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POHow can I use command line arguments with knitr source file?
 

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  1. POHow can I use command line arguments with knitr source file?
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    <p>I have an R script that accepts command line arguments that I want to convert to an Rtex or Rnw file to be knitted with a command like:</p> <pre><code>knit('myScript.Rtex "-args arg1=a arg2=b"') </code></pre> <p>but I cannot figure out how to get my command line arguments into myScript.Rtex [for evaluation therein by <code>args &lt;- commandArgs()</code>]. I am trying to avoid writing temporary files that could contain the same information and be read by myScript.Rtex, because that seems unnecessarily untidy. Please can somebody provide a suggestion/solution?</p> <p>So, long story short, how best to get information into a chunk in a .Rnw file that is equivalent (or at least similar) to processing command line arguments in a .R file?</p> <h2>Edit: Incorporating code from comments below</h2> <p>I want to use them in the computation. For example, I had an R script run like</p> <pre><code>R CMD BATCH --slave --no-save --no-restore "--args input=blah" myScript.R </code></pre> <p>Now I'd like to pass the same argument to <code>myScript.Rnw</code>, which is a version of <code>myScript.R</code>, but interspersed LaTeX and R code chunks. So the broader issue is simply that for knitr report processing to be useful for me I need a way to change the data that the report is run on. I have a workaround - but I'd sure like to know if I can pass command line arguments to a chunk in my .Rnw file. Right now I cannot do that.</p> <p>This is my workaround:</p> <pre><code>#!/bin/bash if [ $# -ne 2 ]; then ` echo "Usage: $0 refdir cmpdir" exit 1` fi export CSPP_VIIRS_EDR_REFERENCE_DIR=$1 export CSPP_VIIRS_EDR_COMPARISON_DIR=$2 script=$(dirname $0)'/viirs_edr_UseR_compare.Rnw' R --slave --no-save --no-restore -e "require(knitr); knit('$script')" &amp;&gt; viirs_edr_UseR_compare.log pdflatex viirs_edr_UseR_compare.tex exit 0 </code></pre> <p>I use <code>Sys.getenv()</code> in *viirs_edr_UseR_compare.Rnw* to extract parameters I want to pass, e.g., <strong>CSPP_VIIRS_EDR_REFERENCE_DIR</strong>.</p>
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    1. USjim davies
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      1. POHow can I use command line arguments with knitr source file?
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      1. POHow can I use command line arguments with knitr source file?
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    1. COThanks for your suggestion. I need to provide a solution called from bash with arguments passed through from the bash command line. So I think I will use the environment of that bash instance and pick up what I need with Sys.getenv(). It is a bit ugly, but I need to push on.
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      1. POHow can I use command line arguments with knitr source file?
      1. USjim davies
    2. CO@jimdavies it is not clear what you want to do. looking at `knit` commandn it expected something like , ..`knit(input, output,...)`
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      1. POHow can I use command line arguments with knitr source file?
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    3. COthis is the shell script I ship with `knitr`: https://github.com/yihui/knitr/blob/master/inst/bin/knit but it is not clear to me what you want to do with the `--args` -- do you want to pass them to `knit()`, or use them in your computation?
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      1. POHow can I use command line arguments with knitr source file?
      1. USYihui Xie
 

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