Translate: 将R函数帮助添加到Quarto文档中

huangapple
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英文:

R functions help into a quarto document

问题

The following code gives the examples [tag:R] codes along their output for first six topics from [tag:stats] [tag:R] library.

title: "Help"
format: pdf

  1. #| echo: false
  2. #| class-output: r
  3. library(purrr)
  4. map(
  5.       .x             = ls("package:stats", all = FALSE)[1:6] 
  6.     , .f             = example
  7.     , package        = "stats"
  8.     , character.only = TRUE
  9.     , type           = "html"
  10.     )

Translate: 将R函数帮助添加到Quarto文档中

I want to tweak this output a little bit.

Expected Output

Wondering how to add each topic title as a section and then its corresponding code and output.

Edited

The helpExtract from SOfun [tag:R] package can be used to extract specified portions of [tag:R] help files for use in [tag:Sweave] or [tag:R-markdown] documents.

remotes::install_github("mrdwab/SOfun")

library(SOfun)

helpExtract(
Function = acf
, section = c("Description", "Usage", "Arguments", "Details", "Value", "Examples")1
, type = c("m_code", "m_text", "s_code", "s_text")[2]
)

However, can't figure out how to use this function to extract topic title.

Edited (2023-04-19)

@Julian's solution is effective for the [tag:stats] [tag:R] package, but it does not function properly with the [tag:meta] [tag:R] package. When attempting to use it with the [tag:meta] [tag:R] package, the following error is generated:

Error in purrr::map():i In index: 1.Caused by error in file():! cannot open the connectionError in vctrs_vec_compat(.y, .purrr_user_env): object 'topic_title' not foundError in cat(res, sep = "\n"): object 'res' not found1

英文:

The following code gives the examples [tag:R] codes along their output for first six topics from [tag:stats] [tag:R] library.

  1. ---
  2. title: "Help"
  3. format: pdf
  4. ---
  6. ```{r}
  7. #| echo: false
  8. #| class-output: r
  9. library(purrr)
  10. map(
  11.       .x             = ls("package:stats", all = FALSE)[1:6] 
  12.     , .f             = example
  13.     , package        = "stats"
  14.     , character.only = TRUE
  15.     , type           = "html"
  16.     )
  17. ```

Translate: 将R函数帮助添加到Quarto文档中

I want to tweak this output a little bit.

Expected Output

Wondering how to add each topic title as a section and then its corresponding code and output.

Edited

The helpExtract from SOfun [tag:R] package can be used to extract specified portions of [tag:R] help files for use in [tag:Sweave] or [tag:R-markdown] documents.

  1. remotes::install_github("mrdwab/SOfun")
  3. library(SOfun)
  5. helpExtract(
  6.     Function = acf
  7.   , section  = c("Description", "Usage", "Arguments", "Details", "Value", "Examples")[1] 
  8.   , type     = c("m_code", "m_text", "s_code", "s_text")[2]
  9.   )

However, can't figured out how to use this function to extract topic title.

Edited (2023-04-19)

@Julian's solution is effective for the [tag:stats] [tag:R] package, but it does not function properly with the [tag:meta] [tag:R] package. When attempting to use it with the [tag:meta] [tag:R] package, the following error is generated:

> Error in purrr::map():i In index: 1.Caused by error in file():! cannot
> open the connectionError in vctrs_vec_compat(.y, .purrr_user_env):
> object 'topic_title' not foundError in cat(res, sep = "\n"): object
> 'res' not found1

答案1

得分: 2

这是你想要的吗？我添加了一个目录来查看章节是否符合预期（代码思路来自这里和这里）：

  1. ---
  2. title: "帮助"
  3. format: pdf
  4. toc: true
  5. number-sections: true
  6. ---
  1. #| echo: false
  3. # https://stackoverflow.com/questions/8379570/get-functions-title-from-documentation
  4. pkg_topic <- function(package, topic, file = NULL) {
  5.   # 找到主题名称/别名对应的“file”名称
  6.   if (is.null(file)) {
  7.     topics <- pkg_topics_index(package)
  8.     topic_page <- subset(topics, alias == topic, select = file)$file
  10.     if(length(topic_page) < 1)
  11.       topic_page <- subset(topics, file == topic, select = file)$file
  13.     stopifnot(length(topic_page) >= 1)
  14.     file <- topic_page[1]    
  15.   }
  17.   rdb_path <- file.path(system.file("help", package = package), package)
  18.   tools:::fetchRdDB(rdb_path, file)
  19. }
  21. pkg_topics_index <- function(package) {
  22.   help_path <- system.file("help", package = package)
  24.   file_path <- file.path(help_path, "AnIndex")
  25.   if (length(readLines(file_path, n = 1)) < 1) {
  26.     return(NULL)
  27.   }
  29.   topics <- read.table(file_path, sep = "\t", 
  30.     stringsAsFactors = FALSE, comment.char = "", quote = "", header = FALSE)
  32.   names(topics) <- c("alias", "file") 
  33.   topics[complete.cases(topics), ]
  34. }
  1. #| output: asis
  2. #| echo: false
  4. topic <- ls("package:stats", all = FALSE)[1:6]
  5. topic_title <- topic |> 
  6.   purrr::map( \(function_name) {
  7.     target <- gsub("^.+/library/(.+)/help.+$", "\", utils:::index.search("stats", 
  8.                                                                   find.package()))
  9.     doc.txt <- pkg_topic(target, function_name)  # 假设Hadley的两个函数都在这里
  11.     return(doc.txt[[1]][[1]][1])
  12.   })
  15. res <- purrr::map2_chr(topic, topic_title, \(topic, topic_title) {
  16.     knitr::knit_child(text = c(
  17.       "# `r topic_title`",
  18.       "",
  19.       "```{r}",
  20.       "#| echo: false",
  21.       "#| class-output: r",
  22.       "example(topic, package = 'stats', character.only = TRUE, type = 'html')",
  23.       "```",
  24.       "",
  25.       ""
  26.     ), envir = environment(), quiet = TRUE)
  27.   })
  29. cat(res, sep = '\n')

Translate: 将R函数帮助添加到Quarto文档中

  2. <details>
  3. <summary>英文:</summary>
  5. Is this what you want? I added a toc to see whether the chapters are as intended (code idea comes from [here](https://github.com/quarto-dev/quarto-cli/issues/2370) and [here](https://stackoverflow.com/questions/8379570/get-functions-title-from-documentation)):
  8.     ---
  9.     title: &quot;Help&quot;
  10.     format: pdf
  11.     toc: true
  12.     number-sections: true
  13.     ---
  14.     
  15.     
  16.     ```{r}
  17.     #| echo: false
  18.     
  19.     # https://stackoverflow.com/questions/8379570/get-functions-title-from-documentation
  20.     pkg_topic &lt;- function(package, topic, file = NULL) {
  21.       # Find &quot;file&quot; name given topic name/alias
  22.       if (is.null(file)) {
  23.         topics &lt;- pkg_topics_index(package)
  24.         topic_page &lt;- subset(topics, alias == topic, select = file)$file
  25.     
  26.         if(length(topic_page) &lt; 1)
  27.           topic_page &lt;- subset(topics, file == topic, select = file)$file
  28.     
  29.         stopifnot(length(topic_page) &gt;= 1)
  30.         file &lt;- topic_page[1]    
  31.       }
  32.     
  33.       rdb_path &lt;- file.path(system.file(&quot;help&quot;, package = package), package)
  34.       tools:::fetchRdDB(rdb_path, file)
  35.     }
  36.     
  37.     pkg_topics_index &lt;- function(package) {
  38.       help_path &lt;- system.file(&quot;help&quot;, package = package)
  39.     
  40.       file_path &lt;- file.path(help_path, &quot;AnIndex&quot;)
  41.       if (length(readLines(file_path, n = 1)) &lt; 1) {
  42.         return(NULL)
  43.       }
  44.     
  45.       topics &lt;- read.table(file_path, sep = &quot;\t&quot;, 
  46.         stringsAsFactors = FALSE, comment.char = &quot;&quot;, quote = &quot;&quot;, header = FALSE)
  47.     
  48.       names(topics) &lt;- c(&quot;alias&quot;, &quot;file&quot;) 
  49.       topics[complete.cases(topics), ]
  50.     }
  51.     ```
  52.     
  53.     
  54.     
  55.     ```{r}
  56.     #| output: asis
  57.     #| echo: false
  58.     
  59.     topic &lt;- ls(&quot;package:stats&quot;, all = FALSE)[1:6]
  60.     topic_title &lt;- topic |&gt; 
  61.       purrr::map( \(function_name) {
  62.         target &lt;- gsub(&quot;^.+/library/(.+)/help.+$&quot;, &quot;\&quot;, utils:::index.search(&quot;stats&quot;, 
  63.                                                                       find.package()))
  64.         doc.txt &lt;- pkg_topic(target, function_name)  # assuming both of Hadley&#39;s functions are here
  65.     
  66.         return(doc.txt[[1]][[1]][1])
  67.       })
  68.       
  69.     
  70.     
  71.     res &lt;- purrr::map2_chr(topic, topic_title, \(topic, topic_title) {
  72.         knitr::knit_child(text = c(
  73.           &quot;# `r topic_title`&quot;,
  74.           &quot;&quot;, 
  75.           &quot;```{r}&quot;,
  76.           &quot;#| echo: false&quot;,
  77.           &quot;#| class-output: r&quot;,
  78.           &quot;example(topic, package = &#39;stats&#39;, character.only = TRUE, type = &#39;html&#39;)&quot;,
  79.           &quot;```&quot;,
  80.           &quot;&quot;,
  81.           &quot;&quot;
  82.         ), envir = environment(), quiet = TRUE)
  83.       })
  84.     
  85.     cat(res, sep = &#39;\n&#39;)
  86.     ```
  88. [![enter image description here][1]][1]
  91.   [1]: https://i.stack.imgur.com/Sh6Wa.png
  96. </details>

huangapple
  • 本文由 发表于 2023年4月17日 17:25:12
  • 转载请务必保留本文链接：https://go.coder-hub.com/76033607.html
  • documentation
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  • quarto
  • r
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