Code repository for Ebihara and Nitta. "An update and reassessment of fern and lycophyte diversity data in the Japanese Archipelago", Journal of Plant Research (2019). https://doi.org/10.1007/s10265-019-01137-3
Reproducible analysis with Docker
make.R requires various packages to be installed, and may not work properly if package versions have changed. Therefore, a Docker image is provided to run the code reproducibly.
To use it, first install docker.
Clone this repo and download the data as described above.
Navigate to the cloned repository (where
/path/to/repo is the path on your machine), and launch the container:
cd /path/to/repo docker-compose up -d
docker-compose is not available, you can also launch the container using
docker run. Be sure to replace the path on the left side of
: (in this example,
/path/to/japan_ferns_review/) with the path to this repo on your machine.
docker run -d --name japan_ferns_review_analysis_1 -e DISABLE_AUTH=true -v /path/to/japan_ferns_review/:/home/rstudio/japan_ferns_review -w=/home/rstudio/japan_ferns_review joelnitta/japan_ferns_review:3.6.0
Enter the container:
docker exec -it japan_ferns_review_analysis_1 bash
Inside the container, run
You will see the targets being built by
drake, and the final manuscript and figures should be compiled at the end as in the
manuscript folder as
When it's finished, exit the container and take it down:
exit docker-compose down