Package: malariasimulation 2.0.0

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]

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malariasimulation.pdf |malariasimulation.html✨
malariasimulation/json (API)
NEWS

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

Peer review:

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

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

On CRAN:

7.73 score 16 stars 132 scripts 39 exports 42 dependencies

Last updated 2 months agofrom:9b4544105c (on master). Checks:OK: 1 NOTE: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 02 2024
R-4.5-win-x86_64NOTENov 02 2024
R-4.5-linux-x86_64NOTENov 02 2024
R-4.4-win-x86_64NOTENov 02 2024
R-4.4-mac-x86_64NOTENov 02 2024
R-4.4-mac-aarch64NOTENov 02 2024
R-4.3-win-x86_64NOTENov 02 2024
R-4.3-mac-x86_64NOTENov 02 2024
R-4.3-mac-aarch64NOTENov 02 2024

Exports:AL_paramsarab_paramscreate_pev_profileDHA_PQP_paramsfun_paramsgamb_paramsget_correlation_parametersget_init_carrying_capacityget_parametersparameterise_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:BHbriocallrclicrayondescdiffobjdigestdqrngevaluatefansifsgluehmsindividualjsonlitelifecyclemagrittrmalariaEquilibriumMASSpillarpkgbuildpkgconfigpkgloadpraiseprettyunitsprocessxprogresspsR6Rcpprematch2rlangrprojrootsitmostatmodtestthattibbleutf8vctrswaldowithr

Antimalarial Resistance

Rendered fromAntimalarial_Resistance.Rmdusingknitr::rmarkdownon Nov 02 2024.

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

Demography

Rendered fromDemography.Rmdusingknitr::rmarkdownon Nov 02 2024.

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

Mass Drug Administriation and Chemoprevention

Rendered fromMDA.Rmdusingknitr::rmarkdownon Nov 02 2024.

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

Matching EIR to PfPR~2-10~

Rendered fromEIRprevmatch.Rmdusingknitr::rmarkdownon Nov 02 2024.

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

Metapopulation

Rendered fromMetapopulation.Rmdusingknitr::rmarkdownon Nov 02 2024.

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

Model Introduction

Rendered fromModel.Rmdusingknitr::rmarkdownon Nov 02 2024.

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

Modifying the carrying capacity

Rendered fromCarrying-capacity.Rmdusingknitr::rmarkdownon Nov 02 2024.

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

Mosquito species

Rendered fromSetSpecies.Rmdusingknitr::rmarkdownon Nov 02 2024.

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

Parameter Variation

Rendered fromParameter_variation.Rmdusingknitr::rmarkdownon Nov 02 2024.

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

Stochastic Variation

Rendered fromVariation.Rmdusingknitr::rmarkdownon Nov 02 2024.

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

Treatment

Rendered fromTreatment.Rmdusingknitr::rmarkdownon Nov 02 2024.

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

Vaccines

Rendered fromVaccines.Rmdusingknitr::rmarkdownon Nov 02 2024.

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

Vector Control: Bed nets

Rendered fromVectorControl_Bednets.Rmdusingknitr::rmarkdownon Nov 02 2024.

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

Vector Control: Indoor Residual Spraying

Rendered fromVectorControl_IRS.Rmdusingknitr::rmarkdownon Nov 02 2024.

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

Readme and manuals

Help Manual

Help pageTopics
Preset parameters for the AL drugAL_params
Preset parameters for the An. arabiensis vectorarab_params
Calculate the vector carrying capacitycalculate_carrying_capacity
Class: Correlation parametersCorrelationParameters
create a PEV profilecreate_pev_profile
Create progress processcreate_progress_process
Preset parameters for the DHA-PQP drugDHA_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
Parameter drawsparameter_draws
Parameterise total_M and carrying capacity for mosquitos from EIRparameterise_mosquito_equilibrium
Parameterise total_Mparameterise_total_M
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 drugSP_AQ_params
Preset parameters for the An. stephensi vectorsteph_params