Working with knitr using subdirectories

Question

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

.

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.

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 = "..")

```

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()

```

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*

```

But the figures end up in the

project/code/figures

directory instead of

project/figures

.

I have also tried setting

base.dir

but that doesn't seem to change anything. I added the parameter

base.dir = "./figures"

to the

opts_knit$set

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

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

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

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.

Thanks in advance for any help.

Update:

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.

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.

update 2:

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

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 code to convert .md file to .docx -- uses the same folder as the .md file

pandoc("./documents/knitr_output.md", format = "docx”)

output styles (from knitr documentation)

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

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Answer 1

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.

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]))
```

Working with knitr using subdirectories

output styles (from knitr documentation)

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