将Rscript与.Rnw文件和commandArgs（）

Question

我有一个.Rnw文件，其中包含R代码块和LaTeX命令。到目前为止，我一直在Rstudio中开发和测试此代码：单击“编译PDF”以获得一些输出文件和生成的PDF文件。

我现在想使用commandArgs（）来给.Rnw一个单独的参数：一个YAML文件。该文件包含脚本所需的各种参数。

提供一些背景信息：

• 我的.Rnw脚本是一种管道脚本，它被设计为尽可能“通用”。

• 我的.Rnw脚本每次都需要多个参数-这些参数将在每个项目之间变化。为了提供这些参数，我目前（已经）使用YAML配置文件。这意味着我的.Rnw脚本要做的第一件事是导入YAML文件，然后开始执行操作。

我的问题是：我可以同时使用“ Rscript”，“ commandArgs（）”和knitr吗？我希望我的addind可以在.Rnw脚本中添加一些commandArgs（），这样就可以运行所有内容（即在命令行上提供参数以提供YAML文件并编译PDF），如下所示：

Rscript script.Rnw params.yaml

但是，我遇到有关“ \”的错误，我强烈怀疑这与我使用.Rnw文件（这是LaTeX命令的第一件事）有关。然后，我在其他帖子上看到了可能的解决方案，例如：

 Rscript -e "library(knitr); knit('script.Rnw')"
 pdflatex script.tex

但是，这也失败了-毫无疑问，我想是因为我没有给我配置YAML文件。

我意识到我的设计可能有缺陷：通过同时使用commandAgrs（）和knitr，我使事情变得非常复杂。我还意识到，knitr可能并不是真正为为用作管道的脚本制作报告而设计的（至少这是我的印象）。我之所以要使用它，是为了使每个项目都可以生成包含所有结果的快速PDF。

我将不胜感激。这是我的代码示例：

\documentclass[12pt, a4paper]{article}

\usepackage[utf8]{inputenc}
\usepackage{hyperref}
\hypersetup{
colorlinks   = true, %Colours links instead of ugly boxes
urlcolor     = blue, %Colour for external hyperlinks
linkcolor    = blue, %Colour of internal links
citecolor   = blue %Colour of citations
 }
\usepackage{caption}
\setlength{\parindent}{0pt}
\usepackage{authblk}
\usepackage[nomarkers, nolists]{endfloat} %Positions figures at the end of the document and add no list of names (requires that chunk have fig.cap option)
\usepackage{soul} % Allows underline lines to be broken (use \ul{} instead of \underline{})

\usepackage{helvet} %Set up Arial as font
\renewcommand{\familydefault}{\sfdefault}

\newcommand{\Rfunction}[1]{{\texttt{#1}}}
\newcommand{\Rpackage}[1]{{\textit{#1}}}

\title{\textbf{Report}}
\author{Author}
\date{\today}



\begin{document}

\maketitle

\begingroup
\hypersetup{linkcolor=black} % force independent link colours in table of contents
\tableofcontents
\endgroup

\begingroup
\hypersetup{linkcolor=black} % force independent link colours in list of figures
\listoffigures
\endgroup



\newpage
\section{Introduction} 
This report blah blah blah

\newpage
\section{Results}

<<importing-lib, echo=FALSE, message=FALSE, cache=TRUE>>=

###################################################
# Obtain command-line YAML file and set directory #
###################################################

#!/usr/bin/env Rscript
args= commandArgs(trailingOnly=TRUE)

if (length(args) == 0) {
 stop("this script requires a configuration file (.yaml) as input")

 } else if (length(args) > 1) {
  stop("this script requires only one input: a configuration file (.yaml)")

}

params <-  yaml.load_file(args[1])

setwd(params$workdir)

if (dir.exists(file.path(params$workdir, "results")) == FALSE) {
  dir.create(file.path(params$workdir, "results","edgeR"), recursive = TRUE)
  dir.create(file.path(params$workdir, "results", "gsea", "input_files"), recursive = TRUE)
}

print("Hello!")
@

\end{document}

Answer 1

Ok so I have found 2 ways in which it seems to work:

Method 1: using command line knitr() and pdflatex

In this case, everything is one script (called script.Rnw) still but it looks like so:

\documentclass[12pt, a4paper]{article}

\usepackage[utf8]{inputenc}
\usepackage{hyperref}
\hypersetup{
colorlinks   = true, %Colours links instead of ugly boxes
urlcolor     = blue, %Colour for external hyperlinks
linkcolor    = blue, %Colour of internal links
citecolor   = blue %Colour of citations
 }
\usepackage{caption}
\setlength{\parindent}{0pt}
\usepackage{authblk}
\usepackage[nomarkers, nolists]{endfloat} %Positions figures at the end of the document and add no list of names (requires that chunk have fig.cap option)
\usepackage{soul} % Allows underline lines to be broken (use \ul{} instead of \underline{})

\usepackage{helvet} %Set up Arial as font
\renewcommand{\familydefault}{\sfdefault}

\newcommand{\Rfunction}[1]{{\texttt{#1}}}
\newcommand{\Rpackage}[1]{{\textit{#1}}}

\title{\textbf{Test report}}
\date{\today}



\begin{document}

\maketitle

\begingroup
\hypersetup{linkcolor=black} % force independent link colours in table of contents
\tableofcontents
\endgroup

\begingroup
\hypersetup{linkcolor=black} % force independent link colours in list of figures
\listoffigures
\endgroup



\newpage
\section{Introduction} 
This is the introduction.

\newpage
\section{Results}

This is the results.

<<importing-lib, echo=FALSE, message=FALSE>>=

###################################################
# Obtain command-line YAML file and set directory #
###################################################

#!/usr/bin/env Rscript
args= commandArgs(trailingOnly=TRUE)

if (length(args) == 0) {
  stop("this script requires a configuration file (.yaml) as input")

  # } else if (length(args) > 1) {
  # stop("this script requires only one input: a configuration file (.yaml)")

}

library(yaml)
params <- yaml.load_file(args[1])

dir <- getwd()

if (dir.exists(file.path(dir, "results")) == FALSE) {
  dir.create(file.path(dir, "results","part1"), recursive = TRUE)
  dir.create(file.path(dir, "results", "part2", "input_files"), recursive = TRUE)
}

print("Hello!")
print(params$project)
@



\newpage
\section{End}

This is the end!

\end{document}

To run the pipeline:

Rscript -e "library(knitr); knit('script.Rnw')" params.yaml && pdflatex script.tex

Method 2: separating code into a .Rnw file and .R launch file

The script.Rnw looks like so:

\documentclass[12pt, a4paper]{article}

\usepackage[utf8]{inputenc}
\usepackage{hyperref}
\hypersetup{
colorlinks   = true, %Colours links instead of ugly boxes
urlcolor     = blue, %Colour for external hyperlinks
linkcolor    = blue, %Colour of internal links
citecolor   = blue %Colour of citations
 }
\usepackage{caption}
\setlength{\parindent}{0pt}
\usepackage{authblk}
\usepackage[nomarkers, nolists]{endfloat} %Positions figures at the end of the document and add no list of names (requires that chunk have fig.cap option)
\usepackage{soul} % Allows underline lines to be broken (use \ul{} instead of \underline{})

\usepackage{helvet} %Set up Arial as font
\renewcommand{\familydefault}{\sfdefault}

\newcommand{\Rfunction}[1]{{\texttt{#1}}}
\newcommand{\Rpackage}[1]{{\textit{#1}}}

\title{\textbf{Test report}}
\date{\today}



\begin{document}

\maketitle

\begingroup
\hypersetup{linkcolor=black} % force independent link colours in table of contents
\tableofcontents
\endgroup

\begingroup
\hypersetup{linkcolor=black} % force independent link colours in list of figures
\listoffigures
\endgroup



\newpage
\section{Introduction} 
This is the introduction.

\newpage
\section{Results}

This is the results.

<<first-chunk, echo=FALSE, message=FALSE>>=

print("Hello!")
print(params$project)
@



\newpage
\section{End}

This is the end!

\end{document}

The launch.R script looks like so:

#!/usr/bin/env Rscript

library(yaml)
library(knitr)

args= commandArgs(trailingOnly=TRUE)

if (length(args) == 0) {
  stop("this script requires a configuration file (.yaml) as input")

  # } else if (length(args) > 1) {
  # stop("this script requires only one input: a configuration file (.yaml)")

}

params <- yaml.load_file(args[1])

dir <- getwd()

if (dir.exists(file.path(dir, "results")) == FALSE) {
  dir.create(file.path(dir, "results","edgeR"), recursive = TRUE)
  dir.create(file.path(dir, "results", "gsea", "input_files"), recursive = TRUE)
}

knit2pdf('script.Rnw')

To run the script:

Rscript launch.R params.yaml

One difference between the methods: method 1 generates more files (*tex, *toc, *out, *log, *aux), presumably because it's technically 2 commands. Method 2 only generates a .tex and a .pdf file.