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Add the DiseasyActivity module #79

Merged
merged 30 commits into from
Dec 20, 2023
Merged

Add the DiseasyActivity module #79

merged 30 commits into from
Dec 20, 2023

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RasmusSkytte
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@RasmusSkytte RasmusSkytte commented Dec 20, 2023

Intent

This PR replaces #30 which became too large to review conveniently.

This PR is as large, but consists of a number of smaller PRs that have been individually reviewed.

This PR fixes #21 and fixes #31

Approach

The approaches are varied and specified in each PR

Known issues

N/A

Checklist

  • The PR passes all local unit tests
  • I have documented any new features introduced
  • If the PR adds a new feature, please add an entry in NEWS.md
  • A reviewer is assigned to this PR

RasmusSkytte and others added 29 commits November 7, 2023 14:09
* test(DiseasyActivity): make tests more specific
* test(DiseasyActivity): put test value before expected value
* fix(DiseasyActivity): allow scenarios with single activity
* fix(DiseasyActivity): always return scenario activities as list
* feat: translate the `dk_activity_units` and `dk_reference_scenario` data sets

* feat: add contact_basis data set
---------
Co-authored-by: Rasmus Skytte Randløv <[email protected]>
Co-authored-by: LasseEngboChr <[email protected]>
feat(DiseasyActivity): improve `$describe()`, `$scenario_matrix`, and `$add_activities()`
---------

Co-authored-by: Lasse Engbo Christiansen <[email protected]>
feat(DiseasyActivity): improve function signatures for weighing
* fix(dk_activity_units): cross check numerical values
* fix(DiseasyActivity): make normalisation robust

* docs(contact_basis): use country name in description
* docs: use long names for demography
* docs(DiseasyActivity): minor fixes to docs

* test(DiseasyActivity): fix broken tests
@RasmusSkytte RasmusSkytte added the enhancement New feature or request label Dec 20, 2023
@RasmusSkytte RasmusSkytte self-assigned this Dec 20, 2023
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codecov bot commented Dec 20, 2023

Codecov Report

Attention: 46 lines in your changes are missing coverage. Please review.

Comparison is base (27393c7) 83.60% compared to head (b13a84f) 83.98%.

Files Patch % Lines
R/DiseasyActivity.R 83.80% 46 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main      #79      +/-   ##
==========================================
+ Coverage   83.60%   83.98%   +0.37%     
==========================================
  Files           7        8       +1     
  Lines         543      843     +300     
==========================================
+ Hits          454      708     +254     
- Misses         89      135      +46     

☔ View full report in Codecov by Sentry.
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@RasmusSkytte RasmusSkytte changed the title Diseasy activity Add the DiseasyActivity module Dec 20, 2023
@RasmusSkytte
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This PR is a formality to ensure CI tests are working and to provide an account of the changes.
Almost all code this PR adds to the main branch has been reviewed and approved.

@RasmusSkytte RasmusSkytte marked this pull request as ready for review December 20, 2023 15:16
@RasmusSkytte RasmusSkytte merged commit 2557ed3 into main Dec 20, 2023
13 checks passed
@RasmusSkytte RasmusSkytte deleted the diseasy_activity branch January 2, 2024 13:05
RasmusSkytte added a commit that referenced this pull request Dec 16, 2024
Add the DiseasyActivity module
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DiseasyActivity: Add vignette that describes principles DiseasyActivity
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