Hi all,
I am working for nest box occupancy data for birds and would like to
construct a Markov transition matrix, to derive transition probabilities for
ALL years of the study (not separate sets of transition probabilities for
each time step). The actual dataset I'm working with is 125 boxes over 14
years that can be occupied by 7 different species, though I have provided a
slimmed down portion for this question...

A box can be in 1 of 4 "states" (i.e. bird species): 1,2,3,4
Included here are 4 "box histories" over 4 years (y97, y98, y99, y00)
These are the box histories
> b1 < c(1,1,4,2)
> b2 < c(1,4,4,3)
> b3 < c(4,4,1,2)
> b4 < c(3,1,1,1)
> boxes < data.frame(rbind(b1,b2,b3,b4))
> colnames(boxes) < c("y97","y98","y99","y00")
> boxes
y97 y98 y99 y00
b1 1 1 4 2
b2 1 4 4 3
b3 4 4 1 2
b4 3 1 1 1
>
My problem is that there are 16 possible transitions, but not all possible transitions occur at each time step. Therefore, don't think I could do something easy like create a table for each time step and add them together, for example:
> t1.boxes < table(boxes$y98, boxes$y97)
> t1.boxes
1 3 4
1 1 1 0
4 1 0 1
> t2.boxes < table(boxes$y99, boxes$y98)
> t2.boxes
1 4
1 1 1
4 1 1
>
t1.boxes and t2.boxes could not be added together to calculate the frequency of each transition occurring because they are of different dimensions. I'm not quite sure how to deal with this, I have attempted to write a function (shown below), though I'm not sure if it is needed, I am a bit new the programming world. If I could get some help either with the function or a way around it that would be most appreciated! Thank you!
FMAT < matrx(0, nrow=4, ncol=4, byrow=TRUE) #This is the matrix that will store the frequency of each possible transition occurring over the 4 years
nboxes < 4
nyears < 4
for(row in 1:nboxes)
{
for(col in 1:(nyears1))
{
FMAT[boxes[row,col+1], boxes[row,col]] < boxes[boxes[row, col+1],
boxes[row,col]]
#This is the line of code I have been struggling with an am unsure about. I
have tried
#various versions of this and keep getting an assortment of error messages.
}
}
FMAT }
 View this message in context: http://r.789695.n4.nabble.com/Markovtransitionmatricesmissingtransitionsforcertainyearstp3459072p3459072.html Sent from the R help mailing list archive at Nabble.com. ______________________________________________ Rhelp_at_rproject.org mailing list https://stat.ethz.ch/mailman/listinfo/rhelp PLEASE do read the posting guide http://www.Rproject.org/postingguide.html and provide commented, minimal, selfcontained, reproducible code.Received on Tue 19 Apr 2011  04:45:35 GMT
Archive maintained by Robert King, hosted by
the discipline of
statistics at the
University of Newcastle,
Australia.
Archive generated by hypermail 2.2.0, at Tue 19 Apr 2011  18:10:31 GMT.
Mailing list information is available at https://stat.ethz.ch/mailman/listinfo/rhelp. Please read the posting guide before posting to the list.