How to include graphics when using tar_render()? Error: Cannot find the file(s)

[RHReynolds]

Hi,

I would like tar_render() to render an .rmd that includes several external graphics that are stored in a directory in the same location where the .rmd is. However, I keep getting the error Cannot find the file(s): "figures/example.png".

The way I am currently running this is:

• In an RStudio Project, which is where the targets pipeline is defined
• Relative to the project directory, the .rmd is stored in the directory, ./docs/, while figures are stored in ./docs/figures
• I have defined the ./docs/figures in my _targets.R using:

tar_target(
        name = fig_dir,
        command = here::here("docs", "figures"),
        format = "file"
        )

• This target is passed to tar_render(), using the following command:

tar_render(
        name = report,
        path = here::here("docs", "example.rmd"),
        params =
            list(
                ext_figures = fig_dir
            )
    )

• Within the .rmd, I use tar_read in the yaml header to call the path to the target, fig_dir (see below).

params:
    ext_figures: !r targets::tar_read(fig_dir, store = here::here("_targets"))

• Finally, the figure is called within the rmd using: knitr::include_graphics(file.path(params$ext_figures, "example.png"))

Appreciate this is quite a long-winded solution, but it was important that I was (i) able to track the dependencies going into the .rmd, as in more complicated cases, I will be using the outputs of other processes as input to my .rmd and (ii) still able to knit the .rmd using RStudio's knit button. The above solution allows me to knit the .rmd without issues. But unfortunately it doesn't seem to work with tar_render(). Do you have any suggestions as to how to resolve this?

[wlandau]

Seems similar to #116 (comment). Experimenting with regular Markdown syntax and withr::with_dir(knitr::include_graphics(...)) may help. Other than that, it would be easier to help with a runnable reprex.

[RHReynolds]

Thanks for the quick response and suggestions!

I managed to get the following to work both with tar_make() and RStudio knit: withr::with_dir(here::here("docs"), knitr::include_graphics("./figures/example.png"))

Ideally, however, I would like the docs/figures directory to be a "target", so that I can see the dependency between my report and the figure directory in my pipeline. The way I was doing this was by providing the directory as an external parameter to my .rmd (see here), having this directory be a target within _targets.R, and then calling the figure with knitr::include_graphics(file.path(params$ext_figures, "example.png")) in the rmd. This may be very obvious, and I'm just not seeing it, but how would I get the withr solution to work such that I could monitor these dependencies?

I've created a GitHub repo that should help with the reprex: rtargets-reprex.

[wlandau]

Thanks for the reprex. I put together a recommendation at RHReynolds/rtargets-reprex#1. The main changes I proposed are:

• Set the knitr root directory to be the pipeline root.
• Set an option to make knitr::include_graphics() respect absolute paths.
• Supply the absolute path to the figure to knitr::include_graphics().

I also modified the solution to work without here::here() (for users who may not be using here) and simplified it to work without R Markdown parameters. The docs/example.rmd report now looks like this:

---
title: "Example"
date: "`r format(Sys.time(), '%d %B %Y')`"
output: 
  bookdown::html_document2:
    figure_caption: yes
    code_folding: hide
    theme: paper
    highlight: kate
    df_print: paged
    toc: true
    toc_float: true
    number_sections: true
---

```{r setup}
root <- rprojroot::find_root_file(criterion = "_targets.R") # Find the pipeline root directory.
knitr::opts_knit$set(root.dir = root) # Run the report from the pipeline root directory. 
options(knitr.graphics.rel_path = FALSE) # Make knitr::include_graphics() use absolute paths.
```

```{r example-figure, fig.cap = "Example figure"}
knitr::include_graphics(file.path(root, targets::tar_read(fig_dir), "example.png"))
```

[RHReynolds]

Thank you very much for this!!