Corrected bug for continuous time Markov chain simulation with absorb…

…ing states

rtcmc originally could not handle continuous time Markov chains with absorbing states because rexp cannot work with rate zero parameters, which would be input for continuous time Markov chains. Added fix that checks for transition rate of 0 and makes transition time Inf if so. Chain will terminate early if it reaches an absorbing state.

R/ctmcProbabilistic.R

@@ -61,12 +61,17 @@ rctmc <- function(n, ctmc, initDist = numeric(), T = 0, include.T0 = TRUE,
   i <- 1
   while (i <= n){
     idx <- which(ctmc@states == state)
-    t <- t + rexp(1, -ctmc@generator[idx, idx])
-    state <- ctmc@states[sample(1:dim(ctmc), 1, prob = trans[idx, ])]
+    if (ctmc@generator[idx, idx] == 0) {
+      # absorbing state; stay here forever
+      t <- Inf
+    } else {
+      t <- t + rexp(1, -ctmc@generator[idx, idx])
+    }
 
-    if(T > 0 & t > T)
+    if((T > 0 & t > T) | (is.infinite(t)))
       break
 
+    state <- ctmc@states[sample(1:dim(ctmc), 1, prob = trans[idx, ])]
     states <- c(states, state)
     time <- c(time, t)
     i <- i + 1
@@ -84,6 +89,7 @@ rctmc <- function(n, ctmc, initDist = numeric(), T = 0, include.T0 = TRUE,
     stop("Not a valid output type")
 }
 
+
 #' @title Return the generator matrix for a corresponding transition matrix
 #' 
 #' @description Calculate the generator matrix for a