Package: magenta 1.3.5

Oliver Watson

magenta: Individual-Based Simulation Model of Malaria Epidemiology and Genomics

Individual-based simulation model of malaria epidemiology and genomics. magenta extends the imperial malaria model by tracking the infection history of individuals. With this additional genetic characteristics of the parasite can be assessed, including resistance.

Authors:OJ Watson [aut, cre]

magenta_1.3.5.tar.gz
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magenta.pdf |magenta.html✨
magenta/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/ojwatson/magenta/issues

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

On CRAN:

4.08 score 12 scripts 21 exports 52 dependencies

Last updated 5 months agofrom:267650a550. Checks:OK: 1 NOTE: 7 ERROR: 1. Indexed: no.

TargetResultDate
Doc / VignettesOKNov 15 2024
R-4.5-win-x86_64NOTENov 15 2024
R-4.5-linux-x86_64NOTENov 15 2024
R-4.4-win-x86_64NOTENov 15 2024
R-4.4-mac-x86_64NOTENov 15 2024
R-4.4-mac-aarch64NOTENov 15 2024
R-4.3-win-x86_64ERRORNov 15 2024
R-4.3-mac-x86_64NOTENov 15 2024
R-4.3-mac-aarch64NOTENov 15 2024

Exports:%>%convert_barcode_vectorsdrug_list_createequilibrium_init_createintervention_grabmodel_param_list_createparam_list_simulation_finalizer_createparam_list_simulation_get_createparam_list_simulation_init_createparam_list_simulation_saved_init_createparam_list_simulation_update_createpipelinepopulation_get_genetics_df_npopulation_get_genetics_ibd_df_nSimulation_Finalizer_cppSimulation_Get_cppSimulation_Init_cppsimulation_RSimulation_Saved_Init_cppSimulation_Update_cppspl_grab

Dependencies:BHcinterpolateclicolorspacecrayonddedeSolvedigestdplyrfansifarvergenericsggplot2gluegtablehmsisobandjsonlitelabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmeodinpillarpkgconfigplyrprettyunitsprogressR6RColorBrewerRcppreduxreshape2ringrlangscalesstatmodstorrstringdiststringistringrtibbletidyselectutf8vctrsviridisLitewithr

How to use magenta

OJ Watson

Rendered fromIntroduction.Rmdusingknitr::rmarkdownon Nov 15 2024.

Last update: 2024-06-05
Started: 2019-12-10

Resistance

OJ Watson

Rendered fromResistance.Rmdusingknitr::rmarkdownon Nov 15 2024.

Last update: 2021-03-18
Started: 2021-03-18

Readme and manuals

Help Manual

Help pageTopics
Admin level 1 africa seasonal parametersadmin_units_seasonal
Convert human barcodes to numericsconvert_barcode_vectors
Create list describing parameters for drug efficacy and prophlyaxisdrug_create
AL Drug Createdrug_create_al
ASAQ Drug Createdrug_create_asaq
Perfect Drug Createdrug_create_default_no_resistance
DHA-PPQ Drug Createdrug_create_dhappq
Create drug listdrug_list_create
Drug Efficacy by Genotype Tabledrug_table
Equilibrium initialisation list creationequilibrium_init_create
Create housekeeping parameter listhousekeeping_list_create
Importation dataimportations
Intervention grabintervention_grab
IRS for 2000 to 2015irs_2000_2015 irs_2010_2015
ITN for 2000 to 2015itn_2000_2015
Model Parameter List Creationmodel_param_list_create
Create nmf listnmf_list_create
Parameter List creation for magenta simulation finalizerparam_list_simulation_finalizer_create
Parameter List creation for magenta simulation getting (saving to disk)param_list_simulation_get_create
Parameter List creation for magenta simulation initialisationparam_list_simulation_init_create
Parameter List creation for loading saved magenta simulationparam_list_simulation_saved_init_create
Parameter List creation for magenta simulation updatingparam_list_simulation_update_create
Pipeline for cluster submissionpipeline
Returns the population's parasite genetics summarised by coi for given sample size and statepopulation_get_genetics_df_n
Returns the population's parasite genetics for ibd style summarised by pibd for given sample size and statepopulation_get_genetics_ibd_df_n
Returns whole model to R in series of nested listsSimulation_Finalizer_cpp
Returns whole model to R in series of nested listsSimulation_Get_cpp
Creates initial model simulation using paramter list providedSimulation_Init_cpp
simulation_R functionsimulation_R
Creates initial model simulation using a saved model stateSimulation_Saved_Init_cpp
Continues simulation forward for as long as specified in param_listSimulation_Update_cpp
Spatial matrix grabspl_grab
Create vector adaptation listvector_adaptation_list_create