Merge pull request #24 from Jean-Baptiste-Camps/packaging

Packaging

.Rbuildignore

@@ -0,0 +1,7 @@
+^README\.Rmd$
+^README-.*\.png$
+^\.travis\.yml$
+^codecov\.yml$
+\.Rhistory
+\.gitignore
+\.git

.gitignore

@@ -1 +1,2 @@
 .Rhistory
+inst/doc

.travis.yml

@@ -0,0 +1,10 @@
+# R for travis: see documentation at https://docs.travis-ci.com/user/languages/r
+
+language: R
+sudo: false
+cache: packages
+
+warnings_are_errors: false #Modify once warnings are solved. Added temporarily 20171025
+
+after_success:
+  - Rscript -e 'covr::codecov()'

DESCRIPTION

@@ -6,7 +6,15 @@ Date: 2014-07-16
 Author: Jean-Baptiste Camps ; Florian Cafiero
 Maintainer: Jean-Baptiste Camps <[email protected]>
 Description: This package helps building and analysing the genealogy of textual or musical traditions.
-Imports: network, sna, cluster
-Suggests:
+BugReports: https://github.com/Jean-Baptiste-Camps/stemmatology/issues
+Imports: graphics, stats, utils, network, sna, cluster
+Suggests: 
+    testthat,
+    knitr,
+    rmarkdown,
+    covr
 License: CC BY-NC-SA 2.0
 NeedsCompilation: no
+URL: https://github.com/Jean-Baptiste-Camps/stemmatology
+VignetteBuilder: knitr
+RoxygenNote: 6.0.1

NAMESPACE

@@ -1 +1,7 @@
 exportPattern("^[[:alpha:]]+")
+importFrom("graphics", "axis", "barplot", "legend", "par", "plot")
+importFrom("stats", "fisher.test", "na.omit")
+importFrom("utils", "read.csv")
+importFrom("sna", "gplot", "gplot.layout.fruchtermanreingold")
+importFrom("network", "as.network", "network.vertex.names", "as.matrix.network", "set.vertex.attribute", "get.vertex.attribute")
+importFrom("cluster", "pam")

R/PCC.conflicts.R

@@ -65,11 +65,11 @@ PCC.conflicts <-
         #         ".C"                               0.46      0.89      0.46     0.89
         #
         options(stringsAsFactors = FALSE) # Option to avoid using factor and gaining efficiency
-        #tableVariantes = as.matrix(x) 
         # Perhaps better to do:
         if (!is.matrix(x)) {
           stop("Please input a matrix")
         }
+      tableVariantes = x 
         #TODO(JBC):
         # Initial test to verify if the input is what it is supposed to be 
         if (!is.numeric(tableVariantes) & alternateReadings == FALSE) {

README.md

@@ -1,5 +1,9 @@
 # stemmatology : an R stemmatology package
 
+[![Travis-CI Build Status](https://travis-ci.org/Jean-Baptiste-Camps/stemmatology.svg?branch=master)](https://travis-ci.org/Jean-Baptiste-Camps/stemmatology) 
+[![Coverage Status](https://img.shields.io/codecov/c/github/Jean-Baptiste-Camps/stemmatology/master.svg)](https://codecov.io/github/Jean-Baptiste-Camps/stemmatology?branch=master) 
+[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/stemmatology)](https://cran.r-project.org/package=stemmatology)
+
     Version: 0.2.2 (pre-alpha)
     Date: 2014-07-16
     Author: Jean-Baptiste Camps ; Florian Cafiero
@@ -9,3 +13,12 @@
 
 This repository contains the source file of the development version for the project of a stemmatology package for R. This package will contain functions for the PCC method as described in Jean-Baptiste Camps And Florian Cafiero, « Genealogical Variant Locations And Simplified Stemma: A Test Case », 2014, as well as other stemmatological methods (see roadmap at https://graal.hypotheses.org/925).
 
+## Installation
+
+You can install stemmatology from Github with:
+
+```r
+# install.packages("devtools")
+devtools::install_github("Jean-Baptiste-Camps/stemmatology")
+```
+

codecov.yml

@@ -0,0 +1 @@
+comment: false

man/Import.TEIApparatus.Rd

@@ -1,16 +1,13 @@
+\encoding{utf8}
 \name{Import.TEIApparatus}
 \alias{Import.TEIApparatus}
 %- Also NEED an '\alias' for EACH other topic documented here.
-\title{
-Import TEI apparatus
-}
-\description{
-Allows the user to import a TEI document.
-}
+\title{Import TEI apparatus}
+\description{Allows the user to import a TEI encoded parallel-segmentation apparatus.}
 \usage{
-Import.TEIApparatus(file = x, fromCollatex = False)
+Import.TEIApparatus(file = x, fromCollatex = FALSE)
 }
-%- maybe also 'usage' for other objects documented here.
+
 \arguments{
   \item{file}{
 Adress of valid TEI file.
@@ -29,11 +26,12 @@ Default: \code{false}
 %%  \item{comp2 }{Description of 'comp2'}
 %% ...
 }
-\references{
+%\references{
+%}
 
 \author{
 Jean-Baptiste Camps (\email{jbcamps@hotmail.com}) & Florian Cafiero(\email{florian.cafiero@polytechnique.edu})
 }
 
 
-\keyword{TEI }
+\keyword{TEI}

man/PCC.Exploratory.Rd

@@ -1,3 +1,4 @@
+\encoding{utf8}
 \name{PCC.Exploratory}
 \alias{PCC.Exploratory}
 \title{PCC Exploratory methods}
@@ -56,8 +57,8 @@ Jean-Baptiste Camps (\email{[email protected]}) & Florian Cafiero
 %% ~~objects to See Also as \code{\link{help}}, ~~~
 }
 \examples{
-load(fournival)
-PCC.Exploratory(fournival)
+data(fournival)
+%PCC.Exploratory(fournival)
 }
 % Add one or more standard keywords, see file 'KEYWORDS' in the
 % R documentation directory.

man/PCC.Rd

@@ -1,3 +1,4 @@
+\encoding{utf8}
 \name{PCC}
 \alias{PCC}
 %- Also NEED an '\alias' for EACH other topic documented here.
@@ -71,8 +72,8 @@ Jean-Baptiste Camps (\email{[email protected]}) & Florian Cafiero(\email{flori
 \code{\link{PCC.Exploratory}}, \code{\link{PCC.Stemma}}.
 }
 \examples{
-load(fournival)
-PCC(fournival)
+%data(fournival)
+%PCC(fournival)
 }
 % Add one or more standard keywords, see file 'KEYWORDS' in the
 % R documentation directory.

man/PCC.Stemma.Rd

@@ -1,3 +1,4 @@
+\encoding{utf8}
 \name{PCC.Stemma}
 \alias{PCC.Stemma}
 %- Also NEED an '\alias' for EACH other topic documented here.
@@ -53,7 +54,7 @@ Jean-Baptiste Camps (\email{[email protected]}) & Florian Cafiero (\email{flor
 %% ~Make other sections like Warning with \section{Warning }{....} ~
 
 \seealso{
-\code{\link{PCC.disagreement}}, \code{\link{PCC.buildgroup}}, \code{\link{PCC.reconstructModel}}.
+\code{\link{PCC.disagreement}}, \code{\link{PCC.buildGroup}}, \code{\link{PCC.reconstructModel}}.
 }
 \examples{
 

man/PCC.buildGroup.Rd

@@ -1,3 +1,4 @@
+\encoding{utf8}
 \name{PCC.buildGroup}
 \alias{PCC.buildGroup}
 %- Also NEED an '\alias' for EACH other topic documented here.

man/PCC.conflicts.Rd

@@ -1,3 +1,4 @@
+\encoding{utf8}
 \name{PCC.conflicts}
 \alias{PCC.conflicts}
 \title{PCC Exploratory Methods: Conflicts between Variant Locations}
@@ -55,12 +56,12 @@ Jean-Baptiste Camps (\email{[email protected]}) & Florian Cafiero
 }
 \examples{
 %TODO: fignoler globalement les exemples et les reprendre, voire les affiner.
-load(fournival)
+data(fournival)
 myConflicts = PCC.conflicts(fournival)
-myOverconflicting = PCC.overconflicting(myConflicts)
-myNewVariantsTable = PCC.elimination(myOverconflicting)
+%myOverconflicting = PCC.overconflicting(myConflicts)
+%myNewVariantsTable = PCC.elimination(myOverconflicting)
 }
 % Add one or more standard keywords, see file 'KEYWORDS' in the
 % R documentation directory.
 \keyword{stemmatology}
-\keyword{philology}
+%\keyword{philology}

man/PCC.contam.Rd

@@ -1,3 +1,4 @@
+\encoding{utf8}
 \name{PCC.contam}
 \alias{PCC.contam}
 %- Also NEED an '\alias' for EACH other topic documented here.

man/PCC.disagreement.Rd

@@ -1,3 +1,4 @@
+\encoding{utf8}
 \name{PCC.disagreement}
 \alias{PCC.disagreement}
 %- Also NEED an '\alias' for EACH other topic documented here.

man/PCC.distribute.Rd

@@ -1,3 +1,4 @@
+\encoding{utf8}
 \name{PCC.distribute}
 \alias{PCC.distribute}
 %- Also NEED an '\alias' for EACH other topic documented here.
@@ -50,5 +51,5 @@ Jean-Baptiste Camps & Florian Cafiero
 }
 % Add one or more standard keywords, see file 'KEYWORDS' in the
 % R documentation directory.
-\keyword{ ~kwd1 }
-\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line
+\keyword{stemmatology}
+\keyword{data-manipulation}%vérif keywords

man/PCC.elimination.Rd

@@ -1,3 +1,4 @@
+\encoding{utf8}
 \name{PCC.elimination}
 \alias{PCC.elimination}
 %- Also NEED an '\alias' for EACH other topic documented here.
@@ -43,7 +44,4 @@ To spot the conflicts between variants: \code{\link{PCC.conflicts}}
 }
 % Add one or more standard keywords, see file 'KEYWORDS' in the
 % R documentation directory.
-\keyword{over-conflicting}
-\keyword{variants}% __ONLY ONE__ keyword per line
-\keyword{selection}
-\keyword{deletion}
+\keyword{stemmatology}

man/PCC.equipollent.Rd

@@ -1,3 +1,4 @@
+\encoding{utf8}
 \name{PCC.equipollent}
 \alias{PCC.equipollent}
 %- Also NEED an '\alias' for EACH other topic documented here.

man/PCC.overconflicting.Rd

@@ -1,3 +1,4 @@
+\encoding{utf8}
 \name{PCC.overconflicting}
 \alias{PCC.overconflicting}
 %- Also NEED an '\alias' for EACH other topic documented here.
@@ -40,11 +41,11 @@ Jean-Baptiste Camps (\email{[email protected]}) & Florian Cafiero
 %% ~Make other sections like Warning with \section{Warning }{....} ~
 
 \seealso{
-\code{\link{PCC.Exploratory},
+\code{\link{PCC.Exploratory}},
 %About the input for this fonction : 
 \code{\link{PCC.conflicts}},
 %To remove the variants labeled as problematic: 
-\code{\link{PCC.elimination}}.}
+\code{\link{PCC.elimination}}.
 }
 \examples{
 }

man/PCC.reconstructModel.Rd

@@ -1,3 +1,4 @@
+\encoding{utf8}
 \name{PCC.reconstructModel}
 \alias{PCC.reconstructModel}
 %- Also NEED an '\alias' for EACH other topic documented here.
@@ -19,11 +20,12 @@ A PCCbuildGroup object.
 
      Default: \code{FALSE}.
 }
-  \item{limit}{
-The maximum number of severe disagreements expected for witnesses to be in the same group. 
-
-    Default: \code{0}.
-}
+%  \item{limit}{
+%The maximum number of severe disagreements expected for witnesses to be in the same group. 
+%
+%    Default: \code{0}.
+%}
+%TODO: faut-il implementer qqchose de ce genre pour cette fonction?
  \item{recoverNAs}{
   logical; if \code{TRUE}, when an actual witness or reconstructed subarchetype is identified to the reconstructed model of a group, every NA it has is recovered by taking the value of the reconstructed model; if \code{FALSE}, their NAs values are kept. 
 
@@ -56,7 +58,11 @@ Jean-Baptiste Camps (\email{[email protected]}) & Florian Cafiero
 
 %% ~Make other sections like Warning with \section{Warning }{....} ~
 
+\examples{
+
+}
+
 \seealso{
-More about the next step: \code{\link{PCC.stemma}}.
+More about the next step: \code{\link{PCC.Stemma}}.
 More about the input: \code{\link{PCC.buildGroup}}
 }

man/VL.pValues.Rd

@@ -1,3 +1,4 @@
+\encoding{utf8}
 \name{VL.pValues}
 \alias{VL.pValues}
 %- Also NEED an '\alias' for EACH other topic documented here.
@@ -15,7 +16,7 @@ VL.pValues(x)
 }
 }
 \details{
-In order to assess the significance of each variant location, and distinguish
+In order to assess the significance of each variant location, and distinguish
 random polygenesis from contamination (i.e. copying based on several exemplars), this function crosses two by two every possible pair of variant locations, and applies a Fisher exact test. It then counts the number of configurations in which a VL has passed the significance threshold (i.e. p < 0.05).
 }
 \value{
@@ -36,7 +37,7 @@ Jean-Baptiste Camps
 %%  ~~further notes~~
 %}
 
-\warning{This function is still in active development.}
+\note{This function is still in active development.}
 
 %% ~Make other sections like Warning with \section{Warning }{....} ~
 

man/fournival.Rd

@@ -1,3 +1,4 @@
+\encoding{utf8}
 \name{fournival}
 \alias{fournival}
 \docType{data}

man/heinrichi.Rd

@@ -1,3 +1,4 @@
+\encoding{utf8}
 \name{heinrichi}
 \alias{heinrichi}
 \docType{data}
@@ -59,9 +60,6 @@ Roos, Teemu, Heikkilä, Tuomas, and Myllymäki, Petri, « Computer-Assisted Ste
 \references{
 Camps (Jean-Baptiste) & Cafiero (Florian), « Genealogical variant locations and simplified stemma: a test case », in Analysis of Ancient and Medieval Texts and Manuscripts: Digital Approaches, ed. Tara Andrews & Caroline Macé, Turnhout: Brepols, 2015, p. 69‑93 (Lectio, 1), \url{http://dx.doi.org/10.1484/M.LECTIO-EB.5.102565}.
 }
-\references{
-Camps (Jean-Baptiste) & Cafiero (Florian), « Genealogical variant locations and simplified stemma: a test case », in Analysis of Ancient and Medieval Texts and Manuscripts: Digital Approaches, ed. Tara Andrews & Caroline Macé, Turnhout: Brepols, 2015, p. 69‑93 (Lectio, 1), \url{http://dx.doi.org/10.1484/M.LECTIO-EB.5.102565}.
-}
 \examples{
 data(heinrichi)
 }