#' @title Title
#'
#' @description Description
#'
#' @param x A number.
#' @param y A number.
#' @return return value here.
#' @details
#' Additional details here
#' @examples
#' example function call here
#' @export
initialize_module <- function(x, param, init, control, s)
{
#Description:
# runs EpiModel function EpiModel::initialize.net()
# fills in viral load values for initial infected with initialize_infecteds_vl()
# fills in cd4 variable values for initial infected (initial CD4 value based on SPVL)
# with initialize_infecteds_cd4()
# does a few bookkeeping steps with initialize_evonet_misc()
# updates vl of initial infecteds (otw, vl jumps from initial value to spvl in one
# timestep) with viral_update_module_gamma()
# creates and inserts initial values for "popsumm" stats (calculated at end of
# each timestep_ with initialize_popsumm_dynamics()
#sets up basic EpiModel structure
dat <- EpiModel::initialize.net(x, param, init, control,s)
#sets up agent attributes and initial values
dat <- initialize_agents(dat, 1)
#fills in vl variable values for initial infecteds
dat <- initialize_infecteds_vl(dat,1)
#fills in cd4 variable values for initial infecteds
#note, this must come after initialize_infecteds_vl because initial cd4 based on spvl
dat <- initialize_infecteds_cd4(dat,1)
#does a few random bookkeeping steps
dat <- initialize_evonet_misc(dat)
#updates vl of initial infecteds (otw, jumps from initial value to spvl)
#but shouldn't happen for aim3 runs
if(param$VL_Function != "aim3"){
dat <- viral_update_gamma(dat,1)
dat <- viral_update_cd4_intial_pop(dat)
}
#create list, if "save_vl_list" = TRUE to save
#individual agent's vl/cd4 values for each timestep
dat<- summary_vl_list(dat,1)
#creates and fills in initial values for "popsumm" stats (stats calculated at
#end of each timestep)
dat <- summary_popsumm(dat,1)
#keep track of current simulation/replicate
dat$simulation <- s
return(dat)
}
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