Changelog

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 https://github.com/mrc-ide/malariasimulation/pull/349
• run_simulation_with_repetitions() overrides argument replaced with parameters and correlations in https://github.com/mrc-ide/malariasimulation/pull/367

New features

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

Bug fixes

• Fix P. vivax n_bites_per_person being overwritten with multiple mosquito species, resulting in fewer bites than expected in https://github.com/mrc-ide/malariasimulation/pull/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 https://github.com/mrc-ide/malariasimulation/pull/354
• Fix set_equilibrium() to properly overwrite existing entries when called multiple times in https://github.com/mrc-ide/malariasimulation/pull/364
• Fix set_parameter_draw() to work without library(malariasimulation) in https://github.com/mrc-ide/malariasimulation/pull/370
• Fix n_bitten missing from initial output population function in https://github.com/mrc-ide/malariasimulation/pull/361
• Fix incorrect parasite output attribution in epi-outputs function in https://github.com/mrc-ide/malariasimulation/pull/352
• Add validation for bednet s + r + d = 1 in https://github.com/mrc-ide/malariasimulation/pull/349

Documentation

• Improved documentation for severe infection sampling function in https://github.com/mrc-ide/malariasimulation/pull/384
• Added iva_mean and ivm_mean immunity outputs to run_simulation documentation in https://github.com/mrc-ide/malariasimulation/pull/382
• Corrected death_rate() roxygen documentation in https://github.com/mrc-ide/malariasimulation/pull/357
• Updated P. vivax vignette to reflect prophylaxis and EIR model differences in https://github.com/mrc-ide/malariasimulation/pull/383
• Updated bednet vignette in https://github.com/mrc-ide/malariasimulation/pull/346
• Updated Variation vignette in https://github.com/mrc-ide/malariasimulation/pull/365

Other

• Unified P. vivax and P. falciparum EIR calculations to both use adult-level EIR in https://github.com/mrc-ide/malariasimulation/pull/377
• Regenerated R-CMD-check and pkgdown GitHub Actions workflows in https://github.com/mrc-ide/malariasimulation/pull/355

malariasimulation 2.0.2

• P. Vivax model by @rjsheppard

malariasimulation 2.0.1

• Fix PMC bug where timesteps to generate targetted individuals were not increasing

malariasimulation 2.0.0

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

Transparent changes to model behaviour

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

Improved documentation

• Update description of the dt parameter. by @plietar in https://github.com/mrc-ide/malariasimulation/pull/288
• Clarify some intervention parametrization documentation. by @plietar in https://github.com/mrc-ide/malariasimulation/pull/291
• Parameter and output documentation. by @RJSheppard in https://github.com/mrc-ide/malariasimulation/pull/299
• Hex by @pwinskill in https://github.com/mrc-ide/malariasimulation/pull/336

New features

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

Breaking changes

• Custom carrying capacity is set as a relative scaler, not absolute value by @pwinskill in https://github.com/mrc-ide/malariasimulation/pull/272
• Implement time varying coverage for PEV boosters: by @giovannic in https://github.com/mrc-ide/malariasimulation/pull/270
• Add asymmetric transmission in mixing in metapopulation modelling: by @giovannic in https://github.com/mrc-ide/malariasimulation/pull/277 https://github.com/mrc-ide/malariasimulation/pull/259
• lm pcr prevalence explicit by @RJSheppard in https://github.com/mrc-ide/malariasimulation/pull/298

New Contributors

• @lmhaile made their first contribution in https://github.com/mrc-ide/malariasimulation/pull/333

Full Changelog: https://github.com/mrc-ide/malariasimulation/compare/v1.6.0…v2.0.0

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

malariasimulation 1.4.0

• 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

malariasimulation 1.3.0

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

malariasimulation 1.2.0

• added a news.md file to track changes to the package.
• n_inc_clinical includes treated humans
• disaggregate EIR and state counts by mosquito species
• remove redundant Total_M and and global EIR outputs
• new vignette on how to calibrate EIR to prevalence