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I am trying to specify the transition parameters that are calculated by substraction, using the substract.stratum option in the function make.design.data(). I have a dataset of 18 years, and four different sites ("N", "F", "I", "A").

I want all transition parameters with tostratum "A" to be calculated by substraction, and tried to do this by using the following code (according to the Manual of RMark):

> msites <- import.chdata("ch.txt")
> msites.proc = process.data(msites, begin.time= 1992, model= "Multistrata")

> msites.ddl = make.design.data(msites.proc,
parameters=list(Psi=list(substract.stratum=c("A","A","A","A"))))

> table(msites.ddl$Psi[,c("stratum", "tostratum")])

tostratum
stratum A F I N
A 0 136 136 136
F 136 0 136 136
I 136 136 0 136
N 136 136 136 0

I expected the column with tostratum "A" to contain only 0's, but it seems that it just has performed the default with transition to the same site calculated by substraction.
Am I doing something wrong? I use the latest version of RMark (1.8..

I hope anyone can help me with this!

With kind regards,

Tamar Lok

You mispelled subtract as substract. The code does not let you know that you created list elements that do not match and they are just ignored. Something to add in a future verson.

-jeff