog box new temporary password .   responsible delivering new temporary password user. bottom User table, also  checkbox select multiple users followed FORCE SELECTED USERS CHANGE PASSWORD button. button enabled select two users.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/Credential_Manager.html","id":"additional-columns-in-passwords-table","dir":"Articles","previous_headings":"The Credential Manager > Managing Passwords","what":"Additional columns in Passwords table","title":"Credential Manager","text":"Must change column: Indicates whether user change /password next log-. changed column: Indicates user already changed /password. Date Last changed column: Indicates date password updated.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/Deployment.html","id":"installing-vs-forking","dir":"Articles","previous_headings":"","what":"Installing vs Forking","title":"Deployment","text":"discuss deployment methods, note riskassessment application developed using renv form source control. helps maintain stability code base. can install riskassessment Github, strongly recommended use fork riskassessment repository deployment. serve handful purposes organization: can utilize renv deployment help ensure share environment app developers, ensuring consistent behavior. easier access configuration file allowing streamlined deployment several projects.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/Deployment.html","id":"the-db-config-yml-file","dir":"Articles","previous_headings":"","what":"The db-config.yml file","title":"Deployment","text":"Starting {riskassessment} v1.0.0, configuration file can found inst/db-config.yml used initialize application deployment. configuration contains elements vital app initialization grow development continues. Many elements file also editable within application (provided user role privileges ). Currently, db-config.yml contains following major elements: assessment_db: string designating file path assessment SQLite database (created upon initialization). default value database.sqlite. credential_db: string designating file path credentials SQLite database (created upon initialization). default value credentials.sqlite. loggit_json: string designating file path logging JSON file (created upon initialization). default value loggit.json. credentials: list defining user roles privileges assigned roles credentials database. decisions: list defining decision categories, automated decision rules (optional), custom decision category colors (also optional). metric_weights: list containing riskmetric weights use upon initialization. weights used increase decrease priority one metric. look current default configuration fork riskassessment code today:","code":"default:   assessment_db: database.sqlite   loggit_json: loggit.json   credential_db: credentials.sqlite   credentials:     roles:       - admin       - lead       - reviewer     privileges:       admin: [admin, weight_adjust, auto_decision_adjust, final_decision, revert_decision, add_package, delete_package]       lead: [weight_adjust, auto_decision_adjust, final_decision, revert_decision, add_package, delete_package]       reviewer: add_package   decisions:     categories:       - Low Risk       - Medium Risk       - High Risk   metric_weights:     covr_coverage: 0"},{"path":"https://pharmar.github.io/riskassessment/articles/Deployment.html","id":"configuring-the-assessment-database","dir":"Articles","previous_headings":"The db-config.yml file","what":"Configuring the assessment database","title":"Deployment","text":"riskassessment::run_app() function ran, code base check assessment sqlite file exists name give (default database.sqlite) doesn’t, several tables initiated create database just app launches. Note user authority name database file whatever like using inst/db-config.yml file. , can include file path preceding file name wish move location database away root directory. example, following code create database called “database.sqlite” dev/ folder: time vignette authored, database initialize following tables NULL values: comments: stores user comments, including user names associated comment entry, comment type, timestamp community_usage_metrics: stores CRAN package downloads per month metric: stores metric info, including riskmetric name, label, short description, type, weight package_metrics: stores package-specific rismetric metrics package: Contains package information, like name, version, maintainer, etc. also contains riskmetric score, weighted score, decision, timestamp. Note: changes/ updates occur tables new release riskassessment, may need delete database file re-running app. changes announced ‘breaking changes’ app. , remember save copy current database file another directory backup purposes.","code":"default:   assessment_db: ./dev/database.sqlite"},{"path":"https://pharmar.github.io/riskassessment/articles/Deployment.html","id":"database-log-file-config","dir":"Articles","previous_headings":"The db-config.yml file","what":"Database log file config","title":"Deployment","text":"mentioned previously, loggit.json file initiated track general actions performed application, especially reflect change assessment db (database.sqlite file). time vignette authored, ’s summary actions logged: App start User log-ins Enabling/ Disabling changing automated decision rules Decisions initiated users decision automation rules, including pkgs added removed database, issues process, like absence data support certain metrics Re-weighting pkg metrics database issues conflicts may arise loggit “transaction” recorded contains lot info, notably, contain time stamp, record type (“info”, “warn”, “error”), message. database transactions, message usually include query executed. log entries always printed R console convenience. example: Feel free use information see fit! Similar assessment_db parameter inst/db-config, can name file whatever like, save directory ’d like. , save dev/ folder name “loggit.json”:","code":"riskassessment::run_app() > [1] \"Log file set to loggit.json\" > Listening on http://127.0.0.1:4097 > {\"timestamp\": \"2023-03-20T11:46:23-0400\", \"log_lvl\": \"INFO\", \"log_msg\": \"User admin signed on as admin\"} > {\"timestamp\": \"2023-03-20T11:46:33-0400\", \"log_lvl\": \"INFO\", \"log_msg\": \"The following decision rules were implemented by admin (admin): Medium = (0.33__COMMA__ 0.66]; Low = (0__COMMA__ 0.33]; High = (0.66__COMMA__ 1].\"} default:   assessment_db: ./dev/database.sqlite   loggit_json: ./dev/loggit.json"},{"path":"https://pharmar.github.io/riskassessment/articles/Deployment.html","id":"credentials-configuration","dir":"Articles","previous_headings":"The db-config.yml file","what":"Credentials configuration","title":"Deployment","text":"Similar assessment database, riskassessment::run_app() function executes, code base check credentials sqlite file exists name give (default credentials.sqlite) doesn’t, riskassessment initiate new database app launches. Note user authority name database sqlite file whatever desire using inst/db-config.yml. , can include file path preceding file name wish move location database away root directory. example, following code create database called “credentials.sqlite” dev/ folder: Right credentials_db element used, credentials element (two sub-elements: roles privileges) must populated. guide, snippet default values elements, encourage design configuration works (organization). Note “User Roles Privileges” guide entirely dedicated config. full details, please visit & read article!","code":"default:   assessment_db: ./dev/database.sqlite   loggit_json: ./dev/loggit.json   credential_db: ./dev/credentials.sqlite credentials:   roles:     - admin     - lead     - reviewer   privileges:     admin: [admin, weight_adjust, auto_decision_adjust, final_decision, revert_decision, add_package, delete_package]     lead: [weight_adjust, auto_decision_adjust, final_decision, revert_decision, add_package, delete_package]     reviewer: add_package"},{"path":"https://pharmar.github.io/riskassessment/articles/Deployment.html","id":"decisions-configuration","dir":"Articles","previous_headings":"The db-config.yml file","what":"Decisions configuration","title":"Deployment","text":"decisions element contains three sub-elements: categories (mandatory), rules, colors. example configuration ’ll walk together:","code":"decisions:   categories:       - Insignificant Risk       - Minor Risk       - Needs Review       - Moderate Risk       - Major Risk       - Severe Risk     rules:       rule_1:         metric: bugs_status         condition: ~ metric_score(.x) <= .25         decision: Severe Risk       rule_2:         metric: dependencies         condition: ~ length(.x) >= 30         decision: Major Risk       rule_3:         metric: has_vignettes         condition: ~ .x == 0         decision: Moderate Risk       Severe Risk:         - .7         - 1       Insignificant Risk:         - 0         - .1       rule_else:         decision: Needs Review   colors:     Moderate Risk: !expr grDevices::rgb(52, 235, 229, maxColorValue = 255)"},{"path":"https://pharmar.github.io/riskassessment/articles/Deployment.html","id":"categories","dir":"Articles","previous_headings":"The db-config.yml file > Decisions configuration","what":"Categories","title":"Deployment","text":"Notice can set many decision categories wish, must specify least two! ’s suggested category names define ordinal way, first category lowest risk designation last category highest risk. example configuration , can see categories defined low risk category “Insignificant Risk” high risk category “Severe Risk”. non-ordinal category ’d like use, like “Needs Review” example, ’s possible - just don’t list first last.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/Deployment.html","id":"rules","dir":"Articles","previous_headings":"The db-config.yml file > Decisions configuration","what":"Rules","title":"Deployment","text":"Using rules element, may set automated decision rules prior launching app. , package uploaded, automatically get labelled appropriate decision rules condition met. rules executed order, top--bottom, ’s important place rules greatest priority top list. implement decision based risk score, list category name mutually exclusive range values directly beneath label packages whose risk score falls two values. , ’ve defined rules dictate risk scores 0.7 1 automatically categorized “Severe Risk”. Similarly, packages scoring 0 0.1 get labelled “Insignificant Risk”. addition, configuration file can evaluate expressions define rules. , rule needs three elements: metric, condition, decision seen . metric element simply name riskmetric assessment ’d like evaluate. Next, provide R code (including riskmetric code) help define rules using formula syntax. Note: .x translated selected metric’s assessment value. wish convert metric score, use riskmetric::metric_score(.x) shown . Last, provide decision category apply condition met. , specified hypothetical rules 1 - 3 apply decisions manner; , spell expressions sentence format, taking account previous condition isn’t met: packages bug closure rate less 25% considered “Severe Risk” packages 30 dependencies (>25% bug close rate) “Major Risk” packages vignettes (<30 dependencies >25% bug close rate) ”Moderate Risk” Categories addressed rules banner receive automated decisions. However, can provide optional rule_else element define decision category apply packages don’t meet rules . Also, keep mind users privileges edit decision rules may change configuration app later time.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/Deployment.html","id":"colors","dir":"Articles","previous_headings":"The db-config.yml file > Decisions configuration","what":"Colors","title":"Deployment","text":"Last, using colors element can detail specific colors assigned certain categories. Notice element accept expression evaluate launching application. don’t care color used category, color-blind friendly color palette used fill categories specified.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/Deployment.html","id":"metric-weights-configuration","dir":"Articles","previous_headings":"The db-config.yml file","what":"Metric weights configuration","title":"Deployment","text":"metric_weights element contains named list weights. weight supplied, default 1. current list weights can included following: has_vignettes, has_news, news_current, has_bug_reports_url, has_website, has_maintainer, has_source_control, export_help, bugs_status, license, covr_coverage, downloads_1yr. seen , default configuration sets weight covr_coverage 0. want ignore certain metric little value organization, give value zero. metrics explicitly given , app uses default weight 1 , unless course already exists assessment database previously initialized metric weights manually changed. wanted toggle current metrics, harm stating metric weight, set config file look like , example: riskmetric use weights score package according org’s needs!","code":"metric_weights:   has_vignettes: 2   has_news: 0.5   news_current: 2   has_bug_reports_url: 1   has_website: 1   has_maintainer: 1   has_source_control: 1   export_help: 2   bugs_status: 5   license: 1   downloads_1yr.: 3   covr_coverage: 0"},{"path":[]},{"path":"https://pharmar.github.io/riskassessment/articles/Deployment.html","id":"shinyapps-io","dir":"Articles","previous_headings":"Deployment options","what":"shinyapps.io","title":"Deployment","text":"Beware: shinyapps.io offer persistent storage riskassessment’s SQLite database logs. Thus, likely viable deployment option organization group. example, demo application (hosted shinyapps.io) contains pre-prepared database packages can’t permanently altered. CAN altered within session, changes persist outside session.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/Deployment.html","id":"posit-connect-shiny-server","dir":"Articles","previous_headings":"Deployment options","what":"Posit Connect & Shiny Server","title":"Deployment","text":"server, want save files disk, ’ll need set write permissions accordingly folder want save database, logs, auto-decision json file. Posit Connect, need use absolute path specify directory save files. can find information : Persistent Storage Posit Connect.  Beyond , ’s important note strongly encourage deploying app take advantage renv.lock file used maintain package version dependencies. information use renv.lock general dev philosophy pertains package management, please read “Using renv” article. Highly related, encourage use git-backed deployment possible. , immediately update/sync package dependencies using renv, may want run rsconnect::writeManifest() deploying dedicated branch. convenience, maintain current manifest.json follow renv.lock file GitHub repo. , ’ve forked application, able deploy latest version app -, directly master branch. information git-backed deployment & manifest files, please read Posit article git-backed content.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/Deployment.html","id":"shinyproxy","dir":"Articles","previous_headings":"Deployment options","what":"ShinyProxy","title":"Deployment","text":"ShinyProxy, can use Docker volume write files outside application container. application.yml, use can something like specs describing application: container-volumes: [ “/var/log/shinylogs:/root/logs” ] /var/log/shinylogs directory server deploy applications ShinyProxy. /root/logs directory inside Docker image.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/Deployment_V0.1.1.html","id":"the-database-sqlite-file","dir":"Articles","previous_headings":"","what":"The database.sqlite file","title":"Deployment V0.1.1","text":"riskassessment::run_app() function ran, code base check database.sqlite file exists, doesn’t, several tables initiated create database just app launches. Note user authority name database file whatever like using assessment_db_name argument run_app(). addition, can include file path preceding file name wish move location database away root directory. example, following code create database called “test_database.sqlite” dev/ folder: time vignette authored, database initialize following tables NULL values: comments: stores user comments, including user names associated comment entry, comment type, timestamp community_usage_metrics: stores CRAN package downloads per month metric: stores metric info, including riskmetric name, label, short description, type, weight package_metrics: stores package-specific rismetric metrics package: Contains package information, like name, version, maintainer, etc. also contains riskmetric score, weighted score, decision, timestamp. one exception : metric table populated data via initialize_metric_table.sql file. user deploying app wants enter certain weights prior launching application, good place . example, org wants place heavier weight “has_vignettes”, can increase weight value accordingly. course, can still application, require manual change app launched. Similarly, want ignore certain metric little value organization, give value zero . Note: changes/ updates occur tables new release riskassessment, may need delete database file re-running app. changes announced ‘breaking changes’ app. , remember save copy current database file another directory backup purposes.","code":"run_app(assessment_db_name = './dev/test_database.sqlite')"},{"path":"https://pharmar.github.io/riskassessment/articles/Deployment_V0.1.1.html","id":"the-loggit-json-file","dir":"Articles","previous_headings":"","what":"The loggit.json file","title":"Deployment V0.1.1","text":"mentioned previously, loggit.json file initiated track general actions performed application, especially impact change database.sqlite file. time vignette authored, ’s summary actions logged: App start User log-ins Enabling/ Disabling changing automated decision rules Decisions initiated users decision automation rules, including pkgs added removed database, issues process, like absence data support certain metrics Re-weighting pkg metrics database issues conflicts may arise loggit “transaction” recorded contains lot info, notably, contain timestamp, record type (“info”, “warn”, “error”), message. database transactions, message usually include query executed. log entries always printed R console convenience. example: Feel free use information see fit!","code":"riskassessment::run_app() > [1] \"Log file set to loggit.json\" > Listening on http://127.0.0.1:4097 > {\"timestamp\": \"2023-03-20T11:46:23-0400\", \"log_lvl\": \"INFO\", \"log_msg\": \"User admin signed on as admin\"} > {\"timestamp\": \"2023-03-20T11:46:33-0400\", \"log_lvl\": \"INFO\", \"log_msg\": \"The following decision rules were implemented by admin (admin): Medium = (0.33__COMMA__ 0.66]; Low = (0__COMMA__ 0.33]; High = (0.66__COMMA__ 1].\"}"},{"path":"https://pharmar.github.io/riskassessment/articles/Deployment_V0.1.1.html","id":"the-auto_decisions-json-file","dir":"Articles","previous_headings":"","what":"The auto_decisions.json file","title":"Deployment V0.1.1","text":"riskassessment::run_app() executed, search performed see exists auto_decisions.json file root directory. Without file, empty one automatically created. file used keep track decision automation rules. add & edit rules app, json file update accordingly, keeping track categories risk score range. example, following json file coordinates ranges displayed app:","code":"{\"Medium\":[0.33,0.66],\"Low\":[0,0.33],\"High\":[0.66,1]}"},{"path":[]},{"path":"https://pharmar.github.io/riskassessment/articles/Deployment_V0.1.1.html","id":"shinyapps-io","dir":"Articles","previous_headings":"Deployment options","what":"shinyapps.io","title":"Deployment V0.1.1","text":"Beware: shinyapps.io offer persistent storage riskassessment’s SQLite database logs. Thus, likely viable deployment option organization group. example, demo application (hosted shinyapps.io) contains pre-prepared database packages can’t permanently altered. CAN altered within session, changes persist outside session.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/Deployment_V0.1.1.html","id":"posit-connect-shiny-server","dir":"Articles","previous_headings":"Deployment options","what":"Posit Connect & Shiny Server","title":"Deployment V0.1.1","text":"server, want save files disk, ’ll need set write permissions accordingly folder want save database, logs, auto-decision json file. Posit Connect, need use absolute path specify directory save files. can find information : Persistent Storage Posit Connect.  Beyond , ’s important note strongly encourage deploying app take advantage renv.lock file used maintain package version dependencies. information use renv.lock general dev philosophy pertains package management, please read “Using renv” article. Highly related, encourage use git-backed deployment possible. , immediately update/sync package dependencies using renv, may want run rsconnect::writeManifest() deploying dedicated branch. information git-backed deployment & manifest files, please read Posit article git-backed content.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/Deployment_V0.1.1.html","id":"shinyproxy","dir":"Articles","previous_headings":"Deployment options","what":"ShinyProxy","title":"Deployment V0.1.1","text":"ShinyProxy, can use Docker volume write files outside application container. application.yml, use can something like specs describing application: container-volumes: [ “/var/log/shinylogs:/root/logs” ] /var/log/shinylogs directory server deploy applications ShinyProxy. /root/logs directory inside Docker image.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/User_Roles_and_Privileges.html","id":"privileges","dir":"Articles","previous_headings":"","what":"Privileges","title":"User Roles and Privileges","text":"time vignette authored, eight different privileges can assigned role: Administrator (admin): manages users application Weight Adjustment (weight_adjust): manages weights applied riskmetric risk calculation Automated Decision Adjustment (auto_decision_adjust): manages decision automation rules decision category display colors Final Decision (final_decision): makes final decisions regarding packages Revert Decision (revert_decision): can undo final decisions made regarding packages Add Packages (add_package): adds packages consideration Delete Packages (delete_package): can remove packages consideration Overall Commentator (overall_comment): can add/edit overall comment summary package General Commentator (general_comment): can add maintenance community metric comments","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/User_Roles_and_Privileges.html","id":"administrator","dir":"Articles","previous_headings":"Privileges","what":"Administrator","title":"User Roles and Privileges","text":"Basically, admin privilege allows user manage credentials privileges users. credential-heavy features admin privilege discussed length “Credential Manager” guide. Please reference vignette information. return top","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/User_Roles_and_Privileges.html","id":"weight-adjustment","dir":"Articles","previous_headings":"Privileges","what":"Weight Adjustment","title":"User Roles and Privileges","text":"weight_adjust privilege allows user change weights applied riskmetric risk calculation. options can found Assessment Reweighting Administrative Tools tab. high level view:  three buttons page: CONFIRM top right, DOWNLOAD middle left, UPDATE bottom left.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/User_Roles_and_Privileges.html","id":"download-database","dir":"Articles","previous_headings":"Privileges > Weight Adjustment","what":"Download Database","title":"User Roles and Privileges","text":"First, simplest: DOWNLOAD database button.   clicked, button download copy current database (default, called “database.sqlite”). app developers recommend anytime plan make integral changes database (like changing metric weights), anything else.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/User_Roles_and_Privileges.html","id":"updating-weights","dir":"Articles","previous_headings":"Privileges > Weight Adjustment","what":"Updating Weights","title":"User Roles and Privileges","text":"CONFIRM button allows view existing change metric weights used calculate risk score using riskmemtric.   can either select metric Select metric dropdown box select row “CURRENT RISK SCORE WEIGHTS METRIC” table. metric selected, enter new (numeric) weight “Choose new weight” box click CONFIRM button. ’ll notice row change appear highlighted, showing old weight value new weight value:   updated least one metric weight, UPDATE button enabled, allowing apply new weights re-calculated risk package. ’ve made final re-weighting changes, can click “Update” button pictured . Note weight changes take effect packages database, updating risk score .   click UPDATE get confirmation modal, reminding “updating risk metrics reverted”, strongly recommending download copy current database first clicking SUBMIT. modal also details actions take effect app submit changes. Note starting Version 1.0.0, re-calculation stored riskmetric assessments, re-assessment.   click SUBMIT modal dialog box appear indicating applying weights updating risk scores package uploaded. followed brief “updates completed” message.   Now go database overview tab confirm risk scores updated. can also view new weights, including standardized weight Assessment Criteria tab. return top","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/User_Roles_and_Privileges.html","id":"automated-decision-adjustment","dir":"Articles","previous_headings":"Privileges","what":"Automated Decision Adjustment","title":"User Roles and Privileges","text":"Users auto_decision_adjust privilege can edit decision automation rules decision category colors. organization black white rules package risk decisions based solely riskmetric scores, decision automation . leveraged, help automatically classify packages “Low Risk”, “Medium Risk”, “High Risk” decision categories upon upload (default configuration). current automation rules accessible two locations: ‘Upload Package’ Risk Assessment tab & ‘Decision Categories’ Database tab. get started, click small  (gear) button upper right hand corner either section.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/User_Roles_and_Privileges.html","id":"select-category-colors","dir":"Articles","previous_headings":"Privileges > Automated Decision Adjustment","what":"Select Category Colors","title":"User Roles and Privileges","text":"change color one decision categories, select new color either typing desired hexidecimal code use color input.  apply changes, click APPLY COLORS. pop-ask user review confirm selection: modal contains summary decision categories respective new colors. happy selections, simply click SUBMIT database application updated selections.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/User_Roles_and_Privileges.html","id":"automate-decision-by-risk-score","dir":"Articles","previous_headings":"Privileges > Automated Decision Adjustment","what":"Automate Decision by Risk Score","title":"User Roles and Privileges","text":"decision rules applied, ’ll see following decision categories adjacent empty check boxes. setting rules organization, can choose much little automation desired.   example, want set automatic decision “High Risk” scores, need select check box make risk score designation / cut value. , every time package uploaded risk score > 0.67, automatically receive decision label: “High Risk” saves review team time mental capacity reviewing large groups packages.   Similarly, package risk thresholds mapped decision category, apply ! user interface won’t allow slider ranges overlap, allow gaps range. example , adopt automatic decisions packages risk scores less 0.33 greater .67. fictitious example, let’s say organization policy package whose risk score falls 0.33 0.67 need reviewed manually.   apply changes, click APPLY DECISION RULES. pop-ask user review confirm selected automation rules:   Upon clicking submit, automation rules stored users see ‘Upload Package’ tab. uploading new set packages, can see ‘Summary Uploaded Package(s)’ now includes summary decisions made category automatically assigned. example , can see 10 packages uploaded, 7 automatic decisions made: six received “low risk” designation one labeled “high risk”. summary table, can note risk score decision right-hand side. can also observe packages weren’t found don’t exist CRAN.   ‘PACKAGE CONTROL PANEL’, select one packages decision made, see ‘Status’ changed “Reviewed” risk decision slider adjusted accordingly disabled. addition, ‘Overall Comment’ submitted, stating decision made driven via automation rules.  return top","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/User_Roles_and_Privileges.html","id":"final-decision","dir":"Articles","previous_headings":"Privileges","what":"Final Decision","title":"User Roles and Privileges","text":"name suggests, user final_decision privilege can make final decisions category package assigned. Overall comments regarding package also tied privilege.   return top","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/User_Roles_and_Privileges.html","id":"revert-decision","dir":"Articles","previous_headings":"Privileges","what":"Revert Decision","title":"User Roles and Privileges","text":"user revert_decision privilege can undo final decision made. set package’s status “review” re-enable “overall comments” regarding decision.   return top","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/User_Roles_and_Privileges.html","id":"add-packages","dir":"Articles","previous_headings":"Privileges","what":"Add Packages","title":"User Roles and Privileges","text":"user add_package privilege can upload packages database consideration.   return top","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/User_Roles_and_Privileges.html","id":"delete-packages","dir":"Articles","previous_headings":"Privileges","what":"Delete Packages","title":"User Roles and Privileges","text":"user delete_package privilege can remove packages consideration (database).   return top","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/User_Roles_and_Privileges.html","id":"overall-commentator","dir":"Articles","previous_headings":"Privileges","what":"Overall Commentator","title":"User Roles and Privileges","text":"user overall_comment privilege can add/edit two optional high-level summaries package: First, “Overall Comment”, located sidebar, outlet users specify quick synopsis related package decision, Package Summary, located “Build Report” tab, allows user compose long-form, open-ended summary evaluation / review process package interest Unlike maintenance community usage metrics, package can one entry “Overall Comment” “Package Summary”.   return top","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/User_Roles_and_Privileges.html","id":"general-commentator","dir":"Articles","previous_headings":"Privileges","what":"General Commentator","title":"User Roles and Privileges","text":"user general_comment privilege can add comments regarding maintenance community metrics package. meant provide suggestions justifications decision making.   return top","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/User_Roles_and_Privileges.html","id":"roles","dir":"Articles","previous_headings":"","what":"Roles","title":"User Roles and Privileges","text":"User roles group select privileges together providing users different, necessarily mutually exclusive, access application. default configuration contains four user roles: admin, lead, reviewer, viewer. snippet inst/db-config.yml file roles defined:   configuration, admin user access entire application, lead user access privileges except administrative ones (e.g. managing user credentials), reviewer privilege add packages consideration adding comments/descriptions, viewer can view current state assessment. organization can customize user roles support needs. information please reference “Deployment” guide. return top","code":"privileges:   admin: [admin, weight_adjust, auto_decision_adjust, final_decision, revert_decision, add_package, delete_package, overall_comment, general_comment]   lead: [weight_adjust, auto_decision_adjust, final_decision, revert_decision, add_package, delete_package, overall_comment, general_comment]   reviewer: [add_package, general_comment]   viewer:"},{"path":"https://pharmar.github.io/riskassessment/articles/dev_Using_SQLite_Command_Line.html","id":"about-sqlite","dir":"Articles","previous_headings":"","what":"About SQLite","title":"Using SQLite Command Line","text":"SQLite software library provides relational database management system. lite SQLite means lightweight terms setup, database administration, required resources. SQLite following noticeable features: self-contained, serverless, zero-configuration, transactional. information, see SQLite","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/dev_Using_SQLite_Command_Line.html","id":"why-sqlite","dir":"Articles","previous_headings":"","what":"Why SQLite?","title":"Using SQLite Command Line","text":"one obvious reason – riskassessment App data stored SQLite database. Also, one SQLite’s advantages can run nearly anywhere. vignette provide means accessing database outside riskassessment App.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/dev_Using_SQLite_Command_Line.html","id":"download-sqlite-tools","dir":"Articles","previous_headings":"","what":"Download SQLite tools","title":"Using SQLite Command Line","text":"Open download page SQLite Download Page work SQLite Windows, download command-line shell program shown screenshot . using Mac, need download one:   either case, downloaded file ZIP format size quite small.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/dev_Using_SQLite_Command_Line.html","id":"run-sqlite-tools","dir":"Articles","previous_headings":"","what":"Run SQLite tools","title":"Using SQLite Command Line","text":"Installing SQLite simple straightforward. Create new folder e.g., C:\\sqlite. Extract content .zip file downloaded previous section C:\\sqlite folder. see three programs shown :","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/dev_Using_SQLite_Command_Line.html","id":"open-the-command-line-window-","dir":"Articles","previous_headings":"","what":"Open the command line window.","title":"Using SQLite Command Line","text":"Windows, type “cmd” search bar.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/dev_Using_SQLite_Command_Line.html","id":"navigate-to-the-csqlite-folder-","dir":"Articles","previous_headings":"","what":"Navigate to the C:\\sqlite folder.","title":"Using SQLite Command Line","text":"Next, type sqlite3 press enter, see following output: Navigate directory containing riskassessment database. Note: app’s default behavior call database “database.sqlite”, unless ’ve specified otherwise using assessment_db_name arg run_app(). Next, use .open FILENAME command open . example: .open database.sqlite; show tables, type .tables show structure table, type .schema TABLE can also type .help sqlite> prompt see available commands. exit, type .quitor .exit","code":"C:\\cd c:\\sqlite C:\\sqlite> C:\\sqlite>sqlite3  SQLite version 3.33.0 2020-08-14 13:23:32  Enter \".help\" for usage hints.  Connected to a transient in-memory database.  Use \".open FILENAME\" to reopen on a persistent database.  sqlite> sqlite> .tables comments                 metric                   package_metrics community_usage_metrics  package sqlite> sqlite> .schema package_metrics CREATE TABLE package_metrics (   id           INTEGER PRIMARY KEY AUTOINCREMENT,   package_id   INT,    metric_id    INT,   value        CHAR,   /* value == 'pkg_metric_error' indicates an error. */   /* value == NA indicates metric is not applicable for this package. */   weight       REAL,   FOREIGN KEY (package_id) REFERENCES package(id),   FOREIGN KEY (metric_id) REFERENCES metric(id)); sqlite> sqlite> .help .archive ...             Manage SQL archives .auth ON|OFF             Show authorizer callbacks .backup ?DB? FILE        Backup DB (default \"main\") to FILE .bail on|off             Stop after hitting an error.  Default OFF .binary on|off           Turn binary output on or off.  Default OFF .cd DIRECTORY            Change the working directory to DIRECTORY .changes on|off          Show number of rows changed by SQL .check GLOB              Fail if output since .testcase does not match .clone NEWDB             Clone data into NEWDB from the existing database .databases               List names and files of attached databases .dbconfig ?op? ?val?     List or change sqlite3_db_config() options .dbinfo ?DB?             Show status information about the database .dump ?TABLE?            Render database content as SQL .echo on|off             Turn command echo on or off .eqp on|off|full|...     Enable or disable automatic EXPLAIN QUERY PLAN .excel                   Display the output of next command in spreadsheet ... additional output not displayed"},{"path":"https://pharmar.github.io/riskassessment/articles/dev_Using_SQLite_Command_Line.html","id":"command-line-shell","dir":"Articles","previous_headings":"","what":"Command Line Shell","title":"Using SQLite Command Line","text":"can also temporarily add C:\\sqlite Windows path. set PATH=%PATH%;C:\\sqlite Verify typing echo %PATH% riskassessment directory, can just enter following command line: sqlite3 database.sqlite see can also use system2 command execute SQLite commands RStudio command line. can build queries commands SQLite execute . info, see Command Line Shell SQLite","code":"SQLite version 3.33.0 2020-08-14 13:23:32 Enter \".help\" for usage hints. sqlite> > system2(\"C:/sqlite/sqlite3\", args =c(\"database.sqlite\", \".tables\", \".quit\")) comments                 metric                   package_metrics         community_usage_metrics  package > table_name <- \"package\" > query <- glue::glue(\"select * from { table_name } limit 1;\") > frst_row <- system2(\"C:/sqlite/sqlite3\", args =\"database.sqlite\", input = query, stdout = TRUE) >  > frst_row [1] \"1|glue|1.6.2|glue: Interpreted String Literals|An implementation of interpreted string literals, inspired by   Pythons Literal String Interpolation   <https://www.python.org/dev/peps/pep-0498/> and Docstrings   <https://www.python.org/dev/peps/pep-0257/> and Julias Triple-Quoted   String Literals   <https://docs.julialang.org/en/v1.3/manual/strings/#Triple-Quoted-String-Literals-1>.|Jennifer Bryan  <jenny at rstudio.com>|Jim Hester  [aut], Jennifer Bryan    [aut, cre], RStudio [cph, fnd]|MIT + file LICENSE|2022-02-24|0.11|||2022-02-24\""},{"path":"https://pharmar.github.io/riskassessment/articles/dev_Using_SQLite_Command_Line.html","id":"sqlitestudio","dir":"Articles","previous_headings":"","what":"SQLiteStudio","title":"Using SQLite Command Line","text":"SQLiteStudio tool free GUI tool managing SQLite databases. free, portable, intuitive, cross-platform. SQLite tool also provides important features work SQLite databases importing, exporting data various formats including CSV, XML, JSON. Visit SQLite Studio can download SQLiteStudio installer portable version visiting download page. , can extract (install) download file folder e.g., C: launch . following picture illustrates launch SQLiteStudio:","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/dev_renv.html","id":"overview","dir":"Articles","previous_headings":"","what":"Overview","title":"Developer onboarding - using renv","text":"renv package provides project-local R dependency management projects. helps manage library paths (project-specific state) help isolate project’s R dependencies. renv package helps create reproducible environments R projects. make R packages isolated, portable reproducible.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/dev_renv.html","id":"actions-performed-only-once-in-the-repo","dir":"Articles","previous_headings":"","what":"Actions performed only once in the repo","title":"Developer onboarding - using renv","text":"First someone initialized new project-local environment private R library - can done via renv::init(). action result creation lockfile - named renv.lock root directory. lock file contains ton environment metadata, including developers installed packages & versions, plus repository source packages installed (.e. CRAN, GitHub, RSPM, etc). ’s important note dev team use repo source point production CRAN, want stable (aka unchanging) source pkgs. addition, lockfile () upgraded need important new feature relies latest version new existing pkg lock file. developer working within repo first time need sync packages stored renv.lock file. first time , ’ll need run renv::activate() ask confirm decision. Note new pkg installations impact R project, R system library stored elsewhere.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/dev_renv.html","id":"if-new-packages-installations-are-needed","dir":"Articles","previous_headings":"","what":"If new packages installations are needed","title":"Developer onboarding - using renv","text":"new dependencies needed, can save current state project library renv::snapshot(). However, pkg changes must expressly documented justified PR’s comments section considered ready review. Without , reviewer reject & request changes PR immediately. dev team’s philosophy renv.lock file () upgraded need important new feature/functionality relies different version new existing pkg. Even updating pkg, R sometimes ask want upgrade packages, seen . always say “3: None” possible.    just want test new package committing lockfile, can . Go ahead install package interest want revert back pkg line stored lock file anytime, just run renv::restore(). Similarly, anytime fellow developer(s) submit PR change lock file, ’ll need run renv::restore() sync development rest team. time sync renv.lock file, can run renv::status() see packages ahead behind lock file.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/dev_renv.html","id":"how-to-ignore-files-pkgs-in-the-lock-file","dir":"Articles","previous_headings":"","what":"How to ignore files & pkgs in the lock file","title":"Developer onboarding - using renv","text":"default renv ignores files stated .gitignore file. want extend , can use .renvignore file - specified similar .gitignore file. addition, can ignore package renv thinks need add lock file using following command: renv::settings$ignored.packages(\"<<package name>>\")","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/dev_renv.html","id":"cache-location-on-different-operating-systems","dir":"Articles","previous_headings":"","what":"Cache Location on different Operating Systems","title":"Developer onboarding - using renv","text":"Linux ~/.local/share/renv macOS ~/Library/Application Support/renv Windows %LOCALAPPDATA%/renv","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/dev_renv.html","id":"references","dir":"Articles","previous_headings":"","what":"References","title":"Developer onboarding - using renv","text":"github.io/renv/ Introduction renv","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/riskassessment.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"Get Started with {riskassessment}","text":"Welcome! guide help users get started riskassessment application first time. information deploy application, please reference Deployments [INSERT LINK] guide. note: guide assumes already downloaded riskassessment package & ’s dependencies following installation instructions.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/riskassessment.html","id":"run-deploy-app-r","dir":"Articles","previous_headings":"","what":"Run / Deploy app.R","title":"Get Started with {riskassessment}","text":"application already deployed, can skip step! installed riskassessment package, now able run app locally using provided app.R file. applicable, can specify application options file, using either options() arguments run_app() function (run ?riskassessment::run_app learn ). However, purposes guide, ’ll run function -, accepting defaults: Running code launch application doesn’t already exist, create initial database authentication.","code":"# launch the application riskassessment::run_app()"},{"path":"https://pharmar.github.io/riskassessment/articles/riskassessment.html","id":"first-time-log-in","dir":"Articles","previous_headings":"","what":"First time log in","title":"Get Started with {riskassessment}","text":"first page ’ll see authentication screen default note bottom:  NOTE: LOG FIRST TIME, USE ADMIN USER: ADMIN PASSWORD QWERTY1. recall, application acts central hub organization review assess risk R packages, thus establishing users specific roles vital. start, application needs admin user.   admin user asked change password immediately. supplying new secure password, click “UPDATE NEW PASSWORD”. password successfully updated, ’ll prompted “LOGIN” new credentials.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/riskassessment.html","id":"subsequent-logins","dir":"Articles","previous_headings":"","what":"Subsequent logins","title":"Get Started with {riskassessment}","text":"designated admin user(s) special privileges duties application, including limited creating new users, admin non-admin roles. admins, please see article titled “Credential Manager” create new users. non-admin roles, receive temporary password initial log , ’ll prompted change immediately upon first visit app. subsequent visits, won’t worry first-time log procedures!","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/riskassessment.html","id":"welcome-to-the-app","dir":"Articles","previous_headings":"","what":"Welcome to the app!","title":"Get Started with {riskassessment}","text":"Upon successful log , ’ll notice many tabs panels.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/riskassessment.html","id":"self-guided-tours","dir":"Articles","previous_headings":"Welcome to the app!","what":"Self-guided tours","title":"Get Started with {riskassessment}","text":"Throughout app, small help buttons strategically placed upper right-hand corners page. clicked, empower users walk UI elements visible -screen desired pace. Consider personal tour guide need quick reminder “?”.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/riskassessment.html","id":"upload-a-package","dir":"Articles","previous_headings":"","what":"Upload a package","title":"Get Started with {riskassessment}","text":"Now main event - let’s upload packages review & assess organization. ’s first time using app, empty database initialized app launch populated packages, riskmetric outputs, organization’s assessment preferences. begin filling database package info, ’ll need start upload list packages want review. Risk Assessment tab, main panel titled, R PACKAGE RISK ASSESSMENT APP four tabs . default, ’ll directed Upload Package tab. Uploading packages can done manually typing one () package names prompt , long list packages asses, may convenient upload CSV file package names. CSV file requires two columns: “package” “version.” However, right now riskmetric can tackle current version, version column ignored. meantime, can make life easier setting version “0.0.0” packages CSV. Additionally, third column “decision” can included. can helpful organization already list packages approved use. simplified example acceptable CSV file: Alternatively, may prefer test app typing package, “glue” prompt. Notice text input pre-populate CRAN packages upon click, thus forget spelling case package, auto-complete feature can assist . ready, select red “>” button progress modal like one appear indicating process generating package info various sources begun app start inserting information database. Upon completion, “Summary Uploaded Packages” section display. lists total packages uploaded, number packages new database, number undiscovered (probably misspelled) packages, number duplicate packages, .e. packages already existed database.","code":"package,version stringr,0.0.0 tidyr,0.0.0"},{"path":"https://pharmar.github.io/riskassessment/articles/riskassessment.html","id":"decision-automation","dir":"Articles","previous_headings":"","what":"Decision Automation","title":"Get Started with {riskassessment}","text":"organization black white rules package risk decisions based solely riskmetric scores, decision automation . leveraged, help automatically classify packages “Low”, “Medium”, “High” risk decision categories upon upload. automation saves review team time mental capacity reviewing large groups packages. current automation rules always displayed ‘Upload Package’ tab. Please note admin users necessary privileges edit. get started, click small gear button upper left hand corner   fictitious example , let’s say admin user adopts automated decision rules packages risk scores less 0.33 greater .66. Perhaps organization policy mandates package whose risk score falls 0.33 0.66 need reviewed manually. uploading new CSV packages, can see ‘Summary Uploaded Package(s)’ displays number decisions made overall risk category. , can see 10 packages uploaded, 5 automatic decisions made: four received “low” designation one labeled “high” risk. summary table, decisions displayed respective risk scores right-hand side. can also observe packages weren’t found don’t exist CRAN.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/riskassessment.html","id":"sidebar","dir":"Articles","previous_headings":"","what":"Sidebar","title":"Get Started with {riskassessment}","text":"Now database populated package data, direct attention PACKAGE CONTROL PANEL left select package (glue) list. package selected, VERSION, STATUS RISK boxes populated information. now, latest version package displayed. Since decision endorse reject package hasn’t made yet, STATUS “Review”. Third, RISK box contains riskmetric score, represented number 0 (low risk) 1 (high risk). also two submission buttons : SUBMIT DECISION SUBMIT OVERALL COMMENT. goal thorough review info contain application, user well informed enough categorize package’s risk either “low”, “medium”, “high” risk using slider. Clicking submit completes review package organization can undone admin user. ’re looking submit something less formal, submitting decision, consider submitting “overall comment” summarizing high level thoughts package. Though ’s required, ’s recommended always submit “overall comment” submitting final decision.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/riskassessment.html","id":"package-metrics-review-tabs","dir":"Articles","previous_headings":"","what":"‘Package Metrics’ Review Tabs","title":"Get Started with {riskassessment}","text":"Package Metrics tab contains riskmetric derived assessments one place, consolidates different like-kind groups convenience-sake. , metrics sorted either “Maintenance” “Community Usage” categories. latest version app, 3rd category added better support analysis “Dependencies”, can selected via drop top tab: ’s tabs bulk automated review occurs metric provides context determines final riskmetric score. highly encourage users become familiar metrics decide important organization. available riskmetric, riskassessment allows admin users set organization-wide metric weights risk score based meaningful metrics, reduces influence less important metrics. Thus, metric un-important org, highly recommend weighting 0. learn options, please read “Metric weights configuration” guide.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/riskassessment.html","id":"maintenance-metrics","dir":"Articles","previous_headings":"‘Package Metrics’ Review Tabs","what":"Maintenance Metrics","title":"Get Started with {riskassessment}","text":"look Maintenance Metrics output “glue” package: metric tab measures something related package maintenance best practices, whether storing code public URL, providing vignettes guide users, package authors sufficiently giving attention bugs. Note metrics report assessment “Found”. ’s application uses “pkg_cran_remote” source compiling metrics, capability gather info possible metrics. -going effort build information remote metrics. learn , please explore package assessment topics riskmetric documentation. Note can add replace comments Maintenance Metrics package, review paste comments made users. great platform form opinions, write others organization read consider evaluation.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/riskassessment.html","id":"community-usage-metrics","dir":"Articles","previous_headings":"‘Package Metrics’ Review Tabs","what":"Community Usage Metrics","title":"Get Started with {riskassessment}","text":"first look Community Usage Metrics “glue” package:   metric tab measures something related package’s usage community. user community plays important role open source software development. words, exposure package community, ad-hoc testing exposed . time “better packages” tend rise top, leading downloads increased exposure. Note riskmetric considers metric called Number download last year Reverse Dependencies risk score calculation. data presented tab accessories help user explore idea community usage. Notably, tab includes highly interactive visual, shows number downloads month since package first released. information metrics, explore package assessments riskmetric documentation. , can add replace comments Community Usage metrics package.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/riskassessment.html","id":"the-source-explorer-tab","dir":"Articles","previous_headings":"","what":"The ‘Source Explorer’ Tab","title":"Get Started with {riskassessment}","text":"Introduced v2.0.0 riskassessment, Source Explorer tab offers users manual, hands-approach assessing packages exploring source contents package. Just developer forking repository explore code, can now page files bundled stored CRAN. exceptions, however: certain file types don’t display well file browser, like RDS example, aren’t compatible. ; example, viewing DESCRIPTION file (doesn’t extension) glue package. possibilities truly endless access source code: can browse R scripts containing exported (non-exported) functions, read contents LICENSE file, even explore tests/ folder inspect robustness ’s unit tests. Just expand file tree left hand side reveal contents folders.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/riskassessment.html","id":"the-build-report-tab","dir":"Articles","previous_headings":"","what":"The ‘Build Report’ Tab","title":"Get Started with {riskassessment}","text":"top portion Build Report tab. tab pulls information viewed previous tabs consolidates easy browse report, downloaded HTML, DOCX, PDF. However, first gives user ample control care see report using check boxes, pre-checked default. Optionally, “Package Summary” section allows reviewers log information explicit acknowledged metrics, plots, risk-based decision, comments. field allow organizations satisfy custom documentation needs app privy . Note one summary can logged per package, submitted, add another, must edit existing summary acceptable.   Directly beneath configurations “report preview” can see first-hand configs & review efforts impact report download.  addition metric info, can see contains vital metadata assessment performed app. quick view metadata referenced . ’s vital understand context report & score calculated. Users encouraged send information rich reports choose, especially savvy riskassessment app… yet.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/riskassessment.html","id":"make-a-decision","dir":"Articles","previous_headings":"","what":"Make a decision","title":"Get Started with {riskassessment}","text":", ’ve uploaded package, reviewed ’s metrics, package score, double-checked metric weights, even read co-workers comments. ’s really nothing left make final decision. waiting ! Let’s ! Head Package Control Panel. First ’ll start “Overall Comment”. Write words ’ve learned evaluation recommend brief succinct .   clicking submit, ’ll receive prompt just confirms wrote. Click dismiss now turn attention decision slider, options “Low”, “Medium”, “High”. Consider organization may treat category? example, “Low” might mean ’s permitted use regulatory environments, “Medium” may mean package isn’t fully endorsed yet, needs stay holding patter. “High” course means rejection.   purposes guide, submitted decision selection “Low” received following dialogue box asking us confirm decision:   clicking ‘Submit’, ’ll notice STATUS updated “REVIEWED” decision slider now disabled & grayed . logged admin user, button now displays “RESET DECISION” non-admin users option.   Congratulations! ’ve reviewed first package! goal, accomplished . Now keep going, waiting ? time guide authored, 19,038 packages CRAN organization may want use !","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/riskassessment.html","id":"other-tabs","dir":"Articles","previous_headings":"","what":"Other Tabs","title":"Get Started with {riskassessment}","text":"may noticed navigation tabs top app contain following four tabs.   work performed first tab: Risk Assessment. ’ll painfully brief touch tabs , just know -depth guides exist .","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/riskassessment.html","id":"database","dir":"Articles","previous_headings":"Other Tabs","what":"Database","title":"Get Started with {riskassessment}","text":"second tab, Database shows, package loaded, package name version, ’s riskmetric score, whether decision made, decision, timestamp last comment provided. Reports (either .html, .docx, .pdf format) can downloaded selected package(s). multiple packages selected, really helpful","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/riskassessment.html","id":"assessment-criteria","dir":"Articles","previous_headings":"Other Tabs","what":"Assessment Criteria","title":"Get Started with {riskassessment}","text":"third tab, Assessment Criteria provides detailed description assessment criteria used Risk Calculation, Maintenance Metrics, Community Usage Metrics, Testing metrics. metric even short description included riskmetric. Risk Calculation tab shown . Browse tab information.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/riskassessment.html","id":"administrative-tools","dir":"Articles","previous_headings":"Other Tabs","what":"Administrative Tools","title":"Get Started with {riskassessment}","text":"fourth tab, Administrative tools, contains two sub-tabs: Credential Manager Assessment Reweighting. former allows admin users add delete users well change passwords others. details provided “Credential Manager” guide   Assessment Reweighting tab admin users fine tune package risk score generated riskmetric manipulating value placed metrics assessed app. Changes made apply packages database, plus packages uploaded future. details provided “User Roles Privileges” guide.","code":""},{"path":"https://pharmar.github.io/riskassessment/articles/riskassessment.html","id":"where-to-go-from-here","dir":"Articles","previous_headings":"","what":"Where to go from here?","title":"Get Started with {riskassessment}","text":"Check riskmetric riskassessment presentations www.pharmar.org/present/. read prepared guides boost knowledge become power user!","code":""},{"path":"https://pharmar.github.io/riskassessment/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Aaron Clark. Author, maintainer. Robert Krajcik. Author. Jeff Thompson. Author. Lars Andersen. Author. Andrew Borgman. Author. Munshi Imran Hossain. Contributor. Scott Schumacker. Contributor. Marly Gotti. Author. Maya Gans. Author. Aravind Reddy Kallem. Author. Eduardo Almeida. Contributor. Narayanan Iyer. Contributor. Fission Labs India Pvt Ltd. Author. PSI special interest group Application Implementation Methodologies Statistics. Copyright holder, funder. R Validation Hub. Copyright holder, funder. GSK contributors. Contributor.            Author 'pharmaR/pkg_explorer' repo Appsilon. Contributor.","code":""},{"path":"https://pharmar.github.io/riskassessment/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Clark , Krajcik R, Thompson J, Andersen L, Borgman , Gotti M, Gans M, Kallem , Fission Labs India Pvt Ltd (2024). riskassessment: web app designed interface 'riskmetric' package. R package version 3.1.0, https://pharmar.github.io/riskassessment/, https://github.com/pharmaR/riskassessment.","code":"@Manual{,   title = {riskassessment: A web app designed to interface with the `riskmetric` package},   author = {Aaron Clark and Robert Krajcik and Jeff Thompson and Lars Andersen and Andrew Borgman and Marly Gotti and Maya Gans and Aravind Reddy Kallem and {Fission Labs India Pvt Ltd}},   year = {2024},   note = {R package version 3.1.0, https://pharmar.github.io/riskassessment/},   url = {https://github.com/pharmaR/riskassessment}, }"},{"path":"https://pharmar.github.io/riskassessment/index.html","id":"the-riskassessment-application-","dir":"","previous_headings":"","what":"A web app designed to interface with the `riskmetric` package","title":"A web app designed to interface with the `riskmetric` package","text":"riskassessment R package containing shiny front-end augment utility riskmetric package within organizational context. ’re honored announce app recently awarded title “Best App” Shiny Conf 2023 (see Recognition section ).   riskmetric framework quantify R package’s “risk use” assessing number meaningful metrics designed evaluate package development best practices, code documentation, community engagement, development sustainability. Together, riskassessment app riskmetric package aim provide context validation within regulated industries. app extends functionality riskmetric allowing reviewer : analyze riskmetric output without need write code R contribute personalized comments value individual metrics categorize package overall assessment (.e., low, medium, high risk) based subjective opinions tabulating user(s) consensus evaluating metric output download static reports package risk, metrics outputs, reviewer summary & comments, plus store assessments database future viewing historical backup user authentication privileges & admin-defined roles manage users tasks performed app","code":""},{"path":"https://pharmar.github.io/riskassessment/index.html","id":"echo-ing-riskmetrics-approach-to-validation-","dir":"","previous_headings":"","what":"Echo-ing {riskmetric}’s Approach to Validation","title":"A web app designed to interface with the `riskmetric` package","text":"Validation can serve umbrella various terms, admittedly, companies diverge may “correct approach”. riskassessment app built rismetric-foundation, whose developers follow validation philosophy proposed white paper published R Validation Hub. , scope riskassessment riskmetric designed support decision making view point. full robustness reliability software may (likely ) require deeper inspection reviewing party. Note: Development riskassessment riskmetric made possible thanks R Validation Hub, collaboration support adoption R within biopharmaceutical regulatory setting.","code":""},{"path":"https://pharmar.github.io/riskassessment/index.html","id":"usage","dir":"","previous_headings":"","what":"Usage","title":"A web app designed to interface with the `riskmetric` package","text":"new using riskassessment app, welcome! ’d highly encourage start exploring demo version app currently deployed shinyapps.io. , ’ll find number pre-loaded packages just waiting assessed. Hands experience help become familiar general layout app poke around explore. said, immediately recognize app requires authentication, since ’s intended use within organization. several pre-defined roles, important admin user. default, admin can add/delete users, download entire copy database, modify metric weights used calculation risk scores, define custom decision categories, automation rules base risk scores. demo version app tells prompts log initially. However, launch app.R file locally, admin user leverage password QWERTY1 initially. log credential, app immediately prompt change password repeat process new credentials. want quick overview project demo application, highly recommend watching following video walk Shiny Conf 2023. conference, riskassessment voted “best application” conference attendees! app also featured Rstudio::Global 2021.","code":""},{"path":"https://pharmar.github.io/riskassessment/index.html","id":"installation","dir":"","previous_headings":"Usage","what":"Installation","title":"A web app designed to interface with the `riskmetric` package","text":"recommend run/deploy application controlled development environment. course, can install latest version GitHub using code , doesn’t take consideration environment dependencies… example, using different version riskmetric dev team? Thus, development team can’t guarantee ’s stability, recommend clone repo’s R project locally instead. cloned/ forked, run following code order take advantage renv.lock file set’s project dependencies: step complete, can simply run contents app.R launch /deploy application default settings! information dev philosophy pertains package management, please read “Using renv” article. , learn manipulate app’s configuration away defaults reading guide “Deployment” covers use app’s configuration file tailor app needs.","code":"# DON'T RUN THIS CODE! There's a better way! remotes::install_github(\"pharmaR/riskmetric\") remotes::install_github(\"pharmaR/riskassessment\")  # Run the application  riskassessment::run_app() # First, clone the repo from GitHub, then... # Get dependcies synced using {renv} renv::activate() renv::restore()"},{"path":"https://pharmar.github.io/riskassessment/index.html","id":"user-guides-and-user-feedback","dir":"","previous_headings":"","what":"User Guides and User Feedback","title":"A web app designed to interface with the `riskmetric` package","text":"’re constantly improving app ’s documentation. Please explore user guides developed date, available riskassessment documentation site. sure read ‘Get Started’ tab perhaps another article two! course, ever specific feedback developers, encounter problem / bug within app, recommend opening new issue GitHub ’ll address promptly.  also want align users big picture, strategic topics. Specifically, want hear groups ’ve built (currently building) R-package validation process, whether use riskmetric / riskassessment ! Ideally, goal form consensus companies regarding validation approach can make riskmetric riskassessment better. example, ’d love understand users currently weighting metrics used calculate package’s risk score. ’d also love learn companies leverage certain risk score thresholds make GxP environment inclusion (exclusion) decisions package. facilitate gathering information, ’ve created incredibly brief questionnaire let us know ’re .","code":""},{"path":"https://pharmar.github.io/riskassessment/index.html","id":"deployment","dir":"","previous_headings":"User Guides and User Feedback","what":"Deployment","title":"A web app designed to interface with the `riskmetric` package","text":"might expect, certain deployment environments offer persistent storage others . example, shinyapps.io . means even demo app ’s hosted shinyapps.io contains package database can’t permanently altered. ’s advantageous since organization needs continually add new packages, publish comments, make decisions packages. Thus, ’d recommend exploring deployment options (allow persistent storage): Shiny Server Posit Connect ShinyProxy information , highly recommend reading ‘Deployment’ article.","code":""},{"path":"https://pharmar.github.io/riskassessment/index.html","id":"recognition","dir":"","previous_headings":"User Guides and User Feedback","what":"Recognition","title":"A web app designed to interface with the `riskmetric` package","text":"March 2023, Appsilon hosted 2nd annual Shiny Conf fully virtual, boasting approximately 4k registrants. Aaron Clark, package maintainer R Validation Hub Executive member, presented riskassessment app work “Shiny Showcase” among 20+ app submissions. end conference, riskassessment awarded title “Best App” popular vote.","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/aboutInfoServer.html","id":null,"dir":"Reference","previous_headings":"","what":"Server Logic for 'About' Module — aboutInfoServer","title":"Server Logic for 'About' Module — aboutInfoServer","text":"Server Logic '' Module","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/aboutInfoServer.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Server Logic for 'About' Module — aboutInfoServer","text":"","code":"aboutInfoServer(id, metric_weights)"},{"path":"https://pharmar.github.io/riskassessment/reference/aboutInfoServer.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Server Logic for 'About' Module — aboutInfoServer","text":"id module id name metric_weights object outputted reweightViewServer()","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/aboutInfoUI.html","id":null,"dir":"Reference","previous_headings":"","what":"UI for 'About' Module — aboutInfoUI","title":"UI for 'About' Module — aboutInfoUI","text":"UI '' Module","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/aboutInfoUI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"UI for 'About' Module — aboutInfoUI","text":"","code":"aboutInfoUI(id)"},{"path":"https://pharmar.github.io/riskassessment/reference/aboutInfoUI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"UI for 'About' Module — aboutInfoUI","text":"id module id name","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/addCommentServer.html","id":null,"dir":"Reference","previous_headings":"","what":"addComment module's server logic — addCommentServer","title":"addComment module's server logic — addCommentServer","text":"addComment module's server logic","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/addCommentServer.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"addComment module's server logic — addCommentServer","text":"","code":"addCommentServer(id, metric_abrv, user, credentials, pkg_name)"},{"path":"https://pharmar.github.io/riskassessment/reference/addCommentServer.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"addComment module's server logic — addCommentServer","text":"id module id name metric_abrv placeholder pkg_name string name package user_name placeholder user_role placeholder","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/addCommentUI.html","id":null,"dir":"Reference","previous_headings":"","what":"The UI for the 'addComment' module — addCommentUI","title":"The UI for the 'addComment' module — addCommentUI","text":"Module display comments specified metric. comments update user inserts comments.","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/addCommentUI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The UI for the 'addComment' module — addCommentUI","text":"","code":"addCommentUI(id)"},{"path":"https://pharmar.github.io/riskassessment/reference/addCommentUI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The UI for the 'addComment' module — addCommentUI","text":"id module id name","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/add_shinymanager_auth.html","id":null,"dir":"Reference","previous_headings":"","what":"Add an Authentication Screen — add_shinymanager_auth","title":"Add an Authentication Screen — add_shinymanager_auth","text":"Adds authentication screen via shinymanager::secure_app().","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/add_shinymanager_auth.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add an Authentication Screen — add_shinymanager_auth","text":"","code":"add_shinymanager_auth(app_ui, app_ver, login_note)"},{"path":"https://pharmar.github.io/riskassessment/reference/add_shinymanager_auth.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add an Authentication Screen — add_shinymanager_auth","text":"app_ui app_ui function application. app_ver See identical param run_app(). login_note See identical param run_app().","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/add_tags.html","id":null,"dir":"Reference","previous_headings":"","what":"The 'Add tags' function — add_tags","title":"The 'Add tags' function — add_tags","text":"'Add tags' function","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/add_tags.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The 'Add tags' function — add_tags","text":"","code":"add_tags(ui, ...)"},{"path":"https://pharmar.github.io/riskassessment/reference/add_tags.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The 'Add tags' function — add_tags","text":"ui placeholder ... placeholder","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/app_theme.html","id":null,"dir":"Reference","previous_headings":"","what":"Application Theme — app_theme","title":"Application Theme — app_theme","text":"sets riskassessment Application theme object using bslib's bs_theme() function. app_theme object gets used run_app.R, addition app_ui.R","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/app_theme.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Application Theme — app_theme","text":"","code":"app_theme()"},{"path":"https://pharmar.github.io/riskassessment/reference/app_theme.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Application Theme — app_theme","text":"bs_theme object several classes","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/assessmentInfoServer.html","id":null,"dir":"Reference","previous_headings":"","what":"Server Logic for 'Assessment Info' Module — assessmentInfoServer","title":"Server Logic for 'Assessment Info' Module — assessmentInfoServer","text":"Server Logic 'Assessment Info' Module","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/assessmentInfoServer.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Server Logic for 'Assessment Info' Module — assessmentInfoServer","text":"","code":"assessmentInfoServer(id, metric_weights)"},{"path":"https://pharmar.github.io/riskassessment/reference/assessmentInfoServer.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Server Logic for 'Assessment Info' Module — assessmentInfoServer","text":"id module id name metric_weights placeholder","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/assessmentInfoUI.html","id":null,"dir":"Reference","previous_headings":"","what":"UI for 'Assessment Info' Module — assessmentInfoUI","title":"UI for 'Assessment Info' Module — assessmentInfoUI","text":"UI 'Assessment Info' Module","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/assessmentInfoUI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"UI for 'Assessment Info' Module — assessmentInfoUI","text":"","code":"assessmentInfoUI(id)"},{"path":"https://pharmar.github.io/riskassessment/reference/assessmentInfoUI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"UI for 'Assessment Info' Module — assessmentInfoUI","text":"id module id name","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/auto_font.html","id":null,"dir":"Reference","previous_headings":"","what":"Automatic font re-sizer — auto_font","title":"Automatic font re-sizer — auto_font","text":"function adjusts number (used font size) proportional length text string. longer text string, smaller font. Used MetricBox.R.","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/auto_font.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Automatic font re-sizer — auto_font","text":"","code":"auto_font(txt, txt_max = 45, size_min = 0.75, size_max = 1.5, num_bins = NULL)"},{"path":"https://pharmar.github.io/riskassessment/reference/auto_font.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Automatic font re-sizer — auto_font","text":"txt string txt_max integer specify length text considered \"long\" continue toggle font size size_min integer specifying smallest font size like see output size_max integer specifying largest font size like see output num_bins NULL (default), accepts integer bins continuous font size categorical one.","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/build_comm_cards.html","id":null,"dir":"Reference","previous_headings":"","what":"The 'Build Community Cards' function — build_comm_cards","title":"The 'Build Community Cards' function — build_comm_cards","text":"'Build Community Cards' function","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/build_comm_cards.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The 'Build Community Cards' function — build_comm_cards","text":"","code":"build_comm_cards(   data,   db_name = golem::get_golem_options(\"assessment_db_name\") )"},{"path":"https://pharmar.github.io/riskassessment/reference/build_comm_cards.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The 'Build Community Cards' function — build_comm_cards","text":"data data.frame","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/build_comm_plotly.html","id":null,"dir":"Reference","previous_headings":"","what":"Build a plotly of community usage metrics — build_comm_plotly","title":"Build a plotly of community usage metrics — build_comm_plotly","text":"Responsible building interactive {plotly} graphic containing trend line number CRAN pkg downloads month.","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/build_comm_plotly.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Build a plotly of community usage metrics — build_comm_plotly","text":"","code":"build_comm_plotly(data = NULL, pkg_name = NULL)"},{"path":"https://pharmar.github.io/riskassessment/reference/build_comm_plotly.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Build a plotly of community usage metrics — build_comm_plotly","text":"data data.frame containing monthly download data, built using generate_comm_data(). argument optional, NULL, pkg_name must provided. pkg_name string package name. parameter optional. pkg_name provided, data argument NULL.","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/build_comm_plotly.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Build a plotly of community usage metrics — build_comm_plotly","text":"plotly object interactive plotly object","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/build_comm_plotly.html","id":"example","dir":"Reference","previous_headings":"","what":"Example","title":"Build a plotly of community usage metrics — build_comm_plotly","text":"","code":"build_comm_plotly(pkg_name = \"ggplot2\")"},{"path":[]},{"path":"https://pharmar.github.io/riskassessment/reference/build_db_cards.html","id":null,"dir":"Reference","previous_headings":"","what":"The 'Build Database Cards' function — build_db_cards","title":"The 'Build Database Cards' function — build_db_cards","text":"'Build Database Cards' function","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/build_db_cards.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The 'Build Database Cards' function — build_db_cards","text":"","code":"build_db_cards(data)"},{"path":"https://pharmar.github.io/riskassessment/reference/build_db_cards.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The 'Build Database Cards' function — build_db_cards","text":"data data.frame","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/build_dep_cards.html","id":null,"dir":"Reference","previous_headings":"","what":"The 'Build Dependency Cards' function — build_dep_cards","title":"The 'Build Dependency Cards' function — build_dep_cards","text":"'Build Dependency Cards' function","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/build_dep_cards.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The 'Build Dependency Cards' function — build_dep_cards","text":"","code":"build_dep_cards(data, loaded, toggled)"},{"path":"https://pharmar.github.io/riskassessment/reference/build_dep_cards.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The 'Build Dependency Cards' function — build_dep_cards","text":"data data.frame loaded vector package names loaded db","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/communityMetricsServer.html","id":null,"dir":"Reference","previous_headings":"","what":"Community Usage Metrics server logic — communityMetricsServer","title":"Community Usage Metrics server logic — communityMetricsServer","text":"Community Usage Metrics server logic","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/communityMetricsServer.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Community Usage Metrics server logic — communityMetricsServer","text":"","code":"communityMetricsServer(id, selected_pkg, community_metrics, user, credentials)"},{"path":"https://pharmar.github.io/riskassessment/reference/communityMetricsServer.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Community Usage Metrics server logic — communityMetricsServer","text":"id module id name selected_pkg placeholder community_metrics placeholder user placeholder","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/communityMetricsUI.html","id":null,"dir":"Reference","previous_headings":"","what":"Community Usage Metrics UI function — communityMetricsUI","title":"Community Usage Metrics UI function — communityMetricsUI","text":"Community Usage Metrics UI function","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/communityMetricsUI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Community Usage Metrics UI function — communityMetricsUI","text":"","code":"communityMetricsUI(id)"},{"path":"https://pharmar.github.io/riskassessment/reference/communityMetricsUI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Community Usage Metrics UI function — communityMetricsUI","text":"id module id name","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/create_credentials_db.html","id":null,"dir":"Reference","previous_headings":"","what":"Create credentials database — create_credentials_db","title":"Create credentials database — create_credentials_db","text":"Note: credentials_db_name object assigned deployment user R/run_app.R","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/create_credentials_db.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create credentials database — create_credentials_db","text":"","code":"create_credentials_db(db_name, admin_role = \"\")"},{"path":"https://pharmar.github.io/riskassessment/reference/create_credentials_db.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create credentials database — create_credentials_db","text":"db_name string denoting name database admin_role string denoting initialized privileges admin","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/create_credentials_dev_db.html","id":null,"dir":"Reference","previous_headings":"","what":"Create credentials dev database — create_credentials_dev_db","title":"Create credentials dev database — create_credentials_dev_db","text":"Create credentials dev database","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/create_credentials_dev_db.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create credentials dev database — create_credentials_dev_db","text":"","code":"create_credentials_dev_db(db_name)"},{"path":"https://pharmar.github.io/riskassessment/reference/create_credentials_dev_db.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create credentials dev database — create_credentials_dev_db","text":"db_name string denoting name database","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/create_db.html","id":null,"dir":"Reference","previous_headings":"","what":"Create package database — create_db","title":"Create package database — create_db","text":"Note: database_name object assigned deployment users R/run_app.R","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/create_db.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create package database — create_db","text":"","code":"create_db(db_name)"},{"path":"https://pharmar.github.io/riskassessment/reference/create_db.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create package database — create_db","text":"db_name string denoting name database","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/databaseViewServer.html","id":null,"dir":"Reference","previous_headings":"","what":"Server logic for 'Database View' module — databaseViewServer","title":"Server logic for 'Database View' module — databaseViewServer","text":"Server logic 'Database View' module","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/databaseViewServer.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Server logic for 'Database View' module — databaseViewServer","text":"","code":"databaseViewServer(id, user, uploaded_pkgs, metric_weights, changes, parent)"},{"path":"https://pharmar.github.io/riskassessment/reference/databaseViewServer.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Server logic for 'Database View' module — databaseViewServer","text":"id module id name user user name uploaded_pkgs vector uploaded package names metric_weights reactive data.frame holding metric weights changes reactive value integer count parent parent (calling module) session information","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/databaseViewUI.html","id":null,"dir":"Reference","previous_headings":"","what":"UI for 'Database View' module — databaseViewUI","title":"UI for 'Database View' module — databaseViewUI","text":"UI 'Database View' module","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/databaseViewUI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"UI for 'Database View' module — databaseViewUI","text":"","code":"databaseViewUI(id)"},{"path":"https://pharmar.github.io/riskassessment/reference/databaseViewUI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"UI for 'Database View' module — databaseViewUI","text":"id module id name","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/generate_comm_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate Community Usage Data — generate_comm_data","title":"Generate Community Usage Data — generate_comm_data","text":"Extracts community usage metrics given package.","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/generate_comm_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate Community Usage Data — generate_comm_data","text":"","code":"generate_comm_data(pkg_name)"},{"path":"https://pharmar.github.io/riskassessment/reference/generate_comm_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate Community Usage Data — generate_comm_data","text":"pkg_name string containing name package.","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/generate_comm_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate Community Usage Data — generate_comm_data","text":"tibble community usage metrics data.frame includes downloads per month given pkg","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/generate_comm_data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Generate Community Usage Data — generate_comm_data","text":"","code":"if( interactive()) { ggplot_comm_df <- generate_comm_data(\"ggplot2\") head(ggplot_comm_df) }"},{"path":"https://pharmar.github.io/riskassessment/reference/getTimeStamp.html","id":null,"dir":"Reference","previous_headings":"","what":"getTimeStamp — getTimeStamp","title":"getTimeStamp — getTimeStamp","text":"Retrieves Sys.time(), transforms slightly","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/getTimeStamp.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"getTimeStamp — getTimeStamp","text":"","code":"getTimeStamp()"},{"path":"https://pharmar.github.io/riskassessment/reference/get_date_span.html","id":null,"dir":"Reference","previous_headings":"","what":"The 'Get Date Span' function — get_date_span","title":"The 'Get Date Span' function — get_date_span","text":"Function accepts start date optional end date ","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/get_date_span.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The 'Get Date Span' function — get_date_span","text":"","code":"get_date_span(start, end = get_Date())"},{"path":"https://pharmar.github.io/riskassessment/reference/get_date_span.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The 'Get Date Span' function — get_date_span","text":"start starting date end ending date","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/get_latest_pkg_info.html","id":null,"dir":"Reference","previous_headings":"","what":"Get the package general information from CRAN/local — get_latest_pkg_info","title":"Get the package general information from CRAN/local — get_latest_pkg_info","text":"Get package general information CRAN/local","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/get_latest_pkg_info.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get the package general information from CRAN/local — get_latest_pkg_info","text":"","code":"get_latest_pkg_info(pkg_name)"},{"path":"https://pharmar.github.io/riskassessment/reference/get_latest_pkg_info.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get the package general information from CRAN/local — get_latest_pkg_info","text":"pkg_name string name package","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/initialize_raa.html","id":null,"dir":"Reference","previous_headings":"","what":"Initialize riskassessment Application Settings — initialize_raa","title":"Initialize riskassessment Application Settings — initialize_raa","text":"sets environment running riskassessment Application. sets log file, initializes package database missing, initializes credentials database missing.","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/initialize_raa.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Initialize riskassessment Application Settings — initialize_raa","text":"","code":"initialize_raa(assess_db, cred_db, configuration)"},{"path":"https://pharmar.github.io/riskassessment/reference/initialize_raa.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Initialize riskassessment Application Settings — initialize_raa","text":"assess_db string denoting name assessment database. cred_db string denoting name credentials database. configuration list dictating configuration databases","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/initialize_raa.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Initialize riskassessment Application Settings — initialize_raa","text":"return value. function run side effects.","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/introJSServer.html","id":null,"dir":"Reference","previous_headings":"","what":"Server logic for introJS module — introJSServer","title":"Server logic for introJS module — introJSServer","text":"Server logic introJS module","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/introJSServer.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Server logic for introJS module — introJSServer","text":"","code":"introJSServer(id, text, user, credentials)"},{"path":"https://pharmar.github.io/riskassessment/reference/introJSServer.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Server logic for introJS module — introJSServer","text":"id module id text data.frame containing info step: element names, text strings guiding users, position place text relationship element. Please see R/introJSText.R data.frames populate argument app user placeholder","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/introJSUI.html","id":null,"dir":"Reference","previous_headings":"","what":"UI for Module to display introJS button and functionality. — introJSUI","title":"UI for Module to display introJS button and functionality. — introJSUI","text":"UI Module display introJS button functionality.","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/introJSUI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"UI for Module to display introJS button and functionality. — introJSUI","text":"","code":"introJSUI(id)"},{"path":"https://pharmar.github.io/riskassessment/reference/introJSUI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"UI for Module to display introJS button and functionality. — introJSUI","text":"id module id","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/maintenanceMetricsServer.html","id":null,"dir":"Reference","previous_headings":"","what":"Maintenance Metrics module's server logic — maintenanceMetricsServer","title":"Maintenance Metrics module's server logic — maintenanceMetricsServer","text":"Maintenance Metrics module's server logic","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/maintenanceMetricsServer.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Maintenance Metrics module's server logic — maintenanceMetricsServer","text":"","code":"maintenanceMetricsServer(   id,   selected_pkg,   maint_metrics,   user,   credentials,   parent )"},{"path":"https://pharmar.github.io/riskassessment/reference/maintenanceMetricsServer.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Maintenance Metrics module's server logic — maintenanceMetricsServer","text":"id module id name selected_pkg placeholder maint_metrics placeholder user placeholder parent parent (calling module) session information","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/maintenanceMetricsUI.html","id":null,"dir":"Reference","previous_headings":"","what":"Maintenance Metrics module's UI. — maintenanceMetricsUI","title":"Maintenance Metrics module's UI. — maintenanceMetricsUI","text":"Maintenance Metrics module's UI.","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/maintenanceMetricsUI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Maintenance Metrics module's UI. — maintenanceMetricsUI","text":"","code":"maintenanceMetricsUI(id)"},{"path":"https://pharmar.github.io/riskassessment/reference/maintenanceMetricsUI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Maintenance Metrics module's UI. — maintenanceMetricsUI","text":"id module id name","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/metricBoxServer.html","id":null,"dir":"Reference","previous_headings":"","what":"Server logic for the 'Metric Box' module — metricBoxServer","title":"Server logic for the 'Metric Box' module — metricBoxServer","text":"Server logic 'Metric Box' module","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/metricBoxServer.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Server logic for the 'Metric Box' module — metricBoxServer","text":"","code":"metricBoxServer(   id,   title,   desc,   value,   score = \"NULL\",   is_perc = FALSE,   is_url = FALSE,   succ_icon = \"check\",   unsucc_icon = \"triangle-exclamation\",   icon_class = \"text-success\",   type = \"information\" )"},{"path":"https://pharmar.github.io/riskassessment/reference/metricBoxServer.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Server logic for the 'Metric Box' module — metricBoxServer","text":"id module id name title title. desc description. value metric value. score metric score, character value is_perc logical value percentage? is_url logical value url succ_icon icon used is_true. unsucc_icon icon used is_true. icon_class string type icon type string color icon (\"information\" \"danger\")","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/metricBoxUI.html","id":null,"dir":"Reference","previous_headings":"","what":"The UI for the 'Metric Box' module — metricBoxUI","title":"The UI for the 'Metric Box' module — metricBoxUI","text":"UI 'Metric Box' module","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/metricBoxUI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The UI for the 'Metric Box' module — metricBoxUI","text":"","code":"metricBoxUI(id)"},{"path":"https://pharmar.github.io/riskassessment/reference/metricBoxUI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The UI for the 'Metric Box' module — metricBoxUI","text":"id module id name","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/metricGridServer.html","id":null,"dir":"Reference","previous_headings":"","what":"Metric Grid module's server logic — metricGridServer","title":"Metric Grid module's server logic — metricGridServer","text":"Metric Grid module's server logic","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/metricGridServer.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Metric Grid module's server logic — metricGridServer","text":"","code":"metricGridServer(id, metrics)"},{"path":"https://pharmar.github.io/riskassessment/reference/metricGridServer.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Metric Grid module's server logic — metricGridServer","text":"id module id name metrics placeholder","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/metricGridUI.html","id":null,"dir":"Reference","previous_headings":"","what":"Metric Grid module's UI. — metricGridUI","title":"Metric Grid module's UI. — metricGridUI","text":"Metric Grid module's UI.","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/metricGridUI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Metric Grid module's UI. — metricGridUI","text":"","code":"metricGridUI(id)"},{"path":"https://pharmar.github.io/riskassessment/reference/metricGridUI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Metric Grid module's UI. — metricGridUI","text":"id module id name","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/metric_gauge.html","id":null,"dir":"Reference","previous_headings":"","what":"Metric Gauge — metric_gauge","title":"Metric Gauge — metric_gauge","text":"HTML meter element, used displaying metric scores app","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/metric_gauge.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Metric Gauge — metric_gauge","text":"","code":"metric_gauge(score)"},{"path":"https://pharmar.github.io/riskassessment/reference/metric_gauge.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Metric Gauge — metric_gauge","text":"score whole number 0 100","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/metric_gauge.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Metric Gauge — metric_gauge","text":"tagList object","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/packageDependenciesServer.html","id":null,"dir":"Reference","previous_headings":"","what":"Package Dependencies module's server logic — packageDependenciesServer","title":"Package Dependencies module's server logic — packageDependenciesServer","text":"Package Dependencies module's server logic","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/packageDependenciesServer.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Package Dependencies module's server logic — packageDependenciesServer","text":"","code":"packageDependenciesServer(id, selected_pkg, user, credentials, parent)"},{"path":"https://pharmar.github.io/riskassessment/reference/packageDependenciesServer.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Package Dependencies module's server logic — packageDependenciesServer","text":"id module id name selected_pkg placeholder user placeholder parent parent (calling module) session information","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/packageDependenciesUI.html","id":null,"dir":"Reference","previous_headings":"","what":"Package Dependencies module's UI. — packageDependenciesUI","title":"Package Dependencies module's UI. — packageDependenciesUI","text":"Package Dependencies module's UI.","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/packageDependenciesUI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Package Dependencies module's UI. — packageDependenciesUI","text":"","code":"packageDependenciesUI(id)"},{"path":"https://pharmar.github.io/riskassessment/reference/packageDependenciesUI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Package Dependencies module's UI. — packageDependenciesUI","text":"id module id name","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/reportPreviewServer.html","id":null,"dir":"Reference","previous_headings":"","what":"Server logic for 'Report Preview' module — reportPreviewServer","title":"Server logic for 'Report Preview' module — reportPreviewServer","text":"Server logic 'Report Preview' module","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/reportPreviewServer.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Server logic for 'Report Preview' module — reportPreviewServer","text":"","code":"reportPreviewServer(   id,   selected_pkg,   maint_metrics,   com_metrics,   com_metrics_raw,   mm_comments,   cm_comments,   dep_comments,   downloads_plot_data,   user,   credentials,   app_version,   metric_weights )"},{"path":"https://pharmar.github.io/riskassessment/reference/reportPreviewServer.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Server logic for 'Report Preview' module — reportPreviewServer","text":"id module id name selected_pkg placeholder maint_metrics placeholder com_metrics placeholder com_metrics_raw placeholder mm_comments placeholder cm_comments placeholder downloads_plot_data placeholder user placeholder app_version placeholder metric_weights placeholder","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/reportPreviewUI.html","id":null,"dir":"Reference","previous_headings":"","what":"UI for 'Report Preview' module — reportPreviewUI","title":"UI for 'Report Preview' module — reportPreviewUI","text":"UI 'Report Preview' module","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/reportPreviewUI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"UI for 'Report Preview' module — reportPreviewUI","text":"","code":"reportPreviewUI(id)"},{"path":"https://pharmar.github.io/riskassessment/reference/reportPreviewUI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"UI for 'Report Preview' module — reportPreviewUI","text":"id module id name","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/reweightViewServer.html","id":null,"dir":"Reference","previous_headings":"","what":"Server logic for the 'Re-weight View' module — reweightViewServer","title":"Server logic for the 'Re-weight View' module — reweightViewServer","text":"Server logic 'Re-weight View' module","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/reweightViewServer.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Server logic for the 'Re-weight View' module — reweightViewServer","text":"","code":"reweightViewServer(id, user, decision_list, credentials)"},{"path":"https://pharmar.github.io/riskassessment/reference/reweightViewServer.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Server logic for the 'Re-weight View' module — reweightViewServer","text":"id module id user user name decision_list list containing decision automation criteria","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/reweightViewUI.html","id":null,"dir":"Reference","previous_headings":"","what":"UI for the 'Re-weight View' module — reweightViewUI","title":"UI for the 'Re-weight View' module — reweightViewUI","text":"UI 'Re-weight View' module","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/reweightViewUI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"UI for the 'Re-weight View' module — reweightViewUI","text":"","code":"reweightViewUI(id)"},{"path":"https://pharmar.github.io/riskassessment/reference/reweightViewUI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"UI for the 'Re-weight View' module — reweightViewUI","text":"id module id","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/riskassessment-package.html","id":null,"dir":"Reference","previous_headings":"","what":"The riskassessment package — riskassessment-package","title":"The riskassessment package — riskassessment-package","text":"riskassessment App interactive web application serving front end application riskmetric R package. riskmetric framework quantify risk assessing number metrics meant evaluate development best practices, code documentation, community engagement, development sustainability. app riskmetric aim provide context validation within regulated industries.","code":""},{"path":[]},{"path":"https://pharmar.github.io/riskassessment/reference/riskassessment-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"The riskassessment package — riskassessment-package","text":"Maintainer: Aaron Clark clark.aaronchris@gmail.com Authors: Robert Krajcik robert.krajcik@biogen.com Jeff Thompson jeff.thompson51317@gmail.com Lars Andersen lars.andersen@boehringer-ingelheim.com Andrew Borgman andrew.borgman@biogen.com Marly Gotti marly.cormar@biogen.com Maya Gans maya.gans@biogen.com Aravind Reddy Kallem Fission Labs India Pvt Ltd contributors: Munshi Imran Hossain [contributor] Scott Schumacker scottschu97@gmail.com [contributor] Eduardo Almeida eduardoalmeida7393@gmail.com [contributor] Narayanan Iyer NarayananSeshan.Iyer@pfizer.com [contributor] PSI special interest group Application Implementation Methodologies Statistics [copyright holder, funder] R Validation Hub [copyright holder, funder] GSK contributors (Author 'pharmaR/pkg_explorer' repo) [contributor] Appsilon [contributor]","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/run_app.html","id":null,"dir":"Reference","previous_headings":"","what":"Run the Shiny Application — run_app","title":"Run the Shiny Application — run_app","text":"Run Shiny Application","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/run_app.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Run the Shiny Application — run_app","text":"","code":"run_app(   onStart = initialize_raa,   options = list(),   enableBookmarking = NULL,   uiPattern = \"/\",   app_ver = NULL,   login_note = NULL,   ... )"},{"path":"https://pharmar.github.io/riskassessment/reference/run_app.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Run the Shiny Application — run_app","text":"onStart function called app actually run. needed shinyAppObj, since shinyAppDir case, global.R file can used purpose. options Named options passed runApp call (can following: \"port\", \"launch.browser\", \"host\", \"quiet\", \"display.mode\" \"test.mode\"). can also specify width height parameters provide hint embedding environment ideal height/width app. enableBookmarking Can one \"url\", \"server\", \"disable\". default value, NULL, respect setting previous calls  enableBookmarking(). See enableBookmarking() information bookmarking app. uiPattern regular expression applied GET request determine whether ui used handle request. Note entire request path must match regular expression order match considered successful. app_ver \"global\" variable passed several modules & reports details installed package version specified. can overwritten include specific version name text string. login_note text string display underneath auth screen's login button, provided guide users ... arguments pass golem_opts. See ?golem::get_golem_options details.","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/run_app.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Run the Shiny Application — run_app","text":"shiny app object","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/showComments.html","id":null,"dir":"Reference","previous_headings":"","what":"showComments — showComments","title":"showComments — showComments","text":"Displays formatted comments","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/showComments.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"showComments — showComments","text":"","code":"showComments(pkg_name, comments, none_txt = \"No comments\")"},{"path":"https://pharmar.github.io/riskassessment/reference/showComments.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"showComments — showComments","text":"pkg_name string name package comments data.frame comments table entry none_txt text show comments object, display text string. Default: \"comments\"","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/showComments.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"showComments — showComments","text":"formatted string comments","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/showHelperMessage.html","id":null,"dir":"Reference","previous_headings":"","what":"showHelperMessage — showHelperMessage","title":"showHelperMessage — showHelperMessage","text":"Displays helper message. default, informs user select package.","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/showHelperMessage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"showHelperMessage — showHelperMessage","text":"","code":"showHelperMessage(message = \"Please select a package\")"},{"path":"https://pharmar.github.io/riskassessment/reference/showHelperMessage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"showHelperMessage — showHelperMessage","text":"message string","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/sidebarServer.html","id":null,"dir":"Reference","previous_headings":"","what":"Sidebar Server Logic — sidebarServer","title":"Sidebar Server Logic — sidebarServer","text":"Also known 'Control Panel', rightfully , controls components app, central function","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/sidebarServer.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sidebar Server Logic — sidebarServer","text":"","code":"sidebarServer(id, user, uploaded_pkgs, credentials)"},{"path":"https://pharmar.github.io/riskassessment/reference/sidebarServer.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sidebar Server Logic — sidebarServer","text":"id module id user username uploaded_pkgs vector packages","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/sidebarUI.html","id":null,"dir":"Reference","previous_headings":"","what":"Sidebar UI — sidebarUI","title":"Sidebar UI — sidebarUI","text":"Also known 'Control Panel', rightfully , controls components app, central function","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/sidebarUI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sidebar UI — sidebarUI","text":"","code":"sidebarUI(id)"},{"path":"https://pharmar.github.io/riskassessment/reference/sidebarUI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sidebar UI — sidebarUI","text":"id module id","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/uploadPackageServer.html","id":null,"dir":"Reference","previous_headings":"","what":"Server logic for the 'Upload Package' module — uploadPackageServer","title":"Server logic for the 'Upload Package' module — uploadPackageServer","text":"Server logic 'Upload Package' module","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/uploadPackageServer.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Server logic for the 'Upload Package' module — uploadPackageServer","text":"","code":"uploadPackageServer(id, user, auto_list, credentials, parent)"},{"path":"https://pharmar.github.io/riskassessment/reference/uploadPackageServer.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Server logic for the 'Upload Package' module — uploadPackageServer","text":"id module id user username auto_list list decision automation rules parent parent (calling module) session information","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/uploadPackageUI.html","id":null,"dir":"Reference","previous_headings":"","what":"'Upload Package' UI — uploadPackageUI","title":"'Upload Package' UI — uploadPackageUI","text":"'Upload Package' UI","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/uploadPackageUI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"'Upload Package' UI — uploadPackageUI","text":"","code":"uploadPackageUI(id)"},{"path":"https://pharmar.github.io/riskassessment/reference/uploadPackageUI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"'Upload Package' UI — uploadPackageUI","text":"id module id","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/upload_pkg_lst.html","id":null,"dir":"Reference","previous_headings":"","what":"Upload a Package List — upload_pkg_lst","title":"Upload a Package List — upload_pkg_lst","text":"Uploads list packages database. Designed used set assessment database deployment application.","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/upload_pkg_lst.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Upload a Package List — upload_pkg_lst","text":"","code":"upload_pkg_lst(   pkg_lst,   assess_db,   repos,   repo_pkgs,   user_name = \"system\",   updateProgress = NULL )"},{"path":"https://pharmar.github.io/riskassessment/reference/upload_pkg_lst.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Upload a Package List — upload_pkg_lst","text":"pkg_lst character vector packages upload assess_db character name (file path) database repos character vector, base URL(s) repositories use repo_pkgs internal use , allows function available.packages() run user_name character name user updateProgress internal use , provides function update progress meter application","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/upload_pkg_lst.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Upload a Package List — upload_pkg_lst","text":"data frame object containing summary upload process","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/viewCommentsServer.html","id":null,"dir":"Reference","previous_headings":"","what":"viewComment module's server logic — viewCommentsServer","title":"viewComment module's server logic — viewCommentsServer","text":"viewComment module's server logic","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/viewCommentsServer.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"viewComment module's server logic — viewCommentsServer","text":"","code":"viewCommentsServer(   id,   pkg_name,   comments,   none_txt = \"No comments\",   label = \"Current Comments\" )"},{"path":"https://pharmar.github.io/riskassessment/reference/viewCommentsServer.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"viewComment module's server logic — viewCommentsServer","text":"id module id name pkg_name string name package comments data.frame comments table entry label string default: Current Comments","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/viewCommentsUI.html","id":null,"dir":"Reference","previous_headings":"","what":"The UI for the 'viewComment' module — viewCommentsUI","title":"The UI for the 'viewComment' module — viewCommentsUI","text":"Module display comments specified metric. comments update user inserts comments.","code":""},{"path":"https://pharmar.github.io/riskassessment/reference/viewCommentsUI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The UI for the 'viewComment' module — viewCommentsUI","text":"","code":"viewCommentsUI(id)"},{"path":"https://pharmar.github.io/riskassessment/reference/viewCommentsUI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The UI for the 'viewComment' module — viewCommentsUI","text":"id module id name","code":""},{"path":[]},{"path":"https://pharmar.github.io/riskassessment/news/index.html","id":"user-enhancements-3-1-0","dir":"Changelog","previous_headings":"","what":"User Enhancements","title":"riskassessment 3.1.0","text":"Allow users specify decisions within CSV file used upload pkgs (#663) Drastically shortened waiting time Code explorer/ Package explorer reading tarballs memory (#707) Added Package Dependencies content Reports (#721) Added option include Suggests pkgs downloadable Reports (#721) Added Decision column Package Dependencies tab’s table output (#774) Added Decision Summary card Package Dependencies tab (#774) Added hyperlink dependencies/reverse dependencies cards, directing users Package Dependencies page detail (#597) Added new table display reverse dependencies highlights pkgs already exist database","code":""},{"path":"https://pharmar.github.io/riskassessment/news/index.html","id":"squashed-bugs-3-1-0","dir":"Changelog","previous_headings":"","what":"Squashed Bugs","title":"riskassessment 3.1.0","text":"Fixed bug causing application crash trying delete zero packages (#781) Fixed bug app doesn’t reset decision decision date fields re-scoring/re-weighting packages (#680) Fixed bug user privileges table aligned available privileges application (#697) Fixed typo privileges table (#719) Fixed bug HTML reports displayed darker green cards’ meters Updated logo reports lighter version match application UI Updated Dependency Cards slightly informative","code":""},{"path":"https://pharmar.github.io/riskassessment/news/index.html","id":"docs-3-1-0","dir":"Changelog","previous_headings":"","what":"Docs","title":"riskassessment 3.1.0","text":"Added page introduce audience project little better, providing useful resources attribution highlights individual contributors Added context metric score card visuals inserting tool tips & creating legend modal describes & interprets possible visuals (#652) Added introjs file browser & function explorer( #581) Added riskmetric assessment documentation URLs tab, Risk Assessment Criteria page.","code":""},{"path":"https://pharmar.github.io/riskassessment/news/index.html","id":"for-devs-3-1-0","dir":"Changelog","previous_headings":"","what":"For Devs","title":"riskassessment 3.1.0","text":"Added non-shinymanager deployment option users may use Posit Credentials instead (#700) Moved package upload process function, allowing devs populate database outside application Added tests Code Explorer Function explorer modules Added repo specification configuration file (#701) Ensured configuration checkers run configuring database Utilized archive parse DESCRIPTION file, increasing speed package upload process Updated manifest file deployments article Updated version riskmetric used v0.2.4.9000 Updated version R v4.3.3 & Posit Package Manager snapshot dates 2024-04-08","code":""},{"path":[]},{"path":"https://pharmar.github.io/riskassessment/news/index.html","id":"enhancements-3-0-0","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"riskassessment 3.0.0","text":"Added “Suggests” pkgs Dependencies tab (#624) Summarized Package Dependencies (#618) Integrated ‘Function Explorer’ offer users function-level browsing source code, unit testing, automatic rendering help documentation (#498) Started showing metric_scores assessment’s card, using html meter (#634) Added default DT based filter Database Overview tab (#586) Allowed users create decision automation rules individual metrics (#483) Added checkbox databaseView select packages reportDownload handler (#649) Allowed users identify store preferred elements include downloaded reports (#526) Add “Explore Metrics” button Uploaded Pkgs Summary tab Upload Packages tab (#653) Added comment module Function Explorer (#643) Made color palette used app even colorblind-friendly created lighter “User Guide” logo (#654)","code":""},{"path":"https://pharmar.github.io/riskassessment/news/index.html","id":"squashed-bugs-3-0-0","dir":"Changelog","previous_headings":"","what":"Squashed Bugs","title":"riskassessment 3.0.0","text":"Fixed app’s logo hyperlink docs functioning expected “zone” (#633) Fixed tests showing “Package Downloads” community usage card non-metric (#621) Removed “Suggests” Riskassessment Criteria weights table (#646) Forced formation new lines cards (#671) Ensured users couldn’t create & select packages CRAN don’t exist Upload Packages tab","code":""},{"path":"https://pharmar.github.io/riskassessment/news/index.html","id":"for-devs-3-0-0","dir":"Changelog","previous_headings":"","what":"For Devs","title":"riskassessment 3.0.0","text":"Migrated jsTreeR {shinyTree} (#585) Removed unneeded/unused dependencies Updated shinytest2 chromote recent versions testing Added correct remotes reference DESCRIPTION file pharmar/riskmetric & rstudio/chromote Stopped using CRAN repo snapshot date renv (#677)","code":""},{"path":[]},{"path":"https://pharmar.github.io/riskassessment/news/index.html","id":"enhancements-2-0-0","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"riskassessment 2.0.0","text":"Expand privileges include commenting metrics packages (#564) Allow admin users edit roles privileges (#541) Download source tarball uploading package database users can explore source contents package (#574) Added card Download Trend linear trend plot community usage metrics (#438) Introduced cards Database tab, reviewing contents db (#587) Prominently display date package added (#486) Fix issue repository used gather information inconsistent Added Package Dependencies page “Package Metrics” tab, two new cards Maintenance Metrics page (#261) Identify non-riskmetric cards (#573)","code":""},{"path":"https://pharmar.github.io/riskassessment/news/index.html","id":"squashed-bugs-2-0-0","dir":"Changelog","previous_headings":"","what":"Squashed Bugs","title":"riskassessment 2.0.0","text":"Fixed busted button introduced #547 (#592)","code":""},{"path":"https://pharmar.github.io/riskassessment/news/index.html","id":"docs-2-0-0","dir":"Changelog","previous_headings":"","what":"Docs","title":"riskassessment 2.0.0","text":"Updated riskassessment vignette reflect new tab structure","code":""},{"path":"https://pharmar.github.io/riskassessment/news/index.html","id":"for-devs-2-0-0","dir":"Changelog","previous_headings":"","what":"For Devs","title":"riskassessment 2.0.0","text":"Disable using Microsoft R Application Network (MRAN) restoring packages Removed legacy code set covr_coverage assessment’s metric weight 0 assessmentInfo mod metric table initialization sql file.","code":""},{"path":[]},{"path":"https://pharmar.github.io/riskassessment/news/index.html","id":"enhancements-1-0-0","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"riskassessment 1.0.0","text":"Updated version riskmetric used V0.2.2 Added decision categories (#459) Added decision automation rules (#459) Added log file designation (#463) Implemented user roles/privileges allow granular access actions application (#527) Allow metric weights initialized (#482) package upload, inserting community metrics database (#516) metric weights changed, re-score instead re-assess, saving huge amounts time (#537) Added Decision-related columns like decision time stamp & decision source Introduced decision category table holistic Report Builder. allows users define content shows report (#348). Users can now compose long form “Package Summary” keep track pertinent items (perhaps items less central {riskmetric} output) rounded package review (#348). Allowed certain users set custom color decision categories (#465) Added code coverage (covr_coverage) card add optimized card layout logic (#533)","code":""},{"path":"https://pharmar.github.io/riskassessment/news/index.html","id":"squashed-bugs-1-0-0","dir":"Changelog","previous_headings":"","what":"Squashed Bugs","title":"riskassessment 1.0.0","text":"Fixed Chromote error (#477) Fixed bug preventing icons displaying admin tab (#427) Fixed button alignment issues (#514) Re-positioned footer bottom visible page (#518) Added new check conditionally delivers message differing pkg versions CSV file loaded (#515) Fixed broken links docs","code":""},{"path":"https://pharmar.github.io/riskassessment/news/index.html","id":"docs-1-0-0","dir":"Changelog","previous_headings":"","what":"Docs","title":"riskassessment 1.0.0","text":"Updated help files build_comm_plotly() include example output (#409). Created new (updated ) user guides explain precisely control app deployment using configuration file. Retired pertinent “old”” user guides case users still running old versions riskassessment","code":""},{"path":"https://pharmar.github.io/riskassessment/news/index.html","id":"for-devs-1-0-0","dir":"Changelog","previous_headings":"","what":"For Devs","title":"riskassessment 1.0.0","text":"Utilized glue::glue_sql() inside update select functions (#520) Improved speed inserting community metrics database (#516) Re-score instead re-assess metric weights changed, meaning now storing pkg assessment (#537) Pass warning instead error default privilege config gets combined another config (#547)","code":""},{"path":[]},{"path":"https://pharmar.github.io/riskassessment/news/index.html","id":"enhancements-0-1-1","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"riskassessment 0.1.1","text":"Upgraded leverage {riskmetric} v0.2.0 impacts risk score calculations Add button redirects pkg metrics Added ‘search’ capability database view tab Added Excel & CSV export options Database View tab Added hyperlink documentation site / user guide within application Added check URLs needed upload packages reachable, just case! Added riskassessment logo docx pdf reports general aesthetic improvements, example: made sure tab headers consistent size","code":""},{"path":"https://pharmar.github.io/riskassessment/news/index.html","id":"squashed-bugs-0-1-1","dir":"Changelog","previous_headings":"","what":"Squashed Bugs","title":"riskassessment 0.1.1","text":"Fixed bug card displaying “Number downloads last 12 months” faulty, summing months previous year none current year. Report headings changed “asis” sentence case avoid altering case package names reports Fix failing tests: prefix AppDriver$new ‘shinytest2::’ Fix Chromote error provided Winston Chang","code":""},{"path":"https://pharmar.github.io/riskassessment/news/index.html","id":"docs-0-1-1","dir":"Changelog","previous_headings":"","what":"Docs","title":"riskassessment 0.1.1","text":"Added User Feedback survey README (#411) Fixed broken R-CMD-CHECK badge README Updated vignettes describe new ‘Decision Automation’ feature","code":""},{"path":"https://pharmar.github.io/riskassessment/news/index.html","id":"for-devs-0-1-1","dir":"Changelog","previous_headings":"","what":"For Devs","title":"riskassessment 0.1.1","text":"Removed {golem} testing option pre_auth_user arguments run_app() Improved stability ease--use testing introJS module Preload information select list packages improve tests utilizing shinytest2 Upgraded R Version v4.2.2","code":""},{"path":[]},{"path":"https://pharmar.github.io/riskassessment/news/index.html","id":"all-new-features-0-1-0","dir":"Changelog","previous_headings":"","what":"All New Features","title":"riskassessment 0.1.0","text":"Allowed users type package names assessed app, instead uploading CSV file. Also allow point--click deletion packages. Added decision automation capabilities user can set decision rules uploaded packages auto-assigned.","code":""},{"path":"https://pharmar.github.io/riskassessment/news/index.html","id":"enhancements-0-1-0","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"riskassessment 0.1.0","text":"Added “PDF report” download option (#280) Added risk score Report Preview tab downloaded reports (#264). Exported generate_comm_data() help users build community usage data needed run build_comm_plotly() (also exported) produce “downloads month”” plot seen Community Usage tab application. (#266).","code":""},{"path":"https://pharmar.github.io/riskassessment/news/index.html","id":"for-deployment-0-1-0","dir":"Changelog","previous_headings":"","what":"For deployment","title":"riskassessment 0.1.0","text":"Created argument run_app() called login_note allows users deploying app add custom log-notes authentication screen. default, displays note use default usernames passwords gain entry first time. Engineered new argument run_app() called app_version allows users deploying application publish custom text string app’s authentication screen downloaded reports. default, display installed version.","code":""},{"path":"https://pharmar.github.io/riskassessment/news/index.html","id":"docs-0-1-0","dir":"Changelog","previous_headings":"","what":"Docs","title":"riskassessment 0.1.0","text":"Updated README include description, ‘Usage’ info, including install & run app first time. Last, included links demo app & short video walk-. brief notes included regarding deployment environments. “Get started riskassessment” vignette “Administrative Tools Options” vignette Designed hex logo updated documentation reflect new repo name ‘riskassessment’ without ’_’ separate two words. suggest installation riskmetric GitHub, CRAN (now)","code":""},{"path":"https://pharmar.github.io/riskassessment/news/index.html","id":"squashed-bugs-0-1-0","dir":"Changelog","previous_headings":"","what":"Squashed Bugs","title":"riskassessment 0.1.0","text":"Fixed bug causing Community Usage metrics fail Mac computers Fixed bug causing report fail Community Metrics available package. Add founders/copyright holders DESCRIPTION file Fixed bug Assessment Criteria tables failing render. Improved metric ‘card’ aesthetics order remove scroll bars (#198). Added console warnings, log-note, modals warn user bug {fontawesome} v0.4.0. info, bug status can tracked . Fixed summary community usage data one package version released month Fixed bug logging file set Fixed package delete button shadow; fix introjs admin/non-admin roles Fixed display ‘Report Bugs’ metric align current riskmetric presentation 0 1","code":""},{"path":"https://pharmar.github.io/riskassessment/news/index.html","id":"for-devs-0-1-0","dir":"Changelog","previous_headings":"","what":"For Devs","title":"riskassessment 0.1.0","text":"general re-organizing package’s infrastructure make testing development easier. Added unit tests attain test coverage >85% (#295). Added renv renv.lock file well corresponding vignette developers/contributors align . Reduce number package dependencies 33 26 Changed risk-based color gradient use colorblind-friendly color palette (#324). Adopt (temporary) CRAN-first data collection method pkg info via riskmetric::pkg_ref()","code":""},{"path":"https://pharmar.github.io/riskassessment/news/index.html","id":"riskassessment-001","dir":"Changelog","previous_headings":"","what":"riskassessment 0.0.1","title":"riskassessment 0.0.1","text":"Initiated simple app.R easier deployment using runURL(\"https://github.com/pharmaR/riskassessment/archive/master.zip\") shiny::runGitHub('riskassessment', 'pharmaR')","code":""},{"path":"https://pharmar.github.io/riskassessment/news/index.html","id":"riskassessment-0009000","dir":"Changelog","previous_headings":"","what":"riskassessment 0.0.0.9000","title":"riskassessment 0.0.0.9000","text":"Added NEWS.md file track changes package. Used golem complete “packagization” riskassessment","code":""}]