RMarkdown - making and using a general Rmd file for re-use

There are some tasks I do a lot and it'd be good to have general .Rmd documents available to report on the outcome of those tasks. Some examples would be a standard report on an ML experiment, or an overview from a data curation pipeline. I've been using rmarkdown for generating reports, but it has some limitations for this. I don't want to have a new Rmd file for every report. I'd like to have a configurable template file that lives in a shared location that I can run each time.

Unfortunately, if you try to do this you'll soon find that rmarkdown expects the Rmd file to be in your working directory - well, the working directory is set to the location of the Rmd file. See the following line in render.R: github-render.R_L96

My current work around for this (and please let me know if you have a better way) is to have a helper script which copies over the Rmd file to the current working directory, generates the report and then removes the temporary files:

	#!/bin/bash -eu
	if [[ $# -ne 4 ]]; then
	echo "Usage: $0 <Rmd file> <config file> <output file> <doc type {html, pdf}>"
	exit 1
	fi
	RMD=$1
	CONFIG=$2
	OUTPUT_FILE=$3
	DOC_TYPE=$4
	RMD_BASE=$(basename $RMD .Rmd)
	TMP_RMD=${RMD_BASE}.$RANDOM.Rmd
	echo $RMD $TMP_RMD $DOC_TYPE $OUTPUT_FILE
	cp $RMD $TMP_RMD
	cp $CONFIG model_report.yaml
	R --vanilla --slave -e "library('rmarkdown'); render('$TMP_RMD', '${DOC_TYPE}_document', output_file='$OUTPUT_FILE')"
	rm $TMP_RMD
	rm model_report.yaml

view raw renderRmd.sh hosted with ❤ by GitHub

The Rmd file has a line for loading in the configuration:
library(yaml)
config <- yaml.load_file("model_report.yaml")

The YAML configuration file contains the project specific variables (e.g. output suffix, flags for adding/subtracting items from a report, important dir locations). This file could easily be generated on the fly via arguments to the bash script.