run_state_trans: Run state_trans function over a given number of timesteps.
In ibmcraftr: Toolkits to Develop Individual-Based Models in Infectious Disease

Description Usage Arguments Value Examples

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

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

`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`.

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

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)