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epiverse-trace / serofoi

Estimates the Force-of-Infection of a given pathogen from population based sero-prevalence studies
https://epiverse-trace.github.io/serofoi/
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Added validation function for `serodata` and `fit_seromodel`. Fixes #148 #154

Closed jpavlich closed 9 months ago

jpavlich commented 9 months ago

Please check that the validations I do for each column in serodata are correct.

codecov-commenter commented 9 months ago

Codecov Report

Attention: 12 lines in your changes are missing coverage. Please review.

Comparison is base (df2322a) 68.26% compared to head (e0d7d1b) 68.63%.

:exclamation: Current head e0d7d1b differs from pull request most recent head 2a5820a. Consider uploading reports for the commit 2a5820a to get more accurate results

Files Patch % Lines
R/modelling.R 84.61% 12 Missing :warning:
Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #154 +/- ## ========================================== + Coverage 68.26% 68.63% +0.37% ========================================== Files 10 10 Lines 1736 1779 +43 ========================================== + Hits 1185 1221 +36 - Misses 551 558 +7 ```

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jpavlich commented 9 months ago

@ntorresd I just added type checking for serodata. Do not merge just yet. As soon as you confirm me the missing checks and the type checks are correct, I will write tests and method documentations, then we can merge this PR.

ntorresd commented 9 months ago

@ntorresd I just added type checking for serodata. Do not merge just yet. As soon as you confirm me the missing checks and the type checks are correct, I will write tests and method documentations, then we can merge this PR.

It seems like all the necessary checks are in place, thanks @jpavlich!

jpavlich commented 9 months ago

@ntorresd Please let me know if validate_prepared_serodata is ok. After merging into main I will open another branch to add documentation and tests

jpavlich commented 7 months ago

Fixes #152 since group_sim_data calls prepare_serodata. The latter performs the required validations that are implemented in this PR