Function reference • magenta

Simulation Functions for running magenta.
`pipeline()`	Pipeline for cluster submission
Pipeline Misc “Functions that are actually being called by pipeline that trigger the simulation to run. These consist of functions that create the parameter lists to be passed to the functions that call the similarly named Rcpp functions. Lastly, two functions that are used to summarise the population genetics using Rcpp functions.”
`param_list_simulation_finalizer_create()`	Parameter List creation for magenta simulation finalizer
`param_list_simulation_get_create()`	Parameter List creation for magenta simulation getting (saving to disk)
`param_list_simulation_init_create()`	Parameter List creation for magenta simulation initialisation
`param_list_simulation_saved_init_create()`	Parameter List creation for loading saved magenta simulation
`param_list_simulation_update_create()`	Parameter List creation for magenta simulation updating
`simulation_R()`	simulation_R function
`Simulation_Finalizer_cpp()`	Returns whole model to R in series of nested lists
`Simulation_Get_cpp()`	Returns whole model to R in series of nested lists
`Simulation_Init_cpp()`	Creates initial model simulation using paramter list provided
`Simulation_Saved_Init_cpp()`	Creates initial model simulation using a saved model state
`Simulation_Update_cpp()`	Continues simulation forward for as long as specified in param_list
`population_get_genetics_df_n()`	Returns the population's parasite genetics summarised by coi for given sample size and state
`population_get_genetics_ibd_df_n()`	Returns the population's parasite genetics for ibd style summarised by pibd for given sample size and state
Pipeline Parameter Creation “Functions to create parameters to be passed to pipeline”
`drug_list_create()`	Create drug list
`model_param_list_create()`	Model Parameter List Creation
`spl_grab()`	Spatial matrix grab
`intervention_grab()`	Intervention grab
`equilibrium_init_create()`	Equilibrium initialisation list creation
`housekeeping_list_create()`	Create housekeeping parameter list
`nmf_list_create()`	Create nmf list
`vector_adaptation_list_create()`	Create vector adaptation list
Drug Functions Functions to create drugs
`drug_create()`	Create list describing parameters for drug efficacy and prophlyaxis
`drug_create_al()`	AL Drug Create
`drug_create_asaq()`	ASAQ Drug Create
`drug_create_dhappq()`	DHA-PPQ Drug Create
`drug_create_default_no_resistance()`	Perfect Drug Create
`drug_table`	Drug Efficacy by Genotype Table
Barcode Misc Functions for converting and manipualting barcodes
`convert_barcode_vectors()`	Convert human barcodes to numerics
Data Objects Internal Data Objects
`admin_units_seasonal`	Admin level 1 africa seasonal parameters
`irs_2000_2015`	IRS for 2000 to 2015
`itn_2000_2015`	ITN for 2000 to 2015
`drug_table`	Drug Efficacy by Genotype Table
`importations`	Importation data

Reference

Simulation

Pipeline Misc

Pipeline Parameter Creation

Drug Functions

Barcode Misc

Data Objects