如何在knitr源文件中使用命令行参数？

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:

我有一个R脚本接受命令行参数，我想将其转换为Rtex或Rnw文件，使用如下命令编写：

knit('myScript.Rtex "-args arg1=a arg2=b"')

but I cannot figure out how to get my command line arguments into myScript.Rtex [for evaluation therein by args <- commandArgs()]. 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?

但我无法弄清楚如何将我的命令行参数放入myScript.Rtex [由args < - commandArgs（）]进行评估。我试图避免编写可能包含相同信息的临时文件，并由myScript.Rtex读取，因为这似乎不必要的不​​整洁。有人可以提供建议/解决方案吗？

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?

那么，长话短说，如何最好地将信息放入.Rnw文件中与.R文件中处理命令行参数等效（或至少类似）的块中？

Edit: Incorporating code from comments below

I want to use them in the computation. For example, I had an R script run like

我想在计算中使用它们。例如，我有一个R脚本运行

R CMD BATCH --slave --no-save --no-restore "--args input=blah" myScript.R

Now I'd like to pass the same argument to myScript.Rnw, which is a version of myScript.R, 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.

现在我想将相同的参数传递给myScript.Rnw，它是myScript.R的一个版本，但是散布了LaTeX和R代码块。因此，更广泛的问题只是针对编织器报告处理对我有用，我需要一种方法来更改运行报告的数据。我有一个解决方法 - 但我肯定想知道我是否可以将命令行参数传递给我的.Rnw文件中的一个块。现在我做不到。

This is my workaround:

这是我的解决方法：

#!/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')" &> viirs_edr_UseR_compare.log
pdflatex viirs_edr_UseR_compare.tex
exit 0

I use Sys.getenv() in *viirs_edr_UseR_compare.Rnw* to extract parameters I want to pass, e.g., CSPP_VIIRS_EDR_REFERENCE_DIR.

我在* viirs_edr_UseR_compare.Rnw *中使用Sys.getenv（）来提取我想要传递的参数，例如CSPP_VIIRS_EDR_REFERENCE_DIR。

2 个解决方案

#1

You could write a R script instead of a bash one:

您可以编写R脚本而不是bash脚本：

my_script_launcher.R

library(knitr)
args <- commandArgs(TRUE)
if (length(args) < 2) stop("Bad args, usage refdir cmpdir")

refdir <- args[1]
cmpdir <- args[2]

knit2pdf('my_script.Rnw')

my_script.Rnw

\documentclass{article}
\begin{document}
refdir=\Sexpr{refdir}
cmpdir=\Sexpr{cmpdir}
\end{document}

Then you launch it like this:

然后你像这样启动它：

Rscript my_script_launcher.R foo bar

#2

I had the same problem and ended up using the following commands (using make):

我有同样的问题，最终使用以下命令（使用make）：

# set parameters
P1=some parameter
P2=some other parameter

# top target
all : report.html

# convert Markdown to HTML
%.html : %.md
    Rscript -e 'require(markdown);markdownToHTML("$<","$@")'

# knit Rmd passing parameters
%.md : %.Rmd
    Rscript -e 'param1<-$(P1);param2<-$(P2);require(knitr);knit("$<")'

In report.Rmd I can use str(c(param1,param2)) in a code chunk and running make will produce an HTML file containing chr [1:2] "some parameter" "some other parameter".

在report.Rmd我可以在代码块中使用str（c（param1，param2））并且运行make将生成包含chr [1：2]“some parameter”“some other parameter”的HTML文件。

If you are not using make, just specify how you want to knit and where you are getting the parameters from and I can help you to adjust my solution to your needs.

如果您不使用make，只需指定您想要编织的方式以及从哪里获取参数，我可以帮助您根据需要调整我的解决方案。