Skeleton setup for a Rmarkdown based workflow using GNU Make as the
taskrunner.
To get started, setup first a new project using a shallow git clone.
$ git clone --depth 1 [email protected]:jsks/skeleton-project.git <project-directory>
# Change origin to desired remote repository
$ cd <project-directory>
$ git remote set-url origin [email protected]:<username>/<project-repo>.gitNext, access the documentation for the default rules in the included Makefile
with the help target.
$ make helpThe barebones Makefile includes support for converting Rmarkdown files to
docx, html, and pdf outputs.
To compile the example skeleton.Rmd file, install R, pandoc, and the
following R packages:
$ Rscript -e "install.packages('rmarkdown', 'dplyr', 'ggplot2', 'ggthemes', 'kableExtra', 'knitr')"
$ make skeleton.pdfAlternatively, a barebones container image from the latest version of r-base
with all necessary packages is also available.
$ docker pull ghcr.io/jsks/skeleton:4.2.0
$ docker run -v $PWD:/proj --rm -it Rbin/ # Shell scripts
data/ # Raw and generated data files
R/ # R scripts
refs/ # Reference files
posteriors/ # Model outputs
stan/ # Stan code
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