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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

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 #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: 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