Cluster input setup

Function for taking benchmark data output by mainpop() and selecting the desired benchmark (EIR, slide prevalence, PCR prevalence, clinical incidence) data to use for input in setting up clusters, plus creating list of intervention parameter values

cluster_input_setup(
  input_list = list(),
  benchmark = "EIR",
  set_n_pt = 1,
  set_n_int = 1,
  age_start = 0,
  age_end = 65,
  plot_flag = FALSE
)

Arguments

input_list	List containing mainpop output data
benchmark	Benchmark to use in choosing clusters ("EIR", "slide_prev", "pcr_prev", or "clin_inc" for new data, "EIR_annual", "slide_prev_annual", "pcr_prev_annual", "clin_inc_annual" for pre-existing annual data in input folder)
set_n_pt	Data point to use (1-max) if using new data
set_n_int	Intervention number to use (1-max) if using new data
age_start	Starting age to use when calculating prevalence or incidence over age range (not used with EIR)
age_end	End age to use when calculating prevalence or incidence over age range (not used with EIR)
plot_flag	Logical operator indicating whether or not to plot graph of read values

Details

Takes in detailed benchmark data as a list and outputs lists of chosen benchmark values and intervention parameter values (as both list and files)