In cjvanlissa/worcs: Workflow for Open Reproducible Code in Science

knitr::opts_chunk$set(
  collapse = TRUE,
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library(worcs)

This vignette describe the worcs package's functionality for automating reproducibility. The basic idea is that the entry point, endpoint (or endpoints), and recipe by which to get to the endpoint from the entry point are all well-defined.

In a typical worcs project, the entry point will be a dynamic document (e.g., manuscript.Rmd), and the endpoint will be the rendered manuscript (e.g., manuscript.pdf). The recipe by which to get from the entry point to the endpoint is often a simple call to rmarkdown::render("manuscript.Rmd").

By default, the entry point and recipe are documented in the .worcs project file when the project is created, if an R-script or Rmarkdown file is selected as the manuscript. Endpoints are not created by default, as it only makes sense to define them when the analyses are complete.

Custom recipes can be added to a project using add_recipe().

Adding endpoints

Users can add endpoints using the function add_endpoint("filename"). When running this function, filename is added to the .worcs project file, and its checksum is computed so that any changes to the contents of the file can be detected.

It is also possible to specify multiple endpoints. For example, maybe the user has finalized the analyses, and wants to track reproducibility for the analysis results - but still wants to make changes to the text of the manuscript without breaking reproducibility checks. In this case, it is useful to track files that contain analysis results instead of the rendered manuscript. Imagine these are intermediary files with analysis results:

• descriptives.csv: A file with the descriptive statistics of study variables
• model_fit.csv: A table with model fit indices for several models
• finalmodel.RData: An RData file with the results of the final model

These three files could be tracked as endpoints by calling add_endpoint("descriptives.csv"); add_endpoint("model_fit.csv"); add_endpoint("finalmodel.RData").

Reproducing a Project

A WORCS project can be reproduced by evaluating the function reproduce(). This function evaluates the recipe defined in the .worcs project file. If no recipe is specified (e.g., when a project was created with an older version of the package), but an entry point is defined, reproduce() will try to evaluate the entry point if it is an Rmarkdown or R source file.

Checking reproducibility

Users can verify that the endpoint remains unchanged after reproducing the project by calling the function check_endpoints(). If any endpoint has changed relative to the version stored in the .worcs project file, this will result in a warning message.

Updating endpoints

To update the endpoints in the .worcs file, call snapshot_endpoints(). Always call this function to log changes to the code that should result in a different end result.

Automating Reproducibility

If a project is connected to a remote repository on GitHub, it is possible to use GitHub actions to automatically check a project's reproducibility and signal the result of this reproducibility check by displaying a badge on the project's readme page (which is the welcome page visitors of the GitHub repository first see).

To do so, follow these steps:

1. Add endpoint using add_endpoint(); for example, if the endpoint of your analyses is a file called 'manuscript/manuscript.md', then you would call add_endpoint('manuscript/manuscript.md')
2. Run github_action_reproduce()
3. You should see a message asking you to copy-paste code for a status badge to your readme.md. If you do not see this message, add the following code to your readme.md manually:
   • [![worcs_endpoints](https://github.com/YOUR_ACCOUNT/PROJECT_REPOSITORY/actions/workflows/worcs_reproduce.yaml/badge.svg)](https://github.com/YOUR_ACCOUNT/PROJECT_REPOSITORY/actions/worcs_reproduce.yaml/worcs_endpoints.yaml)
4. Commit these changes to GitHub using git_update()

Visit your project page on GitHub and select the Actions tab to see that your reproducibility check is running; visit the main project page to see the new badge in your readme.md file.

Automating Endpoint Checks

Sometimes, you may wish to verify that the endpoints of a project remain the same but without reproducing all analyses on GitHub's servers. This may be the case when the project has closed data that are not available on GitHub, or if the analyses take a long time to compute and you want to prevent using unnecessary compute power (e.g., for environmental reasons).

In these cases, you can still use GitHub actions to automatically check whether the endpoints have remained unchanged. If your local changes to the project introduce deviations from the endpoint snapshots, these tests will fail.

If you make intentional changes to the endpoints, you should of course run snapshot_endpoints().

You can display a badge on the project's readme page to signal that the endpoints remain unchanged.

To do so, follow these steps:

1. Add endpoint using add_endpoint(); for example, if the endpoint of your analyses is a file called 'manuscript/manuscript.md', then you would call add_endpoint('manuscript/manuscript.md')
2. Run github_action_check_endpoints()
3. You should see a message asking you to copy-paste code for a status badge to your readme.md. If you do not see this message, add the following code to your readme.md manually:
   • [![worcs_endpoints](https://github.com/YOUR_ACCOUNT/PROJECT_REPOSITORY/actions/workflows/worcs_endpoints.yaml/badge.svg)](https://github.com/YOUR_ACCOUNT/PROJECT_REPOSITORY/actions/workflows/worcs_endpoints.yaml)
4. Commit these changes to GitHub using git_update()

Visit your project page on GitHub and select the Actions tab to see that your reproducibility check is running; visit the main project page to see the new badge in your readme.md file.

cjvanlissa/worcs documentation built on Nov. 7, 2024, 1:20 p.m.