3.0.0

malariasimulation 3.0.0

Breaking changes

• set_bednets() retention parameter is now optional and named, replaced by a choice between log-uniform retention (retention) or logistic decay retention (logistic_half_life, logistic_k) in #349
• run_simulation_with_repetitions() overrides argument replaced with parameters and correlations in #367

New features

• Logistic retention model for bed nets as an alternative to log-uniform retention in #349
• set_equilibrium() gains EIR_population_input argument to accept total-population EIR (converted to adult EIR internally) in #377
• run_simulation_with_repetitions() now supports correlation parameters in #367
• set_parameter_draw() appends the draw index to the parameter list in #365

Bug fixes

• Fix P. vivax n_bites_per_person being overwritten with multiple mosquito species, resulting in fewer bites than expected in #385
• Fix P. vivax liver-stage drug tracking: ls_drug and ls_drug_time now added to variable list, and blood-stage vs liver-stage drugs correctly differentiated in #354
• Fix set_equilibrium() to properly overwrite existing entries when called multiple times in #364
• Fix set_parameter_draw() to work without library(malariasimulation) in #370
• Fix n_bitten missing from initial output population function in #361
• Fix incorrect parasite output attribution in epi-outputs function in #352
• Add validation for bednet s + r + d = 1 in #349

Documentation

• Improved documentation for severe infection sampling function in #384
• Added iva_mean and ivm_mean immunity outputs to run_simulation documentation in #382
• Corrected death_rate() roxygen documentation in #357
• Updated P. vivax vignette to reflect prophylaxis and EIR model differences in #383
• Updated bednet vignette in #346
• Updated Variation vignette in #365

Other

• Unified P. vivax and P. falciparum EIR calculations to both use adult-level EIR in #377
• Regenerated R-CMD-check and pkgdown GitHub Actions workflows in #355

v2.0.2 (P. Vivax)

What's Changed

• Vivax competing hazards main parameters by @RJSheppard in #315
• p.v constant asymptomatic infectivity by @RJSheppard in #316
• Remove blood immunity from p.v model by @RJSheppard in #317
• p.v sub-patent duration is immunity dependent. by @RJSheppard in #318
• Remove severe immunity for P.v by @RJSheppard in #319
• Allow p.v subpatent infections by @RJSheppard in #320
• Fix merging named lists and add custom function to utils by @CosmoNaught in #340
• Add hypnozoites to the P.v model by @RJSheppard in #321
• Add equilibrium solution to P.v model by @RJSheppard in #322
• PMC age subsetting has a mistake in it. timesteps and time_index in s… by @RJSheppard in #341
• Update vector_parameters.R references by @nilani-chandradeva1 in #344
• Vivax competing hazards main drugs by @RJSheppard in #330
• Vivax outputs by @RJSheppard in #345
• v2.0.2 Dev by @giovannic in #348

New Contributors

• @CosmoNaught made their first contribution in #340
• @nilani-chandradeva1 made their first contribution in #344

Full Changelog: v2.0.1...v2.0.2

v2.0.1

What's Changed

• Fix continuous benchmarking: by @giovannic in #338
• Hotfix/pmc by @RJSheppard in #342

Full Changelog: v2.0.0...v2.0.1

v2.0.0

Release v2.0.0. This will mark our shift to semver 2.0.0 for versioning, i.e:

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.

Transparent changes

• Fix progress bar bug by @pwinskill in #258
• Fix bug with pev min_wait by @giovannic in #264
• Fix competing hazards for mass and EPI pev: by @giovannic in #265
• Improve correlation tests. by @plietar in #287
• Assign names to all processes. by @plietar in #325
• Correcting default average_age parameter by @RJSheppard in #326
• Add a range check to bitset_index. by @plietar in #331
• Rewrite the exponential decay process in C++. by @plietar in #285
• recovery_rates variable has been renamed as (disease) progression_rates. by @RJSheppard in #334

Transparent changes to model behaviour

• Moved mortality to the end of processes to resolve order of competing… by @RJSheppard in #292
• calculate_eir function correction by @RJSheppard in #296
• Older age groups (older than equilibrium age object) are not correctl… by @RJSheppard in #301
• Competing hazards recovery infection resolution by @RJSheppard in #300
• Bug/maternal immunity sampling by @tbreweric in #279

Improved documentation

• Update description of the dt parameter. by @plietar in #288
• Clarify some intervention parametrization documentation. by @plietar in #291
• Parameter and output documentation. by @RJSheppard in #299
• Hex by @pwinskill in #336

New features

• Pausing and resuming of simulations by @plietar in #280 #286 #293 #323
• Function for setting age-structured outputs. by @RJSheppard in #297
• Add GitHub workflow for continuous benchmarking. by @plietar in #304
• adding in n_spray output by @htopazian in #310
• Antimalarial resistance by @tbreweric in #263 #282 #289
• Add R21 PEV profiles by @lmhaile in #333

Breaking changes

• Custom carrying capacity is set as a relative scaler, not absolute value by @pwinskill in #272
• Implement time varying coverage for PEV boosters: by @giovannic in #270
• Add asymmetric transmission in mixing in metapopulation modelling: by @giovannic in #277 #259
• lm pcr prevalence explicit by @RJSheppard in #298

New Contributors

• @lmhaile made their first contribution in #333

Full Changelog: v1.6.0...v2.0.0

v1.6.0

malariasimulation 1.6.0

• Fix MDA bug where undetectable asymptomatics are treated
• New vignettes
• Progress bar for long simulations
• Individual mosquitoes off by default
• New vaccination code:
  • pre-erythrocytic vaccine functions have been renamed to pev
  • pev functions have PEVProfiles for alternate pev vaccines and boosters
• Specify carrying capacity over time

v1.4.3

malariasimulation 1.4.3

• Treatment number rendering for all treatments not just effective
• Default rendering for drug-based interventions
• Bed nets and IRS continue post individual's death
• ITN scheduling does not overwrite on receipt of >1 net

v1.4.1

Here we introduce PMC, metapopulation modelling and make some model parameters more flexible

Changes

• Fix rendering of incidence when there are no infections
• Support metapopulation models (see vignette for documentation)
• Render ITN usage
• Time-varying RTS,S EPI coverage
• Time-varying demography (see vignette for documentation)
• Remove unused birthrate parameterisation
• Minor speed improvement from disease progression re-write
• PMC can now be modelled using set_pmc

v1.3.0

• Custom demography
• Rainfall floor
• Documentation fixes for vector controls
• Simple model for severe disease
• Alignment of immunity function with legacy model

v1.2.0

malariasimulation 1.2.0

• added a NEWS.md file to track changes to the package.
• n_inc_clinical now includes treated humans
• EIR and mosquito state counts are now disaggregated by species
• redundant Total_M and and aggregate EIR outputs are no longer output
• new vignette on how to calibrate EIR to match a given prevalence (See Matching PfPR2-10 to EIR vignette)
• p_ outputs for smoother prevalence/incidence outputs (See Variation vignette)
• small speed improvements related to individual@0.1.7

v1.1.0

Changes:

• EPI strategy for vaccination
• new prevalence outputs including numerator and denominator
• BREAKING: prevalence outputs have been removed
• Mosquito model renamed to aquatic mosquito model