如何像‘ source (‘ myfile.r’)’一样来源 R Markdown 文件？

我经常有一个主 R Markdown 文件或编织 LaTeX 文件，其中我 source一些其他 R 文件(例如，数据处理)。然而，我认为在某些情况下，让这些来源文件成为它们自己的可重复文档是有益的(例如，R Markdown 文件不仅包含数据处理命令，而且还生成可重复文档来解释数据处理决策)。

因此，我希望在我的主 R Markdown 文件中有一个类似 source('myfile.rmd')的命令。它将提取和源代码所有的 R 代码在 myfile.rmd的 R 代码块中。当然，这会导致一个错误。

以下命令可以工作:

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

其中，如果需要输出，可以省略 results='hide'。

然而，这似乎并不完美:

  • 它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。

所以我的问题是: 有没有一种更优雅的方法来源于 R Markdown 文件的 R 代码？

48770 次浏览
小开

If you are just after the code I think something along these lines should work:

  1. Read the markdown/R file with readLines
  2. Use grep to find the code chunks, searching for lines that start with <<< for example
  3. Take subset of the object that contains the original lines to get only the code
  4. Dump this to a temporary file using writeLines
  5. Source this file into your R session

Wrapping this in a function should give you what you need.

小开
最佳答案

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()), ...)
}

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.

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.

小开

Factor the common code out into a separate R file, and then source that R file into each Rmd file you want it in.

so for example let's say I have two reports I need to make, Flu Outbreaks and Guns vs Butter Analysis. Naturally I'd create two Rmd documents and be done with it.

Now suppose boss comes along and wants to see the variations of Flu Outbreaks versus Butter prices (controlling for 9mm ammo).

  • Copying and pasting the code to analyze the reports into the new report is a bad idea for code reuse, etc.
  • I want it to look nice.

My solution was to factor the project into these files:

  • Flu.Rmd
    • flu_data_import.R
  • Guns_N_Butter.Rmd
    • guns_data_import.R
    • butter_data_import.R

within each Rmd file I'd have something like:

```{r include=FALSE}
source('flu_data_import.R')
```

The problem here is that we lose reproducibility. My solution to that is to create a common child document to include into each Rmd file. So at the end of every Rmd file I create, I add this:

```{r autodoc, child='autodoc.Rmd', eval=TRUE}
```

And, of course, autodoc.Rmd:

Source Data & Code
----------------------------
<div id="accordion-start"></div>


```{r sourcedata, echo=FALSE, results='asis', warnings=FALSE}


if(!exists(autodoc.skip.df)) {
autodoc.skip.df <- list()
}


#Generate the following table:
for (i in ls(.GlobalEnv)) {
if(!i %in% autodoc.skip.df) {
itm <- tryCatch(get(i), error=function(e) NA )
if(typeof(itm)=="list") {
if(is.data.frame(itm)) {
cat(sprintf("### %s\n", i))
print(xtable(itm), type="html", include.rownames=FALSE, html.table.attributes=sprintf("class='exportable' id='%s'", i))
}
}
}
}
```
### Source Code
```{r allsource, echo=FALSE, results='asis', warning=FALSE, cache=FALSE}
fns <- unique(c(compact(llply(.data=llply(.data=ls(all.names=TRUE), .fun=function(x) {a<-get(x); c(normalizePath(getSrcDirectory(a)),getSrcFilename(a))}), .fun=function(x) { if(length(x)>0) { x } } )), llply(names(sourced), function(x) c(normalizePath(dirname(x)), basename(x)))))


for (itm in fns) {
cat(sprintf("#### %s\n", itm[2]))
cat("\n```{r eval=FALSE}\n")
cat(paste(tryCatch(readLines(file.path(itm[1], itm[2])), error=function(e) sprintf("Could not read source file named %s", file.path(itm[1], itm[2]))), sep="\n", collapse="\n"))
cat("\n```\n")
}
```
<div id="accordion-stop"></div>
<script type="text/javascript">
```{r jqueryinclude, echo=FALSE, results='asis', warning=FALSE}
cat(readLines(url("http://code.jquery.com/jquery-1.9.1.min.js")), sep="\n")
```
</script>
<script type="text/javascript">
```{r tablesorterinclude, echo=FALSE, results='asis', warning=FALSE}
cat(readLines(url("http://tablesorter.com/__jquery.tablesorter.js")), sep="\n")
```
</script>
<script type="text/javascript">
```{r jqueryuiinclude, echo=FALSE, results='asis', warning=FALSE}
cat(readLines(url("http://code.jquery.com/ui/1.10.2/jquery-ui.min.js")), sep="\n")
```
</script>
<script type="text/javascript">
```{r table2csvinclude, echo=FALSE, results='asis', warning=FALSE}
cat(readLines(file.path(jspath, "table2csv.js")), sep="\n")
```
</script>
<script type="text/javascript">
$(document).ready(function() {
$('tr').has('th').wrap('<thead></thead>');
$('table').each(function() { $('thead', this).prependTo(this); } );
$('table').addClass('tablesorter');$('table').tablesorter();});
//need to put this before the accordion stuff because the panels being hidden makes table2csv return null data
$('table.exportable').each(function() {$(this).after('<a download="' + $(this).attr('id') + '.csv" href="data:application/csv;charset=utf-8,'+encodeURIComponent($(this).table2CSV({delivery:'value'}))+'">Download '+$(this).attr('id')+'</a>')});
$('#accordion-start').nextUntil('#accordion-stop').wrapAll("<div id='accordion'></div>");
$('#accordion > h3').each(function() { $(this).nextUntil('h3').wrapAll("<div>"); });
$( '#accordion' ).accordion({ heightStyle: "content", collapsible: true, active: false });
</script>

N.B., this is designed for the Rmd -> html workflow. This will be an ugly mess if you go with latex or anything else. This Rmd document looks through the global environment for all the source()'ed files and includes their source at the end of your document. It includes jquery ui, tablesorter, and sets the document up to use an accordion style to show/hide sourced files. It's a work in progress, but feel free to adapt it to your own uses.

Not a one-liner, I know. Hope it gives you some ideas at least :)

小开

Probably one should start thinking different. My issue is the following: Write every code you normally would have had in a .Rmd chunk in a .R file. And for the Rmd document you use to knit i.e. an html, you only have left

```{R Chunkname, Chunkoptions}
source(file.R)
```

This way you'll probably create a bunch of .R files and you lose the advantage of processing all the code "chunk after chunk" using ctrl+alt+n (or +c, but normally this does not work). But, I read the book about reproducible research by Mr. Gandrud and realized, that he definitely uses knitr and .Rmd files solely for creating html files. The Main Analysis itself is an .R file. I think .Rmd documents rapidly grow too large if you start doing your whole analysis inside.

小开

I would recommend keeping the main analysis and calculation code in .R file and importing the chunks as needed in .Rmd file. I have explained the process here.

小开

The following hack worked fine for me: 

library(readr)
library(stringr)
source_rmd <- function(file_path) {
stopifnot(is.character(file_path) && length(file_path) == 1)
.tmpfile <- tempfile(fileext = ".R")
.con <- file(.tmpfile)
on.exit(close(.con))
full_rmd <- read_file(file_path)
codes <- str_match_all(string = full_rmd, pattern = "```(?s)\\{r[^{}]*\\}\\s*\\n(.*?)```")
stopifnot(length(codes) == 1 && ncol(codes[[1]]) == 2)
codes <- paste(codes[[1]][, 2], collapse = "\n")
writeLines(codes, .con)
flush(.con)
cat(sprintf("R code extracted to tempfile: %s\nSourcing tempfile...", .tmpfile))
source(.tmpfile)
}
小开

I use the following custom function

source_rmd <- function(rmd_file){
knitr::knit(rmd_file, output = tempfile())
}


source_rmd("munge_script.Rmd")
小开

Try the purl function from knitr:

source(knitr::purl("myfile.rmd", quiet=TRUE))

小开

this worked for me 

source("myfile.r", echo = TRUE, keep.source = TRUE)
小开

sys.source("./your_script_file_name.R", envir = knitr::knit_global())

put this command before calling the functions contained in the your_script_file_name.R.

the "./" adding before your_script_file_name.R to show the direction to your file if you already created a Project.

You can see this link for more detail: https://bookdown.org/yihui/rmarkdown-cookbook/source-script.html

小开

I use this one-liner:

```{r optional_chunklabel_for_yourfile_rmd, child = 'yourfile.Rmd'}
```

See: My .Rmd file becomes very lengthy. Is that possible split it and source() it's smaller portions from main .Rmd?

小开

I would say there is not a more elegant way of sourcing an Rmarkdown file. The ethos of Rmd being that the report is reproducible and at best will be self contained. However, adding to the OP's original solution, the below method avoids the permanent creation of the intermediate file on disk. It also makes some extra effort to ensure chunk output does not appear in the renderred document:

knit_loc <- tempfile(fileext = ".R")
knitr::knit("myfile.rmd",
output = knit_loc,
quiet = TRUE,
tangle = TRUE)
invisible(capture.output(source(knit_loc, verbose = FALSE)))

I would also add that if the child markdown dependencies are external to your R environment (eg write a file to disk, download some external resource, interact with a Web api etc), then instead of knit() I would opt for rmarkdown::render() instead:

rmarkdown::render("myfile.rmd")

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