Using here with rmarkdown

The here package enables easy file referencing by using the top-level directory of a file project to easily build file paths. This article demonstrates the case where the working directory is set to a subdirectory of the project root, for instance when rendering an R Markdown document that lives in a subdirectory. See vignette("here") for a more general introduction.

rmarkdown starts in a subdirectory

For demonstration, this article uses a data analysis project that lives in /data/GHE/mpn/deployment/deployments/2021-01-04/renv/library/R-3.6/x86_64-pc-linux-gnu/here/demo-project on my machine. This is the project root. The path will most likely be different on your machine, the here package helps deal with this situation.

The project has the following structure:

#> /data/GHE/mpn/deployment/deployments/2021-01-04/renv/library/R-3.6/x86_64-pc-linux-gnu/here/demo-project
#> ├── analysis
#> │   └── report.Rmd
#> ├── data
#> │   └── penguins.csv
#> ├── demo-project.Rproj
#> └── prepare
#>     └── penguins.R

When report.Rmd is rendered, the working directory is internally set to <project root>/analysis by rmarkdown:

setwd(file.path(project_path, "analysis"))

getwd()
#> [1] "/data/GHE/mpn/deployment/deployments/2021-01-04/renv/library/R-3.6/x86_64-pc-linux-gnu/here/demo-project/analysis"

However, penguins.csv still lives in the data/ subdirectory. The report requires the penguins.csv file to work.

here always uses project-relative paths

To render report.Rmd, you would have to ensure the path to penguins.csv is relative to the analysis/ directory - i.e., ../data/penguins.csv. The chunks would knit properly, but could not be run in the console since the working directory in the console isn’t analysis/.

The here package circumvents this issue by always referring to the project root:

here::i_am("analysis/report.Rmd")
#> here() starts at /data/GHE/mpn/deployment/deployments/2021-01-04/renv/library/R-3.6/x86_64-pc-linux-gnu/here/demo-project

All files accessed by report.Rmd should be referred to using here():

library(here)
here("data", "penguins.csv")
#> [1] "/data/GHE/mpn/deployment/deployments/2021-01-04/renv/library/R-3.6/x86_64-pc-linux-gnu/here/demo-project/data/penguins.csv"
here("data/penguins.csv")
#> [1] "/data/GHE/mpn/deployment/deployments/2021-01-04/renv/library/R-3.6/x86_64-pc-linux-gnu/here/demo-project/data/penguins.csv"

This ensures that penguins.csv can be read both when the report is knit and when the code is run interactively in the console.