使用子目录使用Knitr [英] Working with knitr using subdirectories

问题描述

我有一个项目文件夹，这是我的工作目录.我们称之为 project . project 文件夹下有4个子目录:code，data，figures和documents.

I have a project folder, which is my working directory. Let's call it project. Under the project folder are 4 subdirectories: code, data, figures, and documents.

我想将我的.Rmd文件放在code子目录中.我希望这些图进入figures子目录.我希望.html，.md和.docx文件进入documents子目录.我想从data子目录中读取我的数据.这种组织结构可能吗?我似乎无法使其正常工作.

I would like to put my .Rmd file in the code subdirectory. I would like the figures to go into the figures subdirectory. I would like the .html, .md, and .docx file(s) to go into the documents subdirectory. I would like to read in my data from the data subdirectory. Is this organizational structure possible? I can't seem to get it to work.

我从这里开始将工作目录设置为project，因为我知道knitr会查找具有.Rmd文件的文件夹，如果未指定该目录，则将其视为工作目录.

I start with this to set the working directory to project because I understand that knitr looks to the folder with the .Rmd file and treats it as the working directory if this is not specified.

```{r setglobal, cache = FALSE, include = TRUE}
library(knitr)
opts_knit$set(root.dir = "..")
```

然后我尝试设置相对于工作目录的图形路径.

Then I try setting the figure path relative to the working directory.

```{r setchunk, cache=FALSE, include=TRUE}
opts_chunk$set(fig.path = "./figures/")
getwd()
```

工作目录正确报告为project.可以从data子目录中正确读取数据.正确渲染了所有输出，并运行了所有代码.

The working directory is correctly reported as project. The data is correctly read from the data subdirectory. All output is rendered properly and all code runs.

```{r readdata}
crctx <- readRDS("./data/crctx.rds")
getwd()
*run lots of analyses here*
```

但是这些数字最终出现在project/code/figures目录而不是project/figures.

But the figures end up in the project/code/figures directory instead of project/figures.

我也尝试过设置base.dir，但这似乎并没有改变任何东西.我添加了参数

I have also tried setting base.dir but that doesn't seem to change anything. I added the parameter

base.dir = "./figures" 

到opts_knit$set列表.我什至尝试对完整路径进行硬编码.但是似乎没有什么可以改变这一点.

to the opts_knit$set list. I even tried hard-coding the full path. But nothing seems to be able to change this.

我正在使用R 3.10和RStudio 0.98.953.这是Mac 0SX 10.9.4.

I am using R 3.10 and RStudio 0.98.953. This is Mac 0SX 10.9.4.

我错过了什么吗?有没有办法将输出文件放在自己的目录中?

Am I missing something? And is there a way to put the output files in their own directory?

之所以重要，是因为我希望我们的公司都使用相同的目录结构，这将使我们能够更好地组织项目.

The reason this is important is that I would like our company to all use the same directory structure, and this will allow us to organize our projects better.

在此先感谢您的帮助.

更新:

我意识到opts_chunk$set(fig.path = "./figures/")是不正确的.我假设使用opts_knit$set(root.dir = normalizePath("../"))将根目录设置为项目文件夹将对knitr进行全局更改，因为这是应该这样做的.而且它确实适用于数据子目录，现在可以使用"./data"访问该子目录，从而允许代码运行.但是，全局设置不适用于图形输出.因此，正确的规范是opts_chunk$set(fig.path = "../figures/")-使用../而不是./.我认为Richie Cotton修复了此问题，一段时间以来我还不太清楚.

I realize that opts_chunk$set(fig.path = "./figures/") is incorrect. I assumed that setting the root directory to the project folder using opts_knit$set(root.dir = normalizePath("../")) would make a global change to knitr, since that is what it is supposed to do. And it does work for the data subdirectory, which can now be accessed with "./data" which allows the code to run. However, the global setting doesn't apply to the figure output. Therefore, the correct specification is opts_chunk$set(fig.path = "../figures/") -- using ../ instead of ./. I think Richie Cotton fixed this, and I didn't quite see it for a while.

我还使用OSX中的Terminal来创建从project/documents到project/code/figure的符号链接，该链接默认由knitr创建.这样，knitr会在右侧的子子目录中查找，但是所有内容最终都在projects/documents中.那真的很好.我无法让R使用file.symlink正确创建符号链接.但是它在Terminal中可以正常工作.走吧.

I also used Terminal in OSX to create a symbolic link from project/documents to project/code/figure which is created by default by knitr. With this, knitr looks to the right sub-subdirectory, but everything ends up in projects/documents. That worked really well. I can't get R do create the symbolic link properly using file.symlink. But it works fine in Terminal. Go figure.

更新2 :

我也输出了文件.您必须直接使用knit命令.文本在下面.

I got the output files to work as well. You have to use the knit command directly. The text is below.

用于在代码/分析中使用.Rmd编织降价文档并在输出/报告中进行输出的编织代码: knit("./code/knitr_file.Rmd", "./documents/knitr_output.md)

Knitr code to knit a markdown document with .Rmd in code/analysis and output in output/reports: knit("./code/knitr_file.Rmd", "./documents/knitr_output.md")

Pandoc代码将.md文件转换为.docx-使用与.md文件相同的文件夹 pandoc("./documents/knitr_output.md", format = "docx)

Pandoc code to convert .md file to .docx -- uses the same folder as the .md file pandoc("./documents/knitr_output.md", format = "docx")

pandoc('knitr_output.md', format='html') # HTML pandoc('knitr_output.md', format='latex') # LaTeX/PDF pandoc('knitr_output.md', format='docx') # MS Word pandoc('knitr_output.md', format='odt') # OpenDocument

pandoc('knitr_output.md', format='html') # HTML pandoc('knitr_output.md', format='latex') # LaTeX/PDF pandoc('knitr_output.md', format='docx') # MS Word pandoc('knitr_output.md', format='odt') # OpenDocument

推荐答案

尝试一下.假定您在工作目录project中列出了4个文件夹.它还假定您在data中有一个名为myData.csv的.csv文件.

Try this. It assumes you have the 4 folders you listed inside the working directory project. It also assumes you have a .csv file called myData.csv in data.

编织文件时，图将保存在figures中.最后，代码在code中查找html文件，并将其移至documents.可能有更好的方法.

When you knit the file, the plot will be saved in figures. At the end, the code looks for html files in code and moves them to documents. There's probably a better way to do this.

```{r setup}
  library(knitr)
  opts_knit$set(root.dir=normalizePath('../'))
  opts_chunk$set(fig.path = "../figures/", dev='pdf') # corrected path and added dev
```

```{r import}
  dat <- read.csv("data/myData.csv")
```

```{r plot}
  # pdf(file="figures/test.pdf")  # I do this in setup instead
  plot(dat)
  # dev.off()
```

```{r move}
  files <- list.files("code/")
  index <- grep("html", files)
  file.rename(file.path("code", files[index]),
              file.path("documents", files[index]))
```

这篇关于使用子目录使用Knitr的文章就介绍到这了，希望我们推荐的答案对大家有所帮助，也希望大家多多支持IT屋！