Wrapper for knitr

knitr

#!/bin/bash

# wrapper for knitr

RMD_FILE="$1"
MD_FILE="/tmp/$(basename $0).$$.md"
HTML_FILE="${RMD_FILE%.*}.html"

read -d '' COMMAND << "EOF"
  library(knitr, quietly=TRUE)
  library(markdown, quietly=TRUE)
  knit("%s", "%s")
  invisible(markdownToHTML("%s", "%s", options=c('use_xhtml')))
EOF

printf -v COMMAND "$COMMAND" "$RMD_FILE" "$MD_FILE" "$MD_FILE" "$HTML_FILE"

# collapse command by converting new-lines to semi-colons and execute
Rscript -e "${COMMAND//$'\n'/; }" && rm -f $MD_FILE