Text file of useful R or Rmd things

useful_rmd.txt

if rJava package in R fails to install run: "sudo R CMD javareconf" in bash

Be able to knit rmarkdown from cmd line
first soft link Rstudios pandoc:
Newer Systems (Debian/Ubuntu/Fedora/RHEL6+) 
For newer Linux systems you can make a standalone version of pandoc v1.12.3 available to the system by soft-linking the binaries included with RStudio:
$ sudo ln -s /usr/lib/rstudio/bin/pandoc/pandoc /usr/local/bin 
$ sudo ln -s /usr/lib/rstudio/bin/pandoc/pandoc-citeproc /usr/local/bin 

then:
R CMD -e 'rmarkdown::render("input.Rmd")

Possibly a better way:
Go into RStudio and find the system environment variable for RSTUDIO_PANDOC

Sys.getenv("RSTUDIO_PANDOC")
Then put that in your R script prior to calling the render command.

Sys.setenv(RSTUDIO_PANDOC="--- insert directory here ---")



run rstudio from cmd line with particular install of R:
export RSTUDIO_WHICH_R=/usr/local/bin/R




Dual output and table of contents created on knit:
---
title: "title"
author: "name"
date: '`r format(Sys.Date())`'
output:
  pdf_document:
    toc: yes
  html_document:
    toc: yes
---