# R/state_trans.R In ibmcraftr: Toolkits to Develop Individual-Based Models in Infectious Disease

```#' Make state transitions.
#'
#' Take in the matrix of the states of synthetic population (created by \code{syn_pop} function)
#' and calculate the transitions from one state to other state(s) using the transition rate(s).
#'
#' @param origin A number which represents the column index \code{s.matrix} you want to do the transition from
#' @param new.states A numeric vector or a number which represents the column index \code{s.matrix} you want
#'     as the destination(s) for the transition
#' @param params A numeric vector of similar length to \code{new.states} which serves as the transition rate(s)
#' @param s.matrix A state matrix created from \code{syn_pop} function
#' @return A transition matrix of the same dimension as \code{s.matrix}. -1 indicates that the individual has left
#'     the corresponding state. +1 indicates that the individual has become the corresponding state.
#' @examples
#' pop <- syn_pop(c(19,1,0,0))
#' state_trans(1,2,.1,pop)
#' state_trans(1,4,100,pop)
#'
#' @export
#' @importFrom stats runif

state_trans <- function(origin, new.states, params, s.matrix){
#origin   #single number
#new.states  #a vector of length n (to index the matrix)
#params #a vector of length m (to calculate the probabilities)
#s.matrix  #state.matrix #a matrix cut from the data frame

#dimension check
if(ncol(s.matrix) <  max(c(origin, new.states))) stop("no such states in the input matrix") #stop if the dim requested is higher than input matrix

origin_v <- s.matrix[,origin] #initializing a new vector for calculation
lo <- length(origin_v) #length of origin
org.s.matrix <- s.matrix    #keeping the original matrix ??? for what?

#cummulative probability
#probs <- 1-exp(-params*1) # calc probs from rates

cum_probs <- cumprob(params) #cumprob is a seperate function to calculate the cumulative probabilities

last_prob <- cum_probs[1]

for(i in new.states){
probs_for <- cum_probs[which(new.states==i)+1] #calculating probs_for for transition
rand <- runif(lo)

s.matrix[,i] <- s.matrix[,i]+(s.matrix[,origin]*(rand<probs_for)*(rand>last_prob)) #origin is used here since ??
s.matrix[,origin] <- s.matrix[,origin]-(s.matrix[,origin]*(rand<probs_for)*(rand>last_prob))
#s.matrix[,-c(new.states,origin)] <- 0 #might not do this afterall!
last_prob <- probs_for
}
s.matrix-org.s.matrix
}
```

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ibmcraftr documentation built on May 1, 2019, 11:31 p.m.