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Pleurosoriopsis

Code repository and raw data for Ebihara et al. 2019. "Growth Dynamics of the Independent Gametophytes of Pleurorosiopsis makinoi (Polypodiaceae)" Bulletin of the National Science Museum Series B (Botany) 45:77-86.

Important note

The code base has been updated since original publication. The default branch (main) is kept the same, but for a more modern approach (ca. 2022), see the targets branch: https://github.com/joelnitta/pleurosoriopsis/tree/targets.

Workflow

All code is in R. The drake package is used to manage the workflow. To run all analyses and generate the manuscript, simply clone this repository and 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 and clone this repository.

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

Enter the container:

docker exec -it pleurosoriopsis_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 should be compiled at the end as ms.pdf.

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

exit
docker-compose down