F.cjs.covars: F.cjs.covars

Description

Return an x and y 3-D array for estimation of a traditional time-variant Cormack-Jolly-Seber capture-recapture model.

Usage

F.cjs.covars(nan, ns)

Arguments

nan

Number of individuals/animals.

Number of trap/mark occasions.

Value

A list containing a single component, \$x, that can be used to estimate a classical CJS model when included in a subsequent call to F.cjs.estim. The returned component, \$x, is a 3-D array containing 0's everywhere, except for 1's in certain columns. \$x has dimension nan X ns X ns. Element [i,j,k] of \$x is 1 if j == k, and 0 otherwise. I.e., the k-th "page" of the 3-D array has 1's in the k-th column, 0's elsewhere.

Details

Pages from \$x are designed to useful for fitting classical CJS models with time-variant, but individual-invariant effects. To fit a CJS model using this function, the commands would be something like:

tmp<-F.cjs.covars(nan,ns);F.cjs.estim(capture=~tmp\$x[,,2]+tmp\$x[,,3]+ ..., survival= ~tmp\$x[,,1]+tmp\$x[,,2]+ ..., histories=my.histories)

Examples

Run this code

##  Fit CJS model to dipper data, time-varying capture and survivals.
data(dipper.histories)
xy <- F.cjs.covars( nrow(dipper.histories), ncol(dipper.histories) )
dipper.cjs <- F.cjs.estim( capture=~xy$x[,,2]+xy$x[,,3]+xy$x[,,4]+xy$x[,,5]+xy$x[,,6], 
	survival=~xy$x[,,1]+xy$x[,,2]+xy$x[,,3]+xy$x[,,4]+xy$x[,,5], dipper.histories )
print(dipper.cjs)