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}
答案 0 :(得分：0)
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.