https://github.com/joelnitta/pleurosoriopsis

Growth Dynamics of the Independent Gametophytes of Pleurorosiopsis makinoi (Polypodiaceae)
https://github.com/joelnitta/pleurosoriopsis

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Growth Dynamics of the Independent Gametophytes of Pleurorosiopsis makinoi (Polypodiaceae)

• Host: GitHub
• URL: https://github.com/joelnitta/pleurosoriopsis
• Owner: joelnitta
• Created: 2019-01-31T19:51:47.000Z (almost 6 years ago)
• Default Branch: targets
• Last Pushed: 2022-10-11T02:57:30.000Z (over 2 years ago)
• Last Synced: 2024-08-06T03:04:00.559Z (6 months ago)
• Language: R
• Homepage:
• Size: 22.5 MB
• Stars: 17
• Watchers: 2
• Forks: 2
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# *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.](https://www.kahaku.go.jp/research/publication/botany.html)

## Workflow

All code is in [R](https://cran.r-project.org/). The [targets package](https://docs.ropensci.org/targets/) is used to manage the workflow. To run all analyses and generate the manuscript, [clone this repository](https://git-scm.com/book/en/v2/Git-Basics-Getting-a-Git-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](https://hub.docker.com/r/joelnitta/pleurosoriopsis) to run the code reproducibly.

To use it, first [install docker](https://docs.docker.com/install/).

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  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

```