add get_data_type(), a data type detection function for severity pipeline #163
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
- Add `get_data_type()` to automatically classify input data as "count_data", "incidence", or "linelist" based on structure/columns - Checks for count data via `total_count`/`total_death` arguments - Identifies `incidence` class objects - Validates data frames against required columns (`date`, `cases`, `dead`) and linelist keywords (e.g., "id", "onset", "outcome") - Implements case-insensitive column name matching - Includes error handling for unrecognized formats
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Purpose
This PR adds
get_data_type(), a utility function to automatically classify input data for severity analyses. It supports:total_count/total_deatharguments)incidence-class objectsChanges
R/get_data_type.Rdate,cases,dead)Testing
incidenceobject handlingNotes