Changes in version 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 Changes in version 2.0.2 - P. Vivax model by @rjsheppard Changes in version 2.0.1 - Fix PMC bug where timesteps to generate targetted individuals were not increasing Changes in version 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 Changes in version 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 Changes in version 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 Changes in version 1.3.0 - Custom demography - Rainfall floor - Documentation fixes for vector controls - Simple model for severe disease - Alignment of immunity function with legacy model Changes in version 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