README.Rmd

---
output: github_document
---

<!-- README.md is generated from README.Rmd. Please edit that file -->

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/",
  out.width = "100%",
  eval = FALSE
)
```
# ReportGenerator <img src="man/figures/logo.png" align="right" height="180" />

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## Overview

`ReportGenerator` creates automatic study reports from DARWIN EU® research. It is a Shiny app with an interactive menu where the user can select figures and tables from the Complete Catalogue of Standard Data Analyses.

## Installation

You can install the development version of ReportGenerator like so:

```{r}
install.packages("remotes")
remotes::install_github("darwin-eu-dev/ReportGenerator")
```

`reportGenerator()` takes as an input zip or csv files with results from IncidencePrevalence. To launch the Shiny app just type in the console:

```{r} 
ReportGenerator::reportGenerator()
```

Alternatively, you can access to an [online version here](https://data-dev.darwin-eu.org/content/46c367cd-6e29-4382-9d7d-aff8caaa582a/).

Load your own results from the [IncidencePrevalence](https://darwin-eu.github.io/IncidencePrevalence/) or [TreatmentPatterns](https://darwin-eu-dev.github.io/TreatmentPatterns/) packages. ReportGenerator accepts data from the latest versions, but offers limited legacy support. 

`ReportGenerator()` accepts files in ZIP format from multiple data partners, with the following directory structure, or CSV files to visualise individual results. 

``` 
# IncidencePrevalence ZIP Folders

  C:
  |--results_CHUBX.zip
  |       |--incidence_attrition.csv
  |       |--prevalence_attrition.csv
  |       |--incidence_estimates.csv
  |       |--prevalence_estimates.csv
  |
  |--results_CPRD.zip
  |--results_IMASIS.zip
  |--results_IPCI.zip

# CSV files

  C:
  |
  |--incidence_attrition.csv
  |--prevalence_attrition.csv
  |--incidence_estimates.csv
  |--prevalence_estimates.csv

```

In the same way, the user can load results from TreatmentPatterns in ZIP format, including the metadata file to identify results from each data partner. 

```
# Directory TreatmentPatterns

  C:
  |--results_CPRD.zip
  |       |--countsAge.csv
  |       |--countsSex.csv
  |       |--metadata.csv
  |       |--summaryStatsTherapyDuraion.csv
  |       |--treatmentPathways.csv
  |
  |--results_IMASIS.zip
  |--results_IPCI.zip
  |--results_SIDIAP.zip

```

To test the package, the user can generate some mock data with `ReportGenerator::generateMockData()`, which will create a "Results" folder with data in zip format. 

```{r}
ReportGenerator::generateMockData()
```