p.v constant asymptomatic infectivity #316
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_parameters
branch
from
3386313 to
e1060c0
Compare
RJSheppard
force-pushed
the
vivax_competing_hazards_main_constant_asymptomatic_infectivity
branch
3 times, most recently
from
7236985 to
5cb5a1e
Compare
RJSheppard
force-pushed
the
vivax_competing_hazards_main_parameters
branch
2 times, most recently
from
f48ac97 to
c3dc720
Compare
RJSheppard
force-pushed
the
vivax_competing_hazards_main_constant_asymptomatic_infectivity
branch
from
5cb5a1e to
ac353fd
Compare
RJSheppard
changed the base branch from
vivax_competing_hazards_main_parameters
to
master
RJSheppard
changed the base branch from
dev
to
vivax_competing_hazards_main_parameters
RJSheppard
force-pushed
the
vivax_competing_hazards_main_constant_asymptomatic_infectivity
branch
from
ac353fd to
5cd9688
Compare
RJSheppard
force-pushed
the
vivax_competing_hazards_main_constant_asymptomatic_infectivity
branch
from
5cd9688 to
f5df32d
Compare
Base automatically changed from
vivax_competing_hazards_main_parameters
to
dev
October 1, 2024 14:18
… infectivity is affected by age and immunity. We must therefore change this when asymptomatic infectivity is assigned (when an individual become asymptomatic). This occurs in initial assignments, when someone becomes infected to an asymptomatic status infection and when a clinical diseased individual progresses to asymptomatic. We can use the existing update_infection() function for vivax in human_infection and in disease progression. We can also now remove the gamma1 parameter from the vivax parameter list, used in the falciparum code. The P.v vignette has been extended to include modelled infectivity details.
giovannic
force-pushed
the
vivax_competing_hazards_main_constant_asymptomatic_infectivity
branch
from
f5df32d to
97837f3
Compare
|
/benchmark |
|
/benchmark |
|
This is how benchmark results would change (along with a 95% confidence interval in relative change) if 97837f3 is merged into dev:
Further explanation regarding interpretation and methodology can be found in the documentation. |
giovannic
deleted the
vivax_competing_hazards_main_constant_asymptomatic_infectivity
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.
p.v has a constant asymptomatic infectivity, in contrast to p.f where infectivity is affected by age and immunity. We must therefore change this when asymptomatic infectivity is assigned (when an individual become asymptomatic). This occurs in initial assignments, when someone becomes infected to an asymptomatic status infection and when a clinical diseased individual recovers to asymptomatic. We can now use the existing update_infection() function for vivax in human_infection and in disease progression.
We now remove the gamma1 parameter from the vivax parameter list, used in the falciparum code.