Support thresholded titer values #1118
Merged
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
Adds doctests and logic to support thresholded titer values, to prevent these values from being discarded during titer model fitting. This solution converts values at lower or upper thresholds to half or twice of their threshold values, respectively. Later, we should consider a more robust implementation like the one from Bedford et al. 2014 (https://elifesciences.org/articles/01914#fig8) that treats thresholded values as probabilistic values in some reasonable range based on a normal distribution of observed log2 values. This implementation is good enough, however, to allow all data to pass through to the measurements panel in flu builds, for example. Changes to functional tests reflect the fact that the data for these tests contained thresholded values that we could not previously parse.
Codecov ReportBase: 67.97% // Head: 67.99% // Increases project coverage by
Additional details and impacted files@@ Coverage Diff @@
## master #1118 +/- ##
==========================================
+ Coverage 67.97% 67.99% +0.02%
==========================================
Files 57 57
Lines 6641 6646 +5
Branches 1632 1634 +2
==========================================
+ Hits 4514 4519 +5
Misses 1823 1823
Partials 304 304
Help us with your feedback. Take ten seconds to tell us how you rate us. Have a feature suggestion? Share it here. ☔ View full report at Codecov. |
rneher
approved these changes
Dec 28, 2022
3 tasks
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Outdated suggestions cannot be applied.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.
Description of proposed changes
Adds doctests and logic to support thresholded titer values, to prevent these values from being discarded during titer model fitting. This solution converts values at lower or upper thresholds to half or twice of their threshold values, respectively. Later, we should consider a more robust implementation like the one from Bedford et al. 2014 that treats thresholded values as probabilistic values in some reasonable range based on a normal distribution of observed log2 values. This implementation is good enough, however, to allow all data to pass through to the measurements panel in flu builds, for example.
Changes to functional tests reflect the fact that the data for these tests contained thresholded values that we could not previously parse.
Testing
Checklist