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japan_ferns_review

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

All code is in R. The drake package is used to manage the workflow.

Raw data (except for a single file, FernGreenListV1.01.xls, which is included in this repo) are kept on Dryad (https://doi.org/10.5061/dryad.4362p32).

To run all analyses and generate the manuscript, first clone this repository. Next, download the raw data from the Dryad repository, unzip it, and move it to the data/ folder. Finally, run make.R.

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

If 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 make.R:

Rscript make.R

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 japan_ferns_review_ms.docx, fig_1.pdf, etc.

When it's finished, exit the container and take it down:

exit
docker-compose down

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An update and reassessment of fern and lycophyte diversity data in the Japanese Archipelago

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