Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Convert {epireview} data into <epidist> #298

Merged
merged 16 commits into from
May 16, 2024
Merged

Conversation

joshwlambert
Copy link
Member

This PR addresses #264 and adds a work-in-progress feature to convert between entries in the {epireview} R package epidemiological parameter tables to <epidist> objects for use in pipelines. The as_epidist() S3 generic is added to the package, with an as_epidist.data.frame() method for converting from {epireview}.

This feature is not fully tested or documented, but is being merged into main to be tested in the WHO EpiParameter workshop for user testing. A future PR will ensure the coercion functions are robust and tested to a more diverse range of input.

A new data object epireview_core_cols is added to the package to identify which <data.frame>s are from {epireview}. The data-raw script is also added to the package.

This PR adds a vignette that describes the as_epidist() methods with various use cases.

The existing coercion methods as.function.epidist() and as.data.frame.epidist() are moved to the new coercion.R file.

@joshwlambert joshwlambert added documentation Improvements or additions to documentation enhancement New feature or request S3-method labels May 16, 2024
@joshwlambert
Copy link
Member Author

The lintr GHA workflow is failing but I will address this in a follow-up PR.

@joshwlambert joshwlambert merged commit 7f69ecf into main May 16, 2024
9 of 10 checks passed
@joshwlambert joshwlambert deleted the convert_epireview branch May 16, 2024 07:06
@joshwlambert joshwlambert mentioned this pull request May 23, 2024
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
documentation Improvements or additions to documentation enhancement New feature or request S3-method
Projects
None yet
Development

Successfully merging this pull request may close these issues.

1 participant