p.v sub-patent duration is immunity dependent. #318
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
pwinskill
requested changes
Jul 8, 2024
|
/benchmark |
pwinskill
approved these changes
Aug 1, 2024
RJSheppard
force-pushed
the
vivax_competing_hazards_main_no_blood_immunity
branch
from
693e212
to
a570996
Compare
RJSheppard
force-pushed
the
vivax_competing_hazards_main_subpatent_duration_disease_progression
branch
5 times, most recently
from
3d918c6
to
8b1c56b
Compare
RJSheppard
force-pushed
the
vivax_competing_hazards_main_no_blood_immunity
branch
from
a570996
to
e733b28
Compare
Base automatically changed from
vivax_competing_hazards_main_no_blood_immunity
to
dev
October 9, 2024 10:54
RJSheppard
force-pushed
the
vivax_competing_hazards_main_subpatent_duration_disease_progression
branch
from
8b1c56b
to
3461513
Compare
…tion/rate of recovery from subpatent infection in the Pv model. These values are now assigned during the variable creation and calculation of disease progression rates. Antiparasite immunity is labelled IAA and IAM for acquired and maternal immunities, where their decay, boosting, maternal immunity and reset at death are now included. The decay of the immunity occurs daily and has an impact of disease progression rate, which is now calculated and updated daily. We must also adjust the prevalence rendering, which for p.f is based on detectability immunity, and for p.v is explicit in the human states. `du` and ID variables and parameters are removed for vivax. Tests are added for du rates and for prevalence rendering. The vignette is extended to include the removal of ID and the sub-patent duration calculation.
RJSheppard
force-pushed
the
vivax_competing_hazards_main_subpatent_duration_disease_progression
branch
from
3461513
to
e25c01b
Compare
|
/benchmark |
|
This is how benchmark results would change (along with a 95% confidence interval in relative change) if e25c01b is merged into dev:
Further explanation regarding interpretation and methodology can be found in the documentation. |
giovannic
deleted the
vivax_competing_hazards_main_subpatent_duration_disease_progression
branch
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.
antiparasite immunity function shapes the duration of subpatent infection/rate of recovery from subpatent infection. These values are now assigned during the variable creation and calculation of recovery rates.
In previous iterations I have kept ID in the vivax model, where it acts as antiparasite immunity. For clarity of thought, I've now added IAA and IAM antiparasite immunities, including their decay, boosting, maternal immunity and reset at death.
We must also adjust the prevalence rendering, which for p.f is based on detectability immunity, and for p.v is explicit in the human states. p_detect_lm is also inappropriate for p.v as the lm_detection is explicit.
du, and ID parameters removed for vivax.
Tests are added for du rates and for prevalence rendering.