knitr to html

knitr

#!/bin/bash
# adapted from https://github.com/jdavis/dotfiles/blob/master/bin/knitr
# make sure the ruby gem 'kicker' is installed
# also make sure the r packages 'knitr' and 'markdown' are installed

FILE="${1}"
RMD="$FILE.Rmd"
MD="$FILE.md"
HTML="$FILE.html"

if [[ $# != 1 ]]; then
    echo "Usage: knitr <Rmd_file_without_extension>"
    exit
fi

if [[ ! -f "${RMD}" ]]; then
    echo "Cannot find: ${RMD}"
    exit
fi

hash kicker 2> /dev/null || {
    echo "Please install the Ruby gem 'kicker', usually the following will work:"
    echo "    $ gem install kicker"
    exit
}

KNITR="echo \"Rerunning Knitr...\"; Rscript -e \"library(knitr); library(markdown); knit('./${RMD}'); markdownToHTML('${MD}', '${HTML}', options=c('use_xhtml', 'base64_images')); browseURL(paste0('file://', file.path(getwd(),'${HTML}')))\""

echo "Watching ${RMD}..."
kicker -e "${KNITR}" ${RMD}