count <- function(chain, states)
{
#
# INPUT: chain - time series of events
#        states - number of states in chain
#
# OUTPUT: the transition matrix for chain
#
# This function returns
# a transition matrix for chain (missing values allowed)
#
# check the number of states
        if(max(chain[!is.na(chain)]) > states)
                        stop(paste("you need", max(chain),
                        "states for your\ndata"))
# initialize the counts
        kount <- matrix(0, nrow = states, ncol = states)
# start counting
        for(i in 2:length(chain))
                if (sum(is.na(chain[(i-1):i]))==0)
                kount[chain[i - 1], chain[i]] <- kount[chain[i - 1], chain[
                        i]] + 1
        return(kount)
}