Master Branch Directory Structure
The raw document files and code are oganized in the master branch in the following directories:
doc This directory only has the .Rmd or .Rnw files for the case report and slides. No html files are stored, as those are stored only in the gh-pages branch.
R This directory has all necessary R code files for code that is not included in the Rchunks of the .Rmd (or .Rnw) document files. It also has a file libraries.R which includes all R libraries necessary for the case
toolsThis directory only has the server.R and ui.R files for the case web application tools.
data All public data used in the case or shared as alternative data for the case analysis are stored in this directory. The directory also includes a README file describing the data. Note: Certain cases use proprietary data. In such situations this directory may not include any data. However, it is highly recommended that at least some set of data is included for users to be able to test the case methods and process.
Finally, all cases have the following files in the parent directory:
REAMDE.md A file providing the case description and instructions for replication and reuse
RunStudy.R An R-file which, when sourced, replicates the study and generates html report and slides. Moreover, the file includes all necessary user parameters of the case which, after modifying and sourcing the RunStudy.R file again, new slides and report for the chosen case parametes are generated