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]

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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'))

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

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

admin_units_seasonal - Admin level 1 africa seasonal parameters
drug_table - Drug Efficacy by Genotype Table
importations - Importation data
irs_2000_2015 - IRS for 2000 to 2015
itn_2000_2015 - ITN for 2000 to 2015

On CRAN:

21 exports 0.82 score 52 dependencies

Last updated 26 days agofrom:267650a550cd5b558fba981e600b1c19a07a503b

Exports:%>%convert_barcode_vectors drug_list_create equilibrium_init_create intervention_grab model_param_list_create param_list_simulation_finalizer_create param_list_simulation_get_create param_list_simulation_init_create param_list_simulation_saved_init_create param_list_simulation_update_create pipeline population_get_genetics_df_n population_get_genetics_ibd_df_n Simulation_Finalizer_cpp Simulation_Get_cpp Simulation_Init_cpp simulation_R Simulation_Saved_Init_cpp Simulation_Update_cpp spl_grab

Dependencies:BH cinterpolate cli colorspace crayon dde deSolve digest dplyr fansi farver generics ggplot2 glue gtable hms isoband jsonlite labeling lattice lifecycle magrittr MASS Matrix mgcv munsell nlme odin pillar pkgconfig plyr prettyunits progress R6 RColorBrewer Rcpp redux reshape2 ring rlang scales statmod storr stringdist stringi stringr tibble tidyselect utf8 vctrs viridisLite withr

How to use magenta

OJ Watson

Rendered fromIntroduction.Rmdusingknitr::rmarkdownon Jun 18 2024.

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

Resistance

OJ Watson

Rendered fromResistance.Rmdusingknitr::rmarkdownon Jun 18 2024.

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Admin level 1 africa seasonal parameters	admin_units_seasonal
Convert human barcodes to numerics	convert_barcode_vectors
Create list describing parameters for drug efficacy and prophlyaxis	drug_create
AL Drug Create	drug_create_al
ASAQ Drug Create	drug_create_asaq
Perfect Drug Create	drug_create_default_no_resistance
DHA-PPQ Drug Create	drug_create_dhappq
Create drug list	drug_list_create
Drug Efficacy by Genotype Table	drug_table
Equilibrium initialisation list creation	equilibrium_init_create
Create housekeeping parameter list	housekeeping_list_create
Importation data	importations
Intervention grab	intervention_grab
IRS for 2000 to 2015	irs_2000_2015 irs_2010_2015
ITN for 2000 to 2015	itn_2000_2015
Model Parameter List Creation	model_param_list_create
Create nmf list	nmf_list_create
Parameter List creation for magenta simulation finalizer	param_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 initialisation	param_list_simulation_init_create
Parameter List creation for loading saved magenta simulation	param_list_simulation_saved_init_create
Parameter List creation for magenta simulation updating	param_list_simulation_update_create
Pipeline for cluster submission	pipeline
Returns the population's parasite genetics summarised by coi for given sample size and state	population_get_genetics_df_n
Returns the population's parasite genetics for ibd style summarised by pibd for given sample size and state	population_get_genetics_ibd_df_n
Returns whole model to R in series of nested lists	Simulation_Finalizer_cpp
Returns whole model to R in series of nested lists	Simulation_Get_cpp
Creates initial model simulation using paramter list provided	Simulation_Init_cpp
simulation_R function	simulation_R
Creates initial model simulation using a saved model state	Simulation_Saved_Init_cpp
Continues simulation forward for as long as specified in param_list	Simulation_Update_cpp
Spatial matrix grab	spl_grab
Create vector adaptation list	vector_adaptation_list_create