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-4.7)malariasimulation_3.0.0.zip(r-4.6)malariasimulation_3.0.0.zip(r-4.5)
malariasimulation_3.0.0.tgz(r-4.6-x86_64)malariasimulation_3.0.0.tgz(r-4.6-arm64)malariasimulation_3.0.0.tgz(r-4.5-x86_64)malariasimulation_3.0.0.tgz(r-4.5-arm64)
malariasimulation_3.0.0.tar.gz(r-4.7-arm64)malariasimulation_3.0.0.tar.gz(r-4.7-x86_64)malariasimulation_3.0.0.tar.gz(r-4.6-arm64)malariasimulation_3.0.0.tar.gz(r-4.6-x86_64)
malariasimulation_3.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
malariasimulation/json (API)

# 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

7.54 score 21 stars 185 scripts 43 exports 38 dependencies

Last updated from:5f63ccd61c (on master). Checks:11 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64NOTE540
linux-devel-x86_64NOTE531
source / vignettesOK856
linux-release-arm64NOTE546
linux-release-x86_64NOTE499
macos-release-arm64NOTE368
macos-release-x86_64NOTE1675
macos-oldrel-arm64NOTE433
macos-oldrel-x86_64NOTE1151
windows-develNOTE635
windows-releaseNOTE634
windows-oldrelNOTE580
wasm-releaseOK176

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:BHbriocallrclicrayondescdiffobjdqrngevaluatefsgluehmsindividualjsonlitelifecyclemagrittrmalariaEquilibriummalariaEquilibriumVivaxMASSotelpkgbuildpkgconfigpkgloadpraiseprettyunitsprocessxprogresspsR6Rcpprlangrprojrootsitmostatmodtestthatvctrswaldowithr

P. vivax Model
Using the P. vivax model | Model details | Parameters | Structure | New Infections | Immunity | Infectivity of LM-detectable infections | Hypnozoites | Drug treatment | Equilibrium | Key Model References
Rendered fromPlasmodium_vivax.Rmdusingknitr::rmarkdown

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

Parameter Variation
Estimating variation in parameters
Rendered fromParameter_variation.Rmdusingknitr::rmarkdown

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

Stochastic Variation
Variation and population size | Parameterisation | Simulations | Stochastic elimination | Estimating variation
Rendered fromVariation.Rmdusingknitr::rmarkdown

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

Vector Control: Bed nets
Setting bed net parameters | Parameterisation | A note on mosquito species | Simulation | Visualisation | Comparing coverage and population bed net usage | Using the netz package
Rendered fromVectorControl_Bednets.Rmdusingknitr::rmarkdown

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

Antimalarial Resistance
Introduction | Using set_antimalarial_resistance() to parameterise resistance | Simulating static resistance | Parameterisation | Simulation | Visualisation | Simulating dynamic resistance | Simulating antimalarial resistance with multiple resistance outcomes | References
Rendered fromAntimalarial_Resistance.Rmdusingknitr::rmarkdown

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

Demography
Age group rendering | Set custom demography | Simulation | Visualisation | Set dynamic demography | Parameterisation
Rendered fromDemography.Rmdusingknitr::rmarkdown

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

Mass Drug Administriation and Chemoprevention
Mass Drug Administration | Parameterisation | Interventions | Simulation | Visualisation | Seasonal Malaria Chemoprevention | Simulations
Rendered fromMDA.Rmdusingknitr::rmarkdown

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

Matching EIR to PfPR~2-10~
PfPR~2-10~ matching using malariaEquilibrium | PfPR~2-10~ matching using malariasimulation | Establish malariasimulation parameters | Run the simulations and calculate PfPR~2-10~ | Fit line of best fit relating initial EIR values to PfPR~2-10~ | Visualisation | Matching EIR to PfPR~2-10~ values | Calibrating PfPR~2-10~ using the cali package
Rendered fromEIRprevmatch.Rmdusingknitr::rmarkdown

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

Metapopulation
Run metapopulation simulation | Parameterisation | Simulation | Visualisation
Rendered fromMetapopulation.Rmdusingknitr::rmarkdown

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

Model Introduction
Model structure | Human Biology | States | Parameters | Mosquito Biology | Key Model References (structure and dynamics) | Run simulation | Code | Output | Additional outputs | Output visualisation | Set equilibrium | Override parameters | Seasonality | Individual mosquitoes | Vignettes
Rendered fromModel.Rmdusingknitr::rmarkdown

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

Modifying the carrying capacity
Seasonality | Custom modification of the mosquito carrying capacity | Larval source management | Invasive species | Full flexibility
Rendered fromCarrying-capacity.Rmdusingknitr::rmarkdown

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

Mosquito species
Setting mosquito species parameters | Single endophilic mosquito species | Single exophilic mosquito species | Plot adult female infectious mosquitoes by species over time | Setting multiple mosquito species
Rendered fromSetSpecies.Rmdusingknitr::rmarkdown

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

Treatment
Setting drugs and clinical treatment | Parameterisation and simulation | Visualisation
Rendered fromTreatment.Rmdusingknitr::rmarkdown

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

Vaccines
Parameterisation | Mass RTS,S | Simulation | Visualisation | Seasonal mass vaccination | RTS,S EPI | RTS,S EPI with seasonal boosters | RTS,S dosing | TBV
Rendered fromVaccines.Rmdusingknitr::rmarkdown

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

Vector Control: Indoor Residual Spraying
Setting IRS parameters | Parameterisation | A note on mosquito species | Simulation | Visualisation
Rendered fromVectorControl_IRS.Rmdusingknitr::rmarkdown

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