Tom*_*Tom 3 yaml r rstudio knitr r-markdown
我在rmarkdown写了一些相关文档,我将通过jekyll编译成一个网站.在这样做的过程中,我遇到了一个问题:
我正在使用的一些Rmd文件调用其他Rmd文件作为子文档.当我使用knitr渲染时,生成的文档包含来自父文档和子文档的yaml前端内容.下面给出一个例子.
到目前为止,当该文档是Rmd时,我没有看到任何方法仅指定子文档的部分内容.有没有人知道一种方法,当他们在knit()中读入父级Rmd时,我可以从子文档中剥离yaml？
我很乐意考虑R之外的答案,最好是我可以嵌入rakefile中.不过,我不想永久改变儿童文件.因此剥离yaml不能永久.最后,yaml的长度因文件而异,所以我猜任何解决方案都需要能够通过regex/grep/sed/etc找到yaml的开头和结尾...
例:
%%%% Parent_Doc.rmd %%%%
---
title: parent doc
layout: default
etc: etc
---
This is the parent...
```{r child import, child="./child_doc."}
```
%%%% child_doc.rmd %%%%
---
title: child doc
layout: default
etc: etc
---
lorem ipsum etc
%%%% output.md %%%%
---
title: parent doc
layout: default
etc: etc
---
This is the parent...
---
title: child doc
layout: default
etc: etc
---
lorem ipsum etc
%%%%理想的Output.md %%%%
---
title: parent doc
layout: default
etc: etc
---
This is the parent...
lorem ipsum etc
同时,也许以下内容适合您; 它是一种丑陋而低效的解决方法(我是knitr的新手并且不是真正的程序员),但它实现了我认为你想要做的事情.
我写了一个类似的个人用途的功能,包括以下相关位 ; 原文是西班牙语,所以我在下面翻译了一些:
extraction <- function(matter, escape = FALSE, ruta = ".", patron) {
require(yaml)
# Gather together directory of documents to be processed
doc_list <- list.files(
path = ruta,
pattern = patron,
full.names = TRUE
)
# Extract desired contents
lapply(
X = doc_list,
FUN = function(i) {
raw_contents <- readLines(con = i, encoding = "UTF-8")
switch(
EXPR = matter,
# !YAML (e.g., HTML)
"no_yaml" = {
if (escape == FALSE) {
paste(raw_contents, sep = "", collapse = "\n")
} else if (escape == TRUE) {
require(XML)
to_be_escaped <- paste(raw_contents, sep = "", collapse = "\n")
xmlTextNode(value = to_be_escaped)
}
},
# YAML header and Rmd contents
"rmd" = {
yaml_pattern <- "[-]{3}|[.]{3}"
limits_yaml <- grep(pattern = yaml_pattern, x = raw_contents)[1:2]
indices_yaml <- seq(
from = limits_yaml[1] + 1,
to = limits_yaml[2] - 1
)
yaml <- mapply(
FUN = function(i) {yaml.load(string = i)},
raw_contents[indices_yaml],
USE.NAMES = FALSE
)
indices_rmd <- seq(
from = limits_yaml[2] + 1,
to = length(x = raw_contents)
)
rmd<- paste(raw_contents[indices_rmd], sep = "", collapse = "\n")
c(yaml, "contents" = rmd)
},
# Anything else (just in case)
{
stop("Matter not extractable")
}
)
}
)
}
说我的主要RMD文件main.Rmd住在my_directory和我的孩子文件,01-abstract.Rmd,02-intro.Rmd,...,06-conclusion.Rmd都装在./sections; 请注意,对于我的业余功能,最好将子文档按顺序保存到主文档中(见下文).我有我的功能extraction.R在./assets.这是我的示例目录的结构:
.
+--assets
| +--extraction.R
+--sections
| +--01-abstract.Rmd
| +--02-intro.Rmd
| +--03-methods.Rmd
| +--04-results.Rmd
| +--05-discussion.Rmd
| +--06-conclusion.Rmd
+--stats
| +--analysis.R
+--main.Rmd
在main.Rmd我导入我的子文档./sections:
---
title: Main
author: me
date: Today
output:
html_document
---
```{r, 'setup', include = FALSE}
opts_chunk$set(autodep = TRUE)
dep_auto()
```
```{r, 'import_children', cache = TRUE, include = FALSE}
source('./assets/extraction.R')
rmd <- extraction(
matter = 'rmd',
ruta = './sections',
patron = "*.Rmd"
)
```
# Abstract
```{r, 'abstract', echo = FALSE, results = 'asis'}
cat(x = rmd[[1]][["contents"]], sep = "\n")
```
# Introduction
```{r, 'intro', echo = FALSE, results = 'asis'}
cat(x = rmd[[2]][["contents"]], sep = "\n")
```
# Methods
```{r, 'methods', echo = FALSE, results = 'asis'}
cat(x = rmd[[3]][["contents"]], sep = "\n")
```
# Results
```{r, 'results', echo = FALSE, results = 'asis'}
cat(x = rmd[[4]][["contents"]], sep = "\n")
```
# Discussion
```{r, 'discussion', echo = FALSE, results = 'asis'}
cat(x = rmd[[5]][["contents"]], sep = "\n")
```
# Conclusion
```{r, 'conclusion', echo = FALSE, results = 'asis'}
cat(x = rmd[[6]][["contents"]], sep = "\n")
```
# References
然后我编织这份文件,只将我儿童文件的内容纳入其中,例如:
---
title: Main
author: me
date: Today
output:
html_document
---
# Abstract
This is **Child Doc 1**, my abstract.
# Introduction
This is **Child Doc 2**, my introduction.
- Point 1
- Point 2
- Point *n*
# Methods
This is **Child Doc 3**, my "Methods" section.
| method 1 | method 2 | method *n* |
|---------------|---------------|----------------|
| fffffffffffff | fffffffffffff | fffffffffffff d|
| fffffffffffff | fffffffffffff | fffffffffffff d|
| fffffffffffff | fffffffffffff | fffffffffffff d|
# Results
This is **Child Doc 4**, my "Results" section.
## Result 1
```{r}
library(knitr)
```
```{r, 'analysis', cache = FALSE}
source(file = '../stats/analysis.R')
```
# Discussion
This is **Child Doc 5**, where the results are discussed.
# Conclusion
This is **Child Doc 6**, where I state my conclusions.
# References
上述文件是针织版main.Rmd,即main.md.请注意## Result 1,在我的子文档中04-results.Rmd,我采购了一个外部R脚本,./stats/analysis.R现在在我的编织文档中作为新的knitr块加入; 因此,我现在需要再次编织该文件.
当子文档也包含块时,.md我会将主文档编织成另一个.Rmd,就像我有嵌套块一样多次,例如,继续上面的例子:
knit(input = './main.Rmd', output = './main_2.Rmd'),而不是编织main.Rmd成main.md,我会编织到另一个.Rmd,以便能够编织包含新导入的块生成的文件,例如,我的[R脚本analysis.R以上.main_2.Rmd成main.md或呈现为main.html通过rmarkdown::render(input = './main_2.Rmd', output_file = './main.html').注意:在上面的示例中main.md,我的R脚本的路径是../stats/analysis.R.这是相对于源文件的子文档的路径./sections/04-results.Rmd.一旦我将子文档导入位于根目录的主文档my_directory,即,./main.md或者./main_2.Rmd,路径就会出错; 因此,我必须./stats/analysis.R在下一个针织之前手动纠正它.
我在上面提到过,最好将子文档保存为与导入主文档的顺序相同的顺序.这是因为我的简单函数extraction()只是将指定给它的所有文件的内容存储在一个未命名的列表中,因此我必须main.Rmd按编号访问每个文件,即rmd[[5]][["contents"]]引用子文档./sections/05-discussion.Rmd; 考虑:
> str(rmd)
List of 6
$ :List of 4
..$ title : chr "child doc 1"
..$ layout : chr "default"
..$ etc : chr "etc"
..$ contents: chr "\nThis is **Child Doc 1**, my abstract."
$ :List of 4
..$ title : chr "child doc 2"
..$ layout : chr "default"
..$ etc : chr "etc"
..$ contents: chr "\nThis is **Child Doc 2**, my introduction.\n\n- Point 1\n- Point 2\n- Point *n*"
$ :List of 4
..$ title : chr "child doc 3"
..$ layout : chr "default"
..$ etc : chr "etc"
..$ contents: chr "\nThis is **Child Doc 3**, my \"Methods\" section.\n\n| method 1 | method 2 | method *n* |\n|--------------|--------------|----"| __truncated__
$ :List of 4
..$ title : chr "child doc 4"
..$ layout : chr "default"
..$ etc : chr "etc"
..$ contents: chr "\nThis is **Child Doc 4**, my \"Results\" section.\n\n## Result 1\n\n```{r}\nlibrary(knitr)\n```\n\n```{r, cache = FALSE}\nsour"| __truncated__
$ :List of 4
..$ title : chr "child doc 5"
..$ layout : chr "default"
..$ etc : chr "etc"
..$ contents: chr "\nThis is **Child Doc 5**, where the results are discussed."
$ :List of 4
..$ title : chr "child doc 6"
..$ layout : chr "default"
..$ etc : chr "etc"
..$ contents: chr "\nThis is **Child Doc 6**, where I state my conclusions."
所以,extraction()这里实际上存储了指定子文档的R Markdown内容,以及它们的YAML,以防你也使用它(我自己也这样做).
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