getHostData: Extracts specific data from a 'nosoiSim' object

In slequime/nosoi: A Forward Agent-Based Transmission Chain Simulator

Extracts specific data from a nosoiSim object

Description

This function extracts data user-defined data (i.e. table.hosts, N.infected, table.state or popStructure) from a nosoiSim object.

Usage

getHostData(
  nosoi.output,
  what = c("table.hosts", "N.infected", "table.state", "popStructure"),
  pop = "A"
)

Arguments

nosoi.output	an object of class nosoiSim
what	the data to get, among table.hosts, N.infected, table.state or popStructure.
pop	the population to be extracted (one of "A" or "B")

Value

Returns a data.table with the requested data.

See Also

To directly extract table.hosts or table.state, you can also use getTableHosts and getTableState respectively.

Examples

t_incub_fct <- function(x){rnorm(x,mean = 5,sd=1)}
p_max_fct <- function(x){rbeta(x,shape1 = 5,shape2=2)}
p_Exit_fct  <- function(t){return(0.08)}

proba <- function(t,p_max,t_incub){
  if(t <= t_incub){p=0}
  if(t >= t_incub){p=p_max}
  return(p)
}

time_contact <- function(t){round(rnorm(1, 3, 1), 0)}

test.nosoi <- nosoiSim(type="single", popStructure="none",
                       length=40,
                       max.infected=100,
                       init.individuals=1,
                       nContact=time_contact,
                       param.nContact=NA,
                       pTrans = proba,
                       param.pTrans = list(p_max=p_max_fct,
                                           t_incub=t_incub_fct),
                       pExit=p_Exit_fct,
                       param.pExit=NA)


data.extracted <- getHostData(test.nosoi, "table.hosts", "A")

slequime/nosoi documentation built on Aug. 10, 2024, 9:13 p.m.