dipper: Dipper capture-recapture data

In marked: Mark-Recapture Analysis for Survival and Abundance Estimation

Dipper capture-recapture data

Description

A capture-recapture data set on European dippers from France that accompanies MARK as an example analysis using the CJS and POPAN models. The dipper data set was orginally described as an example by Lebreton et al (1992).

Format

A data frame with 294 observations on the following 2 variables.

ch

a character vector containing the encounter history of each bird

sex

the sex of the bird: a factor with levels Female Male

Details

This is a data set that accompanies program MARK as an example for CJS and POPAN analyses. The data can be stratified using sex as a grouping variable. The functions run.dipper, run.dipper.alternate, run.dipper.popan defined below in the examples mimic the models used in the dbf file that accompanies MARK. Note that the models used in the MARK example use PIM coding with the sin link function which is often better at identifying the number of estimable parameters. The approach used in the R code uses design matrices and cannot use the sin link and is less capable at counting parameters. These differences are illustrated by comparing the results of run.dipper and run.dipper.alternate which fit the same set of "CJS" models. The latter fits the models with constraints on some parameters to achieve identifiability and the former does not. Although it does not influence the selection of the best model it does infleunce parameter counts and AIC ordering of some of the less competitive models. In using design matrices it is best to constrain parameters that are confounded (e.g., last occasion parameters in Phi(t)p(t) CJS model) when possible to achieve more reliable counts of the number of estimable parameters.

Note that the covariate "sex" defined in dipper has values "Male" and "Female". It cannot be used directly in a formula for MARK without using it do define groups because MARK.EXE will be unable to read in a covariate with non-numeric values. By using groups="sex" in the call the process.data a factor "sex" field is created that can be used in the formula. Alternatively, a new covariate could be defined in the data with say values 0 for Female and 1 for Male and this could be used without defining groups because it is numeric. This can be done easily by translating the values of the coded variables to a numeric variable. Factor variables are numbered 1..k for k levels in alphabetic order. Since Female < Male in alphabetic order then it is level 1 and Male is level 2. So the following will create a numeric sex covariate.

 dipper$numeric.sex=as.numeric(dipper$sex)-1 

Source

Lebreton, J.-D., K. P. Burnham, J. Clobert, and D. R. Anderson. 1992. Modeling survival and testing biological hypotheses using marked animals: case studies and recent advances. Ecol. Monogr. 62:67-118.

marked documentation built on Oct. 19, 2023, 5:06 p.m.