使用 knitr 编译 .Rmd 文件时调用第二个文件中的函数
Calling functions in a second file when compiling .Rmd files with knitr
我想用knitr格式化一个R markdown文件，我们就叫它Main.rmd。 Main.rmd 中的一些代码依赖于第二个文件中的辅助函数，我们称之为 Functions.rmd。
当我先 运行 Functions.rmd 然后 Main.rmd 时， Main.rmd 运行 中的代码很好。当我先运行Functions.rmd再尝试编织Main.rmd的时候，收到评价：
Error "Object 'myfunction' not found
如何在不将 Main.rmd 和 Functions.rmd 合并到一个文档中的情况下解决此问题，我想避免这样做？
编辑：我在下面添加了一个玩具示例。到目前为止，对于如何从 Main.rmd 调用 Functions.rmd 中的函数，有非常有用的建议，但它们都需要将 Functions.rmd 转换为 .R 文件。但是，对于我目前的目的，重要的是 Functions.rmd 也可以作为独立的降价文档来阅读。
首先，Main.rmd：
---
title: "Main_test"
author: "Matt Nolan"
date: "25/06/2018"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
## Background.
This is the main body of text and code used to display results of analyses, some of which are created by calling functions in Functions.Rmd.
```{r cars}
myexamplefunction(1,2)
```
还有，这里是 Functions.rmd:
---
title: "Functions_test"
author: "Matt Nolan"
date: "25/06/2018"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
## Background
This is a document containing functions used in the document "Main_test".
Because it contains functions and formatted text to explain the functions for an interested reader, it should be usable as a standalone markdown document.
For example, this is a function that adds two numbers.
```{r cars}
myexamplefunction <- function(a, b) {a + b}
```
30Jun2018 更新：R Markdown 不支持合并 Rmd 文件
Matt 的 25Jun2018 更新澄清了这个问题，询问如何将一个 Rmd 文档嵌入到另一个 Rmd 文档中。根据 R Markdown 网站，R Markdown 需要 一个 Rmd 文件。它目前不支持将一个 Rmd 文件嵌入到另一个 Rmd 文档中。
也就是说，使用 bookdown 包，您可以将 Rmd 文件构建为书中的章节，其中每个 Rmd 文件都是书中的一个章节。有关详细信息，请参阅 Bookdown：使用 R Markdown 1.4 - Two Rendering Approaches, the Getting Started page, and the Bookdown Demo github 库中内置的示例书籍的存储库 bookdown。
2018 年 6 月 25 日更新：打印附录中的代码
根据 OP 的评论，将函数包含在 Rmd 文件而不是 R 文件中的原因是为了获得附录中代码的格式化打印输出。这可以通过我最初发布的技术加上一些更改来实现。
- 使用命名块将代码放在附录中，并使用参数
echo=TRUE和eval=FALSE避免多次执行。
- 通过
ref.label=参数在文档的主流程中执行附录中的代码，并通过echo=FALSE参数使代码不在主文档中打印。
- 除了使用
source()函数外，还必须在附录中的另一个块中打印每个函数，以获得每个函数的格式化打印。
下面列出了我的示例 Rmd 文件的更新版本。
---
title: "TestIncludedFiles"
author: "Len Greski"
date: "June 24, 2018"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
## Background
A question was posted on [Whosebug]( about how to include functions from one Rmd file while knitting another.
If the second file contains R functions to be accessed in the second Rmd file, they're best included as R files rather than Rmd. In this example we'll include three files of functions from the Johns Hopkins University *R Programming* course: `pollutantmean()`, `corr()`, and `complete()`. We'll execute them in a subsequent code block.
After an update to the original post where the original poster noted that he included the functions in an Rmd file in order to provide a formatted printout of the code in the report as an appendix, I've modified this example to account for this additional requirement.
```{r ref.label="sourceCode",echo=FALSE}
# execute sourceCode chunk from appendix
```
## Executing the sourced files
Now that the required R functions have been sourced, we'll execute them.
```{r runCode, echo=TRUE}
pollutantmean("specdata","nitrate",70:72)
complete("specdata",1:10)
corr("specdata",threshold=500)
```
# Appendix
```{r sourceCode,echo=FALSE,eval=FALSE}
# use source() function to source the functions we want to execute
source("./rprogramming/oneLine_pollutantmean.r")
source("./rprogramming/oneLine_complete.r")
source("./rprogramming/oneLine_corr.r")
```
The following is an inventory of the functions used in this Rmd file.
```{r }
pollutantmean
complete
corr
```
...以及文档附录部分的输出（为了避免发布 class 编程作业的答案而进行了编辑）。
原答案
如果第二个 Rmd 文件只包含函数，您最好将它们保存为 R 文件并使用 source() 将它们包含在 Main.Rmd 中。例如：
date: "June 24, 2018"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
## Background
A question was posted on [Whosebug]( about how to include functions from one Rmd file while knitting another.
If the second file contains R functions to be accessed in the second Rmd file, they're best included as R files rather than Rmd. In this example we'll include three files of functions from the Johns Hopkins University *R Programming* course: `pollutantmean()`, `corr()`, and `complete()`. We'll execute them in a subsequent code block.
```{r sourceCode,echo=TRUE}
# use source() function to source the functions we want to execute
source("./rprogramming/pollutantmean.r")
source("./rprogramming/complete.r")
source("./rprogramming/corr.r")
```
## Executing the sourced files
Now that the required R functions have been sourced, we'll execute them.
```{r runCode, echo=TRUE}
pollutantmean("specdata","nitrate",70:72)
complete("specdata",1:10)
corr("specdata",threshold=500)
```
...产生以下输出：
披露： 此答案包含我之前在 2016 年作为博客文章发布的技术 ToothGrowth Assignment: Accessing R Code from an Appendix in Knitr。
我想用knitr格式化一个R markdown文件，我们就叫它Main.rmd。 Main.rmd 中的一些代码依赖于第二个文件中的辅助函数，我们称之为 Functions.rmd。
当我先 运行 Functions.rmd 然后 Main.rmd 时， Main.rmd 运行 中的代码很好。当我先运行Functions.rmd再尝试编织Main.rmd的时候，收到评价：
Error "Object 'myfunction' not found
如何在不将 Main.rmd 和 Functions.rmd 合并到一个文档中的情况下解决此问题，我想避免这样做？
编辑：我在下面添加了一个玩具示例。到目前为止，对于如何从 Main.rmd 调用 Functions.rmd 中的函数，有非常有用的建议，但它们都需要将 Functions.rmd 转换为 .R 文件。但是，对于我目前的目的，重要的是 Functions.rmd 也可以作为独立的降价文档来阅读。
首先，Main.rmd：
---
title: "Main_test"
author: "Matt Nolan"
date: "25/06/2018"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
## Background.
This is the main body of text and code used to display results of analyses, some of which are created by calling functions in Functions.Rmd.
```{r cars}
myexamplefunction(1,2)
```
还有，这里是 Functions.rmd:
---
title: "Functions_test"
author: "Matt Nolan"
date: "25/06/2018"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
## Background
This is a document containing functions used in the document "Main_test".
Because it contains functions and formatted text to explain the functions for an interested reader, it should be usable as a standalone markdown document.
For example, this is a function that adds two numbers.
```{r cars}
myexamplefunction <- function(a, b) {a + b}
```
30Jun2018 更新：R Markdown 不支持合并 Rmd 文件
Matt 的 25Jun2018 更新澄清了这个问题，询问如何将一个 Rmd 文档嵌入到另一个 Rmd 文档中。根据 R Markdown 网站，R Markdown 需要 一个 Rmd 文件。它目前不支持将一个 Rmd 文件嵌入到另一个 Rmd 文档中。
也就是说，使用 bookdown 包，您可以将 Rmd 文件构建为书中的章节，其中每个 Rmd 文件都是书中的一个章节。有关详细信息，请参阅 Bookdown：使用 R Markdown 1.4 - Two Rendering Approaches, the Getting Started page, and the Bookdown Demo github 库中内置的示例书籍的存储库 bookdown。
2018 年 6 月 25 日更新：打印附录中的代码
根据 OP 的评论，将函数包含在 Rmd 文件而不是 R 文件中的原因是为了获得附录中代码的格式化打印输出。这可以通过我最初发布的技术加上一些更改来实现。
- 使用命名块将代码放在附录中，并使用参数
echo=TRUE和eval=FALSE避免多次执行。 - 通过
ref.label=参数在文档的主流程中执行附录中的代码，并通过echo=FALSE参数使代码不在主文档中打印。 - 除了使用
source()函数外，还必须在附录中的另一个块中打印每个函数，以获得每个函数的格式化打印。
下面列出了我的示例 Rmd 文件的更新版本。
---
title: "TestIncludedFiles"
author: "Len Greski"
date: "June 24, 2018"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
## Background
A question was posted on [Whosebug]( about how to include functions from one Rmd file while knitting another.
If the second file contains R functions to be accessed in the second Rmd file, they're best included as R files rather than Rmd. In this example we'll include three files of functions from the Johns Hopkins University *R Programming* course: `pollutantmean()`, `corr()`, and `complete()`. We'll execute them in a subsequent code block.
After an update to the original post where the original poster noted that he included the functions in an Rmd file in order to provide a formatted printout of the code in the report as an appendix, I've modified this example to account for this additional requirement.
```{r ref.label="sourceCode",echo=FALSE}
# execute sourceCode chunk from appendix
```
## Executing the sourced files
Now that the required R functions have been sourced, we'll execute them.
```{r runCode, echo=TRUE}
pollutantmean("specdata","nitrate",70:72)
complete("specdata",1:10)
corr("specdata",threshold=500)
```
# Appendix
```{r sourceCode,echo=FALSE,eval=FALSE}
# use source() function to source the functions we want to execute
source("./rprogramming/oneLine_pollutantmean.r")
source("./rprogramming/oneLine_complete.r")
source("./rprogramming/oneLine_corr.r")
```
The following is an inventory of the functions used in this Rmd file.
```{r }
pollutantmean
complete
corr
```
...以及文档附录部分的输出（为了避免发布 class 编程作业的答案而进行了编辑）。
原答案
如果第二个 Rmd 文件只包含函数，您最好将它们保存为 R 文件并使用 source() 将它们包含在 Main.Rmd 中。例如：
date: "June 24, 2018"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
## Background
A question was posted on [Whosebug]( about how to include functions from one Rmd file while knitting another.
If the second file contains R functions to be accessed in the second Rmd file, they're best included as R files rather than Rmd. In this example we'll include three files of functions from the Johns Hopkins University *R Programming* course: `pollutantmean()`, `corr()`, and `complete()`. We'll execute them in a subsequent code block.
```{r sourceCode,echo=TRUE}
# use source() function to source the functions we want to execute
source("./rprogramming/pollutantmean.r")
source("./rprogramming/complete.r")
source("./rprogramming/corr.r")
```
## Executing the sourced files
Now that the required R functions have been sourced, we'll execute them.
```{r runCode, echo=TRUE}
pollutantmean("specdata","nitrate",70:72)
complete("specdata",1:10)
corr("specdata",threshold=500)
```
...产生以下输出：
披露： 此答案包含我之前在 2016 年作为博客文章发布的技术 ToothGrowth Assignment: Accessing R Code from an Appendix in Knitr。