Dev #335
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Dev #335
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* Add rdt testing parameters * Update biting_process to consider rdt testing for mixing
- updating metapop vignette - clarifying row & col meanings
* Add rdt testing parameters * Update biting_process to consider rdt testing for mixing
* refactor transmission mixing code * fix regressions * add time caching
Specify timesteps in create process
* Added export_mixing and import_mixing arguments to run_metapop_... * Update create_transmission_mixer to mix eir on import and foim on export * Fix regression tests
* Add tests for the EPI and mass vaccination processes/listeners * Add checks in the listeners to remove scheduled vaccinations * Update the news for the bug fix * RcppExports updated automatically
Fix competing hazards for mass and EPI pev:
* Update pev-epi min_wait test to directly check sample population * Update pe-epi min_wait test to check that pev_timestep is being updated on the first dose * Copy pev-epi min_wait test to mass pev * Update pev and epi processes to calculate targets based on time of first dose * Update infection immunity function to calculate pev immunity only after 3rd dose
Fix bug with pev min_wait
Custom carrying capacity is set as a relative scaler, not absolute value
* Update documentation * Update parameterisation and tests * Update booster listener to incorporate timed coverage * Update attach_events to pass timed coverage parameters * Test timed coverage sampling * Bonus: fix a biology test
* rename booster_timesteps -> booster_spacing * make booster_coverage a matrix (timestep x booster doses) * update validation * update implementation of attach_booster_listener * fix regression tests * update documentation * update vignettes * fix correlation examples
…he function now calculates the maternally-acquired immunity to severe disease (birth_ivm) using the acquired immunity to severe disease (iva) rather than the acquired immunity to clinical disease (ica)
Implement time varying coverage for PEV boosters:
Function for setting age-structured outputs.
…e age is 7665, which seems to make more sense (7665/365=21).
Correcting default average_age parameter
Thanks to [individual#198], processes in the simulation can now be named. This has no effect on the behaviour of the simulation but helps in debugging and profiling by labelling the call frames with the given names. [individual#198]: mrc-ide/individual#198
Assign names to all processes.
…very_infection_resolution
…tion_resolution Competing hazards recovery infection resolution
The function assumes the two bitsets are the same size, but was never checking for it. If the user passed in a second bitset that is smaller than the first, it could lead to an out-of-bounds access on the underlying std::vector.
Add a range check to bitset_index.
…lation into origin/r21_profiles
I've created two new functions to standardise drug and resistance calculations across treatment and mass treatments: calculate_successful_treatments and update_mass_drug_admin calculate_successful_treatments handles the durg efficacy and antimalarial resistance, generating key outputs for each intervention type and returning a bitset of those treated, a vector of the drugs used to treat those individuals and a vector of treated delays for those individual if resistance (SPC) is switched on. This function is called during calculate_treated, create_mda_listeners and create_pmc_process. update_mass_drug_admin calls update_infection twice,assigning D and LM-detectable A infections to Tr, while non-LM detectable A infections, U and Tr infections to S. Those assigned to S have 0 infectivity and 0 dt, while those who are assigned to Tr are assigned a fraction of their infectivity in the current timestep and dt from the parameter set or calculated using antimalarial resistance.
MDA and PMC code now consistent with each other, correctly update individual variables and take into account antimalarial resistance.
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/benchmark |
Version 2.0.0 will mark our shift to semver 2.0.0: > Given a version number MAJOR.MINOR.PATCH, increment the: > > 1. MAJOR version when you make incompatible API changes > 2. MINOR version when you add functionality in a backward compatible manner > 3. PATCH version when you make backward compatible bug fixes > > Additional labels for pre-release and build metadata are available as extensions to the MAJOR.MINOR.PATCH format.
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This is how benchmark results would change (along with a 95% confidence interval in relative change) if 9eef099 is merged into master:
Further explanation regarding interpretation and methodology can be found in the documentation. |
pwinskill
approved these changes
Sep 12, 2024
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Merging dev in preparation for release v2.0.0. This will mark our shift to semver 2.0.0 for versioning, i.e:
Transparent changes:
New features:
Breaking changes: