What is a neat command line equivalent to RStudio's Knit HTML?
rmarkdown::render("test.Rmd", "html_document")
Following up on the accepted answer, I've drafted a bash script called "knitter" that will do everything needed, all the user needs to do is input: ./knitter file.Rmd file.html
or ./knitter file.Rmd file.pdf
.
The script is below:
#!/bin/sh
### Test usage; if incorrect, output correct usage and exit
if [ "$#" -gt 2 -o "$#" -lt 2 ]; then
echo "********************************************************************"
echo "* Knitter version 1.0 *"
echo "********************************************************************"
echo -e "The 'knitter' script converts Rmd files into HTML or PDFs. \n"
echo -e "usage: knitter file.Rmd file.{pdf,html} \n"
echo -e "Spaces in the filename or directory name may cause failure. \n"
exit
fi
# Stem and extension of file
extension1=`echo $1 | cut -f2 -d.`
extension2=`echo $2 | cut -f2 -d.`
### Test if file exist
if [[ ! -r $1 ]]; then
echo -e "\n File does not exist, or option mispecified \n"
exit
fi
### Test file extension
if [[ $extension1 != Rmd ]]; then
echo -e "\n Invalid input file, must be a Rmd-file \n"
exit
fi
# Create temporary script
# Use user-defined 'TMPDIR' if possible; else, use /tmp
if [[ -n $TMPDIR ]]; then
pathy=$TMPDIR
else
pathy=/tmp
fi
# Tempfile for the script
tempscript=`mktemp $pathy/tempscript.XXXXXX` || exit 1
if [[ $extension2 == "pdf" ]]; then
echo "library(rmarkdown); rmarkdown::render('"${1}"', 'pdf_document')" >> $tempscript
Rscript $tempscript
fi
if [[ $extension2 == "html" ]]; then
echo "library(rmarkdown); rmarkdown::render('"${1}"', 'html_document')" >> $tempscript
Rscript $tempscript
fi
My simpler command-line script, similar to Tyler R.'s:
In your .profile
or similar, add:
function knit() {
R -e "rmarkdown::render('$1')"
}
Then, on command line, type knit file.Rmd
EDIT: For nice autocomplete, see comments
I set up output format in the Rmd header: output: github_document
or similar