Capture History Summary

questions concerning analysis/theory using program MARK

Capture History Summary

Postby cjackson1373 » Mon Apr 25, 2022 5:43 pm

I'm interested in creating a capture history summary table to go along with my analysis. The table would resemble the m-array in RELEASE, however I'd want to include all recaptures, not just "first" recaptures. For example, for a given year of capture/recapture data, I want to be able to summarize:

(1) total number of captures (Mark can do this)
(2) total number of recaptures (all recaptures, not just first recaptures)
(3) which year the animal was originally tagged

Is there a way to do this in Mark? I've examined the FSA package in R as well and it appears I can only get the "first recaptures" summary.

Cody
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Re: Capture History Summary

Postby cooch » Mon Apr 25, 2022 6:50 pm

cjackson1373 wrote:I'm interested in creating a capture history summary table to go along with my analysis. The table would resemble the m-array in RELEASE, however I'd want to include all recaptures, not just "first" recaptures. For example, for a given year of capture/recapture data, I want to be able to summarize:

(1) total number of captures (Mark can do this)
(2) total number of recaptures (all recaptures, not just first recaptures)
(3) which year the animal was originally tagged

Is there a way to do this in Mark? I've examined the FSA package in R as well and it appears I can only get the "first recaptures" summary.

Cody


Not in MARK - but, the most granular summary you can get is the full m(i,j) array, which can be generated in RELEASE. See Chapter 5 in the MARK book, starting ~p. 13.
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Re: Capture History Summary

Postby B.K. Sandercock » Tue Apr 26, 2022 3:24 am

If you are working in an R environment, you can use the following script from Kery and Schaub (2012) to build an m-array from the capture histories. Could customize if you want a different output.

Code: Select all
# Pages 221-222 of Kery and Schaub (2012) Bayesian Population Analysis using WinBUGS
# Function to create a m-array based on capture-histories (CH)
marray <- function(CH){
   nind <- dim(CH)[1]
   n.occasions <- dim(CH)[2]
   m.array <- matrix(data = 0, ncol = n.occasions+1, nrow = n.occasions)
   # Calculate the number of released individuals at each time period
   for (t in 1:n.occasions){
      m.array[t,1] <- sum(CH[,t])
      }
   for (i in 1:nind){
      pos <- which(CH[i,]!=0)
      g <- length(pos)
      for (z in 1:(g-1)){
         m.array[pos[z],pos[z+1]] <- m.array[pos[z],pos[z+1]] + 1
         } #z
      } #i
   # Calculate the number of individuals that is never recaptured
   for (t in 1:n.occasions){
      m.array[t,n.occasions+1] <- m.array[t,1] - sum(m.array[t,2:n.occasions])
      }
   out <- m.array[1:(n.occasions-1),2:(n.occasions+1)]
   return(out)
   }
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