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.

Workflow

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

Reproducible analysis with Docker

_targets.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.

To run the analysis, execute this code in your console:

docker run --rm -v ${PWD}:/wd -w /wd joelnitta/pleurosoriopsis:targets \
  bash /tmp/make.sh

You will see the targets being built by {targets}, and the final manuscript should be compiled at the end as pleurosoriopsis/ms.pdf.

Interacting with the code

You can run RStudio inside the Docker container.

First run this code in your console (must be run from within the pleurosoriopsis folder):

docker run --rm -dt -v ${PWD}:/home/rstudio/ \
  -p 8787:8787 \
  -e DISABLE_AUTH=true \
  --name pleuro \
  joelnitta/pleurosoriopsis:targets

Then, navigate to localhost:8787/ in your browser.

In the RStudio "Files" pane, click Pleurosoriopsis.Rproj to open the project.

When you are done, stop and remove the container:

docker kill pleuro