edwards.eberhardt: Rabbit capture-recapture data

In RMark: R Code for Mark Analysis

Rabbit capture-recapture data

Description

A capture-recapture data set on rabbits derived from Edwards and Eberhardt (1967) that accompanies MARK as an example analysis using the closed population models.

Format

A data frame with 76 observations on the following variable.

ch

a character vector

Details

This data set is used in MARK to illustrate the various closed population models including "Closed", "HetClosed", "FullHet","Huggins","HugHet", and "FullHugHet". The first 3 include N in the likelihood whereas the last 3 are based on the Huggins approach which does not use N in the likelihood. The Het... and FullHet... models are based on the Pledger mixture model approach. Some of the examples demonstrate the use of the share argument in the model.parameters list for parameter p which allows sharing common values for p and c.

Source

Edwards, W.R. and L.L. Eberhardt 1967. Estimating cottontail abundance from live trapping data. J. Wildl. Manage. 31:87-96.

Examples

# This example is excluded from testing to reduce package check time
#
# get data
#
data(edwards.eberhardt)
#
# create function that defines and runs the analyses as defined in 
# MARK example dbf file
#
run.edwards.eberhardt=function()
{
#
#  Define parameter models
#
pdotshared=list(formula=~1,share=TRUE)
ptimeshared=list(formula=~time,share=TRUE)
ptime.c=list(formula=~time+c,share=TRUE)
ptimemixtureshared=list(formula=~time+mixture,share=TRUE)
pmixture=list(formula=~mixture)
#
# Run assortment of models
#
#
#   Capture Closed models
#
#  constant p=c
ee.closed.m0=mark(edwards.eberhardt,model="Closed",
                   model.parameters=list(p=pdotshared),delete=TRUE)
#  constant p and constant c but different
ee.closed.m0c=mark(edwards.eberhardt,model="Closed",delete=TRUE)
#  time varying p=c
ee.closed.mt=mark(edwards.eberhardt,model="Closed",
                   model.parameters=list(p=ptimeshared),delete=TRUE)
#
#  Closed heterogeneity models
#
#  2 mixtures Mh2
ee.closed.Mh2=mark(edwards.eberhardt,model="HetClosed",
                   model.parameters=list(p=pmixture),delete=TRUE)
#  Closed Mth2 - p different for time; mixture additive
ee.closed.Mth2.additive=mark(edwards.eberhardt,model="FullHet",
                   model.parameters=list(p=ptimemixtureshared),adjust=TRUE,delete=TRUE)
#
#    Huggins models
#
# p=c constant over time
ee.huggins.m0=mark(edwards.eberhardt,model="Huggins",
                   model.parameters=list(p=pdotshared),delete=TRUE)
# p constant c constant but different; this is default model for Huggins
ee.huggins.m0.c=mark(edwards.eberhardt,model="Huggins",delete=TRUE)
# Huggins Mt
ee.huggins.Mt=mark(edwards.eberhardt,model="Huggins",
                   model.parameters=list(p=ptimeshared),adjust=TRUE,delete=TRUE)
#
#    Huggins heterogeneity models
#
#  Mh2 - p different for mixture
ee.huggins.Mh2=mark(edwards.eberhardt,model="HugHet",
                   model.parameters=list(p=pmixture),delete=TRUE)
#  Huggins Mth2 - p different for time; mixture additive
ee.huggins.Mth2.additive=mark(edwards.eberhardt,model="HugFullHet",
                   model.parameters=list(p=ptimemixtureshared),adjust=TRUE,delete=TRUE)
#
# Return model table and list of models
#
return(collect.models() )
}
#
# fit models in mark by calling function created above
#
ee.results=run.edwards.eberhardt()

RMark documentation built on Aug. 14, 2022, 1:05 a.m.