A customised template for ProjectTemplate

Modifications to Full Project Layout:

See git for modifications.

Usage

# Setting up the project 
options(ProjectTemplate.templatedir = "statreport_projecttemplate")
ProjectTemplate::create.project("my-new-project", template = "statreport_projecttemplate")
## change name of R project and reports/Statistical_report
## modify packages in global.dcf

# Setting up renv (management of package dependencies)
renv::init() 
install.packages("ProjectTemplate")
## install.packages("Any other packages in global.dcf")
renv::snapshot()

# Setting up git (version control)

## Delete existing git folder .git

## Add to .gitignore in main directory:
## TODO
## OLD
## checks/
## data/
## docs/
## output/

## Create a new remote repository https://github.com/ for the project
## Set up a new git repository with a remote with Git Bash: 
### $ cd "path/my-new-project"
### $ git init
### $ git remote add origin https://github.com/username/my-new-project
### $ git push -u origin master

References

http://projecttemplate.net/

https://www.r-bloggers.com/customising-projecttemplate-in-r/

Example README for project:

R code for the project XXX

The aim of this R code is to be transparent and document the data handling and statistical analyses performed for the project XXX.

Language

English (sprinkled with Swedish).

Data

The data consists of Swedish individual patient data and is not public, and therefore no data is stored in this repository.

Instructions

The project uses the R package projectTemplate, http://projecttemplate.net/ and is structured (and run) accordingly. Renv, https://rstudio.github.io/renv/articles/renv.html, is used for management of package dependencies.

Since the data is not available the code can not be run as is.

Workflow:

1. Run src/load_munge_cache.R or set loading and munging options in ProjectTemplate::reload.project() to TRUE in reports/Statistical_report_XX.Rmd

2. Knit reports/Statistical_report_XX.Rmd

Publication

...