Reference

All functions
Adomako_Ankomah_2017	Multiplicity of infection in Mali using 24-SNP barcode data (Adomako-Ankomah et al., 2017)
Bankole_2018	24-SNP barcode data from two urban cities in Nigeria (Bankole et al., 2018)
Bei_2018	24-SNP barcode data at two time-points in Senegal (Bei et al., 2018)
Briggs_2021	Inferring local and crossborder transmission with human and mobility data, Kanunga District in Southwest Uganda (Briggs et al., 2019)
CI_inc()	Get confidence intervals on incidence data
Chang_2017	SNP data collected from Uganda (Chang et al., 2017)
Charles_2016	24-SNP barcode data showing population structure in Haiti (Charles et al., 2016)
Daniels_2013	24-SNP barcode data showing clonal and epidemic transmission in Senegal (Daniels et al., 2013)
Daniels_2020	24-SNP barcode data from 11 sentinel sites in Haiti (Daniels et al., 2020)
Daniels_2020B	24-SNP barcode data from two trials in Zambia (Daniels et al., 2020)
Daniels_2020C	24-SNP barcode data from Richard Toll, Senegal (Daniels et al., 2020)
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
Galinsky_2015	24-SNP barcode data showing monogenomic and polygenomic infections in Senegal (Galinsky et al., 2015)
Obaldia_2015	24-SNP barcode data from clonal outbreak in Panama (Obaldia et al., 2015)
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
Roh_2019	Microsatellite data across 26 loci, Eswatini (Roh et al., 2019)
SIMPLEGEN	Load system file
Taylor_2017	93-SNP barcode data from Thai-Myanmar border (Taylor et al., 2017)
Taylor_2020	250-SNP barcode reveals connectivity on Colombian-Pacific coast (Taylor et al., 2020)
Tessema_2019	Microsatellite data across 26 loci, Northeast Namibia (Tessema et al., 2019)
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
life_table_Mali()	A life table taken from Mali
plot_flex_distribution()	Generic function for plotting flexible distributions
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
sim_epi()	Simulate from simple individual-based model
simplegen_cols()	A series of internally-used colours
simplegen_file()	Load system file
simplegen_project()	Define new SIMPLEGEN project