[R] Four concurrent Markov chains

[drlucyasher]

Hi,

I am trying to write a simulation of the movements of four animals between
six patches. The movement between patches is based on a first-order Markov
chain so that the next patch they visit depends on the patch they were in
before.

I have written code that allows me to simulate the movement of one animal
but when I add more there seems to be a problem and all chains come back as
N/A. I can fix the problem if I run the animals as separate sub-routines but
whilst this is adequate for this stage of my model it won't allow me to
progress to the next stage. The next stage will be to make the animals move
in reference to each other using a moving average variable. Therefore I
think I need all animals simulated within one subroutine (loop).

I probably haven't explained thie very well but here is the code I have been
working on....

#creation of a 6*6 matrix with the transition probabilities

transitions<-matrix(0,nrow=6,ncol=6); transitions[1,1]<- (0/6);
transitions[1,2]<- (0/6); transitions[1,3]<-(0/6);
transitions[1,4]<-(0/6);transitions[1,5]<-(0/6);
transitions[1,6]<-(6/6);transitions[2,1]<- (1/6);transitions[2,2]<- (1/6);
transitions[2,3]<-(1/6); transitions[2,4]<-(1/6);transitions[2,5]<-(1/6);
transitions[2,6]<-(1/6);transitions[3,1]<- (1/6);transitions[3,2]<- (1/6);
transitions[3,3]<-(1/6); transitions[3,4]<-(1/6);transitions[3,5]<-(1/6);
transitions[3,6]<-(1/6);transitions[4,1]<- (1/6);transitions[4,2]<- (1/6);
transitions[4,3]<-(1/6); transitions[4,4]<-(1/6);transitions[4,5]<-(1/6);
transitions[4,6]<-(1/6);transitions[5,1]<- (1/6);transitions[5,2]<- (1/6);
transitions[5,3]<-(1/6); transitions[5,4]<-(1/6);transitions[5,5]<-(1/6);
transitions[5,6]<-(1/6);transitions[6,1]<- (1/6);transitions[6,2]<- (1/6);
transitions[6,3]<-(1/6); transitions[6,4]<-(1/6);transitions[6,5]<-(1/6);
transitions[6,6]<-(1/6); transitions

# start position probalities
w <- c((1/6), (1/6), (1/6), (1/6), (1/6), (1/6)) 

#length of the chain

n<-241

#matrices creation for birds 1-4
observationb1<-matrix(nrow=n+1,ncol=6)
observationb2<-matrix(nrow=n+1,ncol=6)
observationb3<-matrix(nrow=n+1,ncol=6)
observationb4<-matrix(nrow=n+1,ncol=6)

#chains starting position
i<-1;observationb1[1,2]<-sample(1:6, 1, prob=w, repl=T)
i<-1;observationb2[1,2]<-sample(1:6, 1, prob=w, repl=T)
i<-1;observationb3[1,2]<-sample(1:6, 1, prob=w, repl=T)
i<-1;observationb4[1,2]<-sample(1:6, 1, prob=w, repl=T)



while(i<n+1){

      stateb1<-observationb1[i,2];


      probsb1<-transitions[stateb1,1:6];

      nextstateb1<-rmultinom(1,1,probsb1);

      seqb1<-which.max(nextstateb1);

      j<-i+1;

      observationb1[j,2]<-seqb1;i<-j 
#-------------------------------------if I close the brackets here this
works but I want to inlcude this next bit of code for bird 2

      stateb2<-observationb2[i,2];

      probsb2<-transitions[stateb2,1:6];

      nextstateb2<-rmultinom(1,1,probsb2);

      seqb2<-which.max(nextstateb2);

      j<-i+1;

      observationb2[j,2]<-seqb2;i<-j

#and so on for birds 3 and 4.

Any help you could give me would be much appreciated. 

Lucy
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