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()…

Accepted Answer

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

Solution

Problem

Related problems