run_state_trans {ibmcraftr}

Run state_trans function over a given number of timesteps.

Description

Organize population data and transition parameters to run state_trans function over the given number of timesteps.

Usage

run_state_trans(timesteps, param, pop, transient = "", useC = TRUE)

Arguments

timesteps

A numeric scalar based on which the state_trans function will run for that specific no. of timesteps and accumulate the results.

param

A list of lists. Each low-level list must contain transition parameters required by the state_trans function.

pop

A state matrix created from syn_pop function. This matrix represents the states of the population.

transient

A character vector. Each element must include formula(e)/expression(s) to evaluate dynamic parameters after each timestep.

useC

A logical value, which is TRUE by default, will run state_transition function written in RCPP, stRCPP.

Value

A summary matrix of the states all individuals in the population are in.

Examples

pop <- syn_pop(c(19,1,0,0,0)) #synthesizing population
b <- 2 #effective contact rate
param <- list(
list(1,c(2,5),c(NA,.1)), #transition from state 1 to 2 using FOI lambda
list(2,3,100), #transition from state 2 to 3,
list(3,4,100)  #the 3rd term ensures the transition to the next stage
)

timesteps <- 10
transient <- c("param[[1]][[3]][1] <- rate2prob(b*sum(pop[,2],pop[,3])/sum(pop))")
eval(parse(text=transient))

run_state_trans(timesteps, param, pop, transient)
run_state_trans(timesteps, param, pop, transient, useC = FALSE)