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Package: magenta 1.3.7

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_1.3.7.tar.gz
magenta_1.3.7.zip(r-4.7-x86_64)magenta_1.3.7.zip(r-4.7-arm64)magenta_1.3.7.zip(r-4.6-x86_64)magenta_1.3.7.zip(r-4.6-arm64)magenta_1.3.7.zip(r-4.5-x86_64)
magenta_1.3.7.tgz(r-4.6-x86_64)magenta_1.3.7.tgz(r-4.6-arm64)magenta_1.3.7.tgz(r-4.5-x86_64)magenta_1.3.7.tgz(r-4.5-arm64)
magenta_1.3.7.tar.gz(r-4.7-arm64)magenta_1.3.7.tar.gz(r-4.7-x86_64)magenta_1.3.7.tar.gz(r-4.6-arm64)magenta_1.3.7.tar.gz(r-4.6-x86_64)
magenta_1.3.7.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
magenta/json (API)

# 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

Pkgdown/docs site:https://ojwatson.github.io

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:

cpp

3.30 score 10 scripts 22 exports 46 dependencies

Last updated from:dba6c5c6e7. Checks:13 NOTE, 2 OK. Indexed: no.

Target	Result	Time
linux-devel-arm64	NOTE	256
linux-devel-x86_64	NOTE	224
source / vignettes	OK	277
linux-release-arm64	NOTE	248
linux-release-x86_64	NOTE	224
macos-release-arm64	NOTE	228
macos-release-x86_64	NOTE	436
macos-oldrel-arm64	NOTE	186
macos-oldrel-x86_64	NOTE	330
windows-devel-arm64	NOTE	486
windows-devel-x86_64	NOTE	292
windows-release-arm64	NOTE	527
windows-release-x86_64	NOTE	251
windows-oldrel-x86_64	NOTE	245
wasm-release	OK	181

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 update_saved_state_barcode_plaf

Dependencies:BH cinterpolate cli cpp11 crayon dde deSolve digest dplyr farver generics ggplot2 glue gtable hms isoband jsonlite labeling lifecycle magrittr odin pillar pkgconfig plyr prettyunits progress R6 RColorBrewer Rcpp redux reshape2 ring rlang S7 scales statmod storr stringdist stringi stringr tibble tidyselect utf8 vctrs viridisLite withr

How to use magenta

Rendered fromIntroduction.Rmdusingknitr::rmarkdown

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

Resistance

Overview | Demonstration | Base Model | Summary

Rendered fromResistance.Rmdusingknitr::rmarkdown

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

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
Update saved state barcode vectors to match a target PLAF	update_saved_state_barcode_plaf
Create vector adaptation list	vector_adaptation_list_create

Package: magenta 1.3.7

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

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