如何获取像`source('myfile.r')`这样的R Markdown文件? [英] How to source R Markdown file like `source('myfile.r')`?

问题描述

我经常有一个主要的R Markdown文件或knitr LaTeX文件，其中我source一些其他R文件(例如，用于数据处理).但是，我认为在某些情况下，使这些源文件成为其自己的可复制文档(例如，R Markdown文件不仅包含用于数据处理的命令，而且还生成可解释数据处理的可复制文档，这将是有益的).决定).

I often have a main R Markdown file or knitr LaTeX file where I source some other R file (e.g., for data processing). However, I was thinking that in some instances it would be beneficial to have these sourced files be their own reproducible documents (e.g., an R Markdown file that not only includes commands for data processing, but also produces a reproducible document that explains the data processing decisions).

因此，我想在主R Markdown文件中使用类似source('myfile.rmd')的命令.它将提取并获取myfile.rmd的R代码块内的所有R代码.当然，这会引起错误.

Thus, I would like to have a command like source('myfile.rmd') in my main R Markdown file. that would extract and source all the R code inside the R code chunks of myfile.rmd. Of course, this gives rise to an error.

以下命令有效:

```{r message=FALSE, results='hide'}
knit('myfile.rmd', tangle=TRUE)
source('myfile.R')
```

如果需要输出，可以省略results='hide'.也就是说，knitr将R代码从myfile.rmd输出到myfile.R.

where results='hide' could be omitted if output was desired. I.e., knitr outputs the R code from myfile.rmd into myfile.R.

但是，这似乎并不完美:

However, it doesn't seem perfect:

• 这会导致创建一个额外的文件
• 如果需要控制显示，它需要出现在自己的代码块中.
• 它不像简单的source(...)那样优雅.

• it results in the creation of an extra file
• it needs to appear in it's own code chunk if control over display is required.
• It's not as elegant as simple source(...).

因此，我的问题是: 是否有更优雅的方式来获取R Markdown文件的R代码?

Thus my question: Is there a more elegant way of sourcing the R code of an R Markdown file?

推荐答案

似乎您正在寻找一种衬板.如何将其放入您的.Rprofile?

It seems you are looking for a one-liner. How about putting this in your .Rprofile?

ksource <- function(x, ...) {
  library(knitr)
  source(purl(x, output = tempfile()), ...)
}

但是，我不明白您为什么要source() Rmd文件本身中的代码.我的意思是knit()将运行该文档中的所有代码，并且如果您提取该代码并将其分批运行，则当您knit()该文档时，所有代码将运行两次(在您自己内部运行).这两个任务应该分开.

However, I do not understand why you want to source() the code in the Rmd file itself. I mean knit() will run all the code in this document, and if you extract the code and run it in a chunk, all the code will be run twice when you knit() this document (you run yourself inside yourself). The two tasks should be separate.

如果您真的想运行所有代码，则RStudio使此操作相当容易:Ctrl + Shift + R.它基本上在后台调用purl()和source().

If you really want to run all the code, RStudio has made this fairly easy: Ctrl + Shift + R. It basically calls purl() and source() behind the scene.

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