Package: malariasimulation 3.0.0

Giovanni Charles

malariasimulation: An individual based model for malaria

Specifies the latest and greatest malaria model.

Authors:Giovanni Charles [aut, cre], Peter Winskill [aut], Hillary Topazian [aut], Joseph Challenger [aut], Richard Fitzjohn [aut], Richard Sheppard [aut], Tom Brewer [aut], Kelly McCain [aut], Lydia Haile [aut], Imperial College of Science, Technology and Medicine [cph]

malariasimulation_3.0.0.tar.gz
malariasimulation_3.0.0.zip(r-4.5)
malariasimulation_3.0.0.tgz(r-4.5-x86_64)malariasimulation_3.0.0.tgz(r-4.5-arm64)

malariasimulation_3.0.0.tgz(r-4.5-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
malariasimulation/json (API)
NEWS

# Install 'malariasimulation' in R:
install.packages('malariasimulation', repos = c('https://mrc-ide.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/mrc-ide/malariasimulation/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

Conda:

cpp

7.51 score 21 stars 171 scripts 43 exports 37 dependencies

Last updated from:5f63ccd61c (on master). Checks:6 FAIL, 2 OK, 5 NOTE. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64FAIL144
linux-devel-x86_64FAIL139
source / vignettesOK857
linux-release-arm64NOTE502
linux-release-x86_64NOTE506
macos-release-arm64FAIL93
macos-release-x86_64FAIL183
macos-oldrel-arm64NOTE412
macos-oldrel-x86_64NOTE745
windows-develFAIL114
windows-releaseFAIL80
windows-oldrelNOTE550
wasm-releaseOK175

Exports:AL_paramsarab_paramsCQ_params_vivaxCQ_PQ_params_vivaxCQ_TQ_params_vivaxcreate_pev_profileDHA_PQP_paramsfun_paramsgamb_paramsget_correlation_parametersget_init_carrying_capacityget_parameterskol_paramsparameterise_mosquito_equilibriumparameterise_total_Mpeak_season_offsetr21_booster_profiler21_profilertss_booster_profilertss_profilerun_metapop_simulationrun_resumable_simulationrun_simulationrun_simulation_with_repetitionsset_antimalarial_resistanceset_bednetsset_carrying_capacityset_clinical_treatmentset_demographyset_drugsset_epi_outputsset_equilibriumset_mass_pevset_mdaset_parameter_drawset_pev_episet_pmcset_smcset_speciesset_sprayingset_tbvSP_AQ_paramssteph_params

Dependencies:BHbriocallrclicrayondescdiffobjdqrngevaluatefsgluehmsindividualjsonlitelifecyclemagrittrmalariaEquilibriummalariaEquilibriumVivaxMASSpkgbuildpkgconfigpkgloadpraiseprettyunitsprocessxprogresspsR6Rcpprlangrprojrootsitmostatmodtestthatvctrswaldowithr

Antimalarial Resistance

Rendered fromAntimalarial_Resistance.Rmdusingknitr::rmarkdownon Apr 03 2026.

Last update: 2024-09-12
Started: 2024-09-12

Demography

Rendered fromDemography.Rmdusingknitr::rmarkdownon Apr 03 2026.

Last update: 2024-09-12
Started: 2022-02-11

Mass Drug Administriation and Chemoprevention

Rendered fromMDA.Rmdusingknitr::rmarkdownon Apr 03 2026.

Last update: 2024-09-12
Started: 2020-09-01

Matching EIR to PfPR~2-10~

Rendered fromEIRprevmatch.Rmdusingknitr::rmarkdownon Apr 03 2026.

Last update: 2024-09-12
Started: 2021-11-01

Metapopulation

Rendered fromMetapopulation.Rmdusingknitr::rmarkdownon Apr 03 2026.

Last update: 2024-09-12
Started: 2022-08-08

Model Introduction

Rendered fromModel.Rmdusingknitr::rmarkdownon Apr 03 2026.

Last update: 2024-09-12
Started: 2020-06-11

Modifying the carrying capacity

Rendered fromCarrying-capacity.Rmdusingknitr::rmarkdownon Apr 03 2026.

Last update: 2024-09-12
Started: 2023-07-03

Mosquito species

Rendered fromSetSpecies.Rmdusingknitr::rmarkdownon Apr 03 2026.

Last update: 2024-09-12
Started: 2023-07-03

P. vivax Model

Rendered fromPlasmodium_vivax.Rmdusingknitr::rmarkdownon Apr 03 2026.

Last update: 2026-03-04
Started: 2025-02-13

Parameter Variation

Rendered fromParameter_variation.Rmdusingknitr::rmarkdownon Apr 03 2026.

Last update: 2026-03-04
Started: 2023-07-03

Stochastic Variation

Rendered fromVariation.Rmdusingknitr::rmarkdownon Apr 03 2026.

Last update: 2026-03-04
Started: 2021-11-01

Treatment

Rendered fromTreatment.Rmdusingknitr::rmarkdownon Apr 03 2026.

Last update: 2024-09-12
Started: 2020-08-13

Vaccines

Rendered fromVaccines.Rmdusingknitr::rmarkdownon Apr 03 2026.

Last update: 2024-09-12
Started: 2020-09-01

Vector Control: Bed nets

Rendered fromVectorControl_Bednets.Rmdusingknitr::rmarkdownon Apr 03 2026.

Last update: 2026-03-04
Started: 2023-07-03

Vector Control: Indoor Residual Spraying

Rendered fromVectorControl_IRS.Rmdusingknitr::rmarkdownon Apr 03 2026.

Last update: 2024-09-12
Started: 2023-07-03

Readme and manuals

Help Manual

Help pageTopics
Preset parameters for the AL drug (P. falciparum)AL_params
Preset parameters for the An. arabiensis vectorarab_params
Calculate the vector carrying capacitycalculate_carrying_capacity
Class: Correlation parametersCorrelationParameters
Preset parameters for the CQ drug (P. vivax)CQ_params_vivax
Preset parameters for the CQ-PQ drug (P. vivax)CQ_PQ_params_vivax
Preset parameters for the CQ-TQ drug (P. vivax)CQ_TQ_params_vivax
create a PEV profilecreate_pev_profile
Create progress processcreate_progress_process
Preset parameters for the DHA-PQP drug (P. falciparum)DHA_PQP_params
Calculate the birthrate for a population in equilibriumfind_birthrates
Preset parameters for the An. funestus vectorfun_params
Preset parameters for the An. gambiae s.s vectorgamb_params
Retrieve resistance parametersget_antimalarial_resistance_parameters
Get default correlation parametersget_correlation_parameters
Get initialised carrying capacity for each speciesget_init_carrying_capacity
Get model parametersget_parameters
Preset parameters for the An. koliensis vectorkol_params
Parameter draws (P. falciparum)parameter_draws_pf
Parameter draws (P. vivax)parameter_draws_pv
Parameterise total_M and carrying capacity for mosquitos from EIRparameterise_mosquito_equilibrium
Parameterise total_Mparameterise_total_M
Parasite parametersparasite_parameters
Calculate the yearly offset (in timesteps) for the peak mosquito seasonpeak_season_offset
R21 booster vaccine profiler21_booster_profile
R21 vaccine profiler21_profile
RTS,S booster vaccine profilertss_booster_profile
RTS,S vaccine profilertss_profile
Run a metapopulation modelrun_metapop_simulation
Run the simulation in a resumable wayrun_resumable_simulation
Run the simulationrun_simulation
Run the simulation with repetitionsrun_simulation_with_repetitions
Parameterise antimalarial resistanceset_antimalarial_resistance
Parameterise a bed net strategyset_bednets
Parameterise custom baseline carrying capacityset_carrying_capacity
Parameterise clinical treatmentset_clinical_treatment
Parameterise variable deathratesset_demography
Parameterise drugs to use in the modelset_drugs
Parameterise age grouped output renderingset_epi_outputs
Set equilibriumset_equilibrium
Parameterise a vaccine mass distribution strategyset_mass_pev
Parameterise a Mass Drug Administrationset_mda
Use parameter draw from the join posteriorset_parameter_draw
Parameterise a pre-erythrocytic vaccine with an EPI strategyset_pev_epi
Parameterise a perennial malaria chemoprevention (PMC, formerly IPIi)set_pmc
Parameterise a Seasonal Malaria Chemopreventionset_smc
Parameterise the mosquito species to use in the modelset_species
Parameterise an indoor spraying strategyset_spraying
Parameterise an TBV strategyset_tbv
Preset parameters for the SP-AQ drug (P. falciparum)SP_AQ_params
Preset parameters for the An. stephensi vectorsteph_params