All functions

EIR_prev_beier1999

Measures of annual EIR and prevalence (Beier et al.,1999)

EIR_prev_hay2005

Measures of annual EIR and prevalence within the same site

PCR_micro_age_whittaker2021

Measures of prevalence by PCR and Microscopy, broken down by age

PCR_micro_full_whittaker2021

Measures of prevalence by PCR and Microscopy

SIMPLEGEN

Simulating Plasmodium Epidemiological and Genetic Data

check_SIMPLEGEN_loaded()

Check that SIMPLEGEN package has loaded successfully

define_epi_model_parameters()

Define parameters of transmission simulation model

define_epi_sampling_parameters()

Define outputs produced from the transmission model

define_genetic_params()

Define genetic parameters

get_coalescent_times()

Get coalescent time of two lineages

life_table_Mali()

A life table taken from Mali

plot_EIR_prevalence()

Plot EIR versus prevalence

plot_age_states()

Plot age distribution of states

plot_daily_prevalence()

Plot daily prevalence

plot_epi_distribution()

Generic function for plotting a SIMPLEGEN flexible distribution

plot_treatment_seeking()

Plot distribution of treatment seeking in the population

prev_inc_griffin2014

Data on prevalence and incidence broken down by age, used in Griffin et al. 2014 model fit

prune_transmission_record()

Prune the transmission record

retrieve_prev()

Retrieve prevalence

sim_epi()

Simulate from simple individual-based model

sim_relatedness()

Draw tree of genome-wide relatedness from pruned transmission record

simplegen_file()

Load system file

simplegen_project()

Define new SIMPLEGEN project