dipper: Dipper capture-recapture data

In RMark: R Code for Mark Analysis

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. See adjust.parameter.count for more dicussion on this point.

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 

See export.chdata for an example that creates a .inp file for MARK with sex being used to describe groups and a numeric sex covariate.

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.

Examples

# This example is excluded from testing to reduce package check time
data(dipper)
dipper.model=mark(dipper,delete=TRUE)
run.dipper=function()
{
#
# Process data
#
dipper.processed=process.data(dipper,groups=("sex"))
#
# Create default design data
#
dipper.ddl=make.design.data(dipper.processed)
#
# Add Flood covariates for Phi and p that have different values
#
dipper.ddl$Phi$Flood=0
dipper.ddl$Phi$Flood[dipper.ddl$Phi$time==2 | dipper.ddl$Phi$time==3]=1
dipper.ddl$p$Flood=0
dipper.ddl$p$Flood[dipper.ddl$p$time==3]=1
#
#  Define range of models for Phi
#
Phidot=list(formula=~1)
Phitime=list(formula=~time)
Phisex=list(formula=~sex)
Phisextime=list(formula=~sex+time)
Phisex.time=list(formula=~sex*time)
PhiFlood=list(formula=~Flood)
#
#  Define range of models for p
#
pdot=list(formula=~1)
ptime=list(formula=~time)
psex=list(formula=~sex)
psextime=list(formula=~sex+time)
psex.time=list(formula=~sex*time)
pFlood=list(formula=~Flood)
#
# Run assortment of models
#
dipper.phidot.pdot          =mark(dipper.processed,dipper.ddl,
                 model.parameters=list(Phi=Phidot,p=pdot),delete=TRUE)
dipper.phidot.pFlood      	=mark(dipper.processed,dipper.ddl,
                 model.parameters=list(Phi=Phidot,p=pFlood),delete=TRUE)
dipper.phidot.psex        	=mark(dipper.processed,dipper.ddl,
                 model.parameters=list(Phi=Phidot,p=psex),delete=TRUE)
dipper.phidot.ptime       	=mark(dipper.processed,dipper.ddl,
                 model.parameters=list(Phi=Phidot,p=ptime),delete=TRUE)
dipper.phidot.psex.time		=mark(dipper.processed,dipper.ddl,
                 model.parameters=list(Phi=Phidot,p=psex.time),delete=TRUE)
dipper.phitime.ptime      	=mark(dipper.processed,dipper.ddl,
                 model.parameters=list(Phi=Phitime, p=ptime),delete=TRUE)
dipper.phitime.pdot       	=mark(dipper.processed,dipper.ddl,
                 model.parameters=list(Phi=Phitime,p=pdot),delete=TRUE)
dipper.phitime.psex		=mark(dipper.processed,dipper.ddl,
                 model.parameters=list(Phi=Phitime,p=psex),delete=TRUE)
dipper.phitime.psex.time	=mark(dipper.processed,dipper.ddl,
                 model.parameters=list(Phi=Phitime,p=psex.time),delete=TRUE)
dipper.phiFlood.pFlood    	=mark(dipper.processed,dipper.ddl,
                 model.parameters=list(Phi=PhiFlood, p=pFlood),delete=TRUE)
dipper.phisex.pdot        	=mark(dipper.processed,dipper.ddl,
                 model.parameters=list(Phi=Phisex,p=pdot),delete=TRUE)
dipper.phisex.psex        	=mark(dipper.processed,dipper.ddl,
                 model.parameters=list(Phi=Phisex,p=psex),delete=TRUE)
dipper.phisex.psex.time        	=mark(dipper.processed,dipper.ddl,
                 model.parameters=list(Phi=Phisex,p=psex.time),delete=TRUE)
dipper.phisex.ptime       	=mark(dipper.processed,dipper.ddl,
                 model.parameters=list(Phi=Phisex,p=ptime),delete=TRUE)
dipper.phisextime.psextime	=mark(dipper.processed,dipper.ddl,
                 model.parameters=list(Phi=Phisextime,p=psextime),delete=TRUE)
dipper.phisex.time.psex.time	=mark(dipper.processed,dipper.ddl,
                 model.parameters=list(Phi=Phisex.time,p=psex.time),delete=TRUE)
dipper.phisex.time.psex 	=mark(dipper.processed,dipper.ddl,
                 model.parameters=list(Phi=Phisex.time,p=psex),delete=TRUE)
dipper.phisex.time.pdot		=mark(dipper.processed,dipper.ddl,
                 model.parameters=list(Phi=Phisex.time,p=pdot),delete=TRUE)
dipper.phisex.time.ptime	=mark(dipper.processed,dipper.ddl,
                 model.parameters=list(Phi=Phisex.time,p=ptime),delete=TRUE)
#
# Return model table and list of models
#
return(collect.models() )
}

dipper.results=run.dipper()

run.dipper.alternate=function()
{
#
# Process data
#
dipper.processed=process.data(dipper,groups=("sex"))
#
# Create default design data
#
dipper.ddl=make.design.data(dipper.processed)
#
# Add Flood covariates for Phi and p that have different values
#
dipper.ddl$Phi$Flood=0
dipper.ddl$Phi$Flood[dipper.ddl$Phi$time==2 | dipper.ddl$Phi$time==3]=1
dipper.ddl$p$Flood=0
dipper.ddl$p$Flood[dipper.ddl$p$time==3]=1
#
#  Define range of models for Phi
#
Phidot=list(formula=~1)
Phitime=list(formula=~time)
Phitimec=list(formula=~time,fixed=list(time=6,value=1))
Phisex=list(formula=~sex)
Phisextime=list(formula=~sex+time)
Phisex.time=list(formula=~sex*time)
PhiFlood=list(formula=~Flood)
#
#  Define range of models for p
#
pdot=list(formula=~1)
ptime=list(formula=~time)
ptimec=list(formula=~time,fixed=list(time=7,value=1))
psex=list(formula=~sex)
psextime=list(formula=~sex+time)
psex.time=list(formula=~sex*time)
psex.timec=list(formula=~sex*time,fixed=list(time=7,value=1))
pFlood=list(formula=~Flood)
#
# Run assortment of models
#
dipper.phidot.pdot          =mark(dipper.processed,dipper.ddl,
                  model.parameters=list(Phi=Phidot,p=pdot),delete=TRUE)
dipper.phidot.pFlood      	=mark(dipper.processed,dipper.ddl,
                  model.parameters=list(Phi=Phidot,p=pFlood),delete=TRUE)
dipper.phidot.psex        	=mark(dipper.processed,dipper.ddl,
                  model.parameters=list(Phi=Phidot,p=psex),delete=TRUE)
dipper.phidot.ptime       	=mark(dipper.processed,dipper.ddl,
                  model.parameters=list(Phi=Phidot,p=ptime),delete=TRUE)
dipper.phidot.psex.time		=mark(dipper.processed,dipper.ddl,
                  model.parameters=list(Phi=Phidot,p=psex.time),delete=TRUE)
dipper.phitime.ptimec      	=mark(dipper.processed,dipper.ddl,
                  model.parameters=list(Phi=Phitime, p=ptimec),delete=TRUE)
dipper.phitime.pdot       	=mark(dipper.processed,dipper.ddl,
                  model.parameters=list(Phi=Phitime,p=pdot),delete=TRUE)
dipper.phitime.psex		=mark(dipper.processed,dipper.ddl,
                  model.parameters=list(Phi=Phitime,p=psex),delete=TRUE)
dipper.phitimec.psex.time	=mark(dipper.processed,dipper.ddl,
                  model.parameters=list(Phi=Phitimec,p=psex.time),delete=TRUE)
dipper.phiFlood.pFlood    	=mark(dipper.processed,dipper.ddl,
                  model.parameters=list(Phi=PhiFlood, p=pFlood),delete=TRUE)
dipper.phisex.pdot        	=mark(dipper.processed,dipper.ddl,
                  model.parameters=list(Phi=Phisex,p=pdot),delete=TRUE)
dipper.phisex.psex        	=mark(dipper.processed,dipper.ddl,
                  model.parameters=list(Phi=Phisex,p=psex),delete=TRUE)
dipper.phisex.psex.time        	=mark(dipper.processed,dipper.ddl,
                  model.parameters=list(Phi=Phisex,p=psex.time),delete=TRUE)
dipper.phisex.ptime       	=mark(dipper.processed,dipper.ddl,
                  model.parameters=list(Phi=Phisex,p=ptime),delete=TRUE)
dipper.phisextime.psextime	=mark(dipper.processed,dipper.ddl,
                  model.parameters=list(Phi=Phisextime,p=psextime),adjust=FALSE,delete=TRUE)
dipper.phisex.time.psex.timec	=mark(dipper.processed,dipper.ddl,
                  model.parameters=list(Phi=Phisex.time,p=psex.timec),delete=TRUE)
dipper.phisex.time.psex 	=mark(dipper.processed,dipper.ddl,
                  model.parameters=list(Phi=Phisex.time,p=psex),delete=TRUE)
dipper.phisex.time.pdot		=mark(dipper.processed,dipper.ddl,
                  model.parameters=list(Phi=Phisex.time,p=pdot),delete=TRUE)
dipper.phisex.time.ptimec	=mark(dipper.processed,dipper.ddl,
                  model.parameters=list(Phi=Phisex.time,p=ptimec),delete=TRUE)
#
# Return model table and list of models
#
return(collect.models() )
}
dipper.results.alternate=run.dipper.alternate()
#
# Merge two sets of models into a single model list and include the 
# initial model as a demo for merge.mark
#
dipper.cjs=merge.mark(dipper.results,dipper.results.alternate,dipper.model)
dipper.cjs
#
# next delete some of the models to show how this is done with remove.mark
#
dipper.cjs=remove.mark(dipper.cjs,c(2,4,9))
dipper.cjs

run.dipper.popan=function()
{
#
# Process data
#
dipper.processed=process.data(dipper,model="POPAN",group="sex")
#
# Create default design data
#
dipper.ddl=make.design.data(dipper.processed)
#
# Add Flood covariates for Phi and p that have different values
#
dipper.ddl$Phi$Flood=0
dipper.ddl$Phi$Flood[dipper.ddl$Phi$time==2 | dipper.ddl$Phi$time==3]=1
dipper.ddl$p$Flood=0
dipper.ddl$p$Flood[dipper.ddl$p$time==3]=1
#
#  Define range of models for Phi
#
Phidot=list(formula=~1)
Phitime=list(formula=~time)
Phisex=list(formula=~sex)
Phisextime=list(formula=~sex+time)
Phisex.time=list(formula=~sex*time)
PhiFlood=list(formula=~Flood)
#
#  Define range of models for p
#
pdot=list(formula=~1)
ptime=list(formula=~time)
psex=list(formula=~sex)
psextime=list(formula=~sex+time)
psex.time=list(formula=~sex*time)
pFlood=list(formula=~Flood)
#
#  Define range of models for pent
#
pentsex.time=list(formula=~sex*time)
#
#  Define range of models for N
#
Nsex=list(formula=~sex)
#
# Run assortment of models
#
dipper.phisex.time.psex.time.pentsex.time=mark(dipper.processed,dipper.ddl,
model.parameters=list(Phi=Phisex.time,p=psex.time,pent=pentsex.time,N=Nsex),
invisible=FALSE,adjust=FALSE,delete=TRUE)
dipper.phisex.time.psex.pentsex.time=mark(dipper.processed,dipper.ddl,
model.parameters=list(Phi=Phisex.time,p=psex,pent=pentsex.time,N=Nsex),
invisible=FALSE,adjust=FALSE,delete=TRUE)
#
# Return model table and list of models
#
return(collect.models() )
}

dipper.popan.results=run.dipper.popan()

# *****************************************************************
# Here is an example of user specified links for each real parameter
 data(dipper)
 dipper.proc=process.data(dipper)
 dipper.ddl=make.design.data(dipper.proc)
# dummy run of make.mark.model to get links and design data. 
# parm.specific set to TRUE so it will create a link for 
# each parameter because for this model they are all the
# same (logit) and if this was not specified you'ld get a vector with one element
 dummy=make.mark.model(dipper.proc,dipper.ddl,simplify=FALSE,parm.specific=TRUE)
 input.links=dummy$links
# get model indices for p where time=4
 log.indices=dipper.ddl$p$model.index[dipper.ddl$p$time==4]
# assign those links to log
 input.links[log.indices]="Log"
# Now these can be used with any call to mark
 mymodel=mark(dipper.proc,dipper.ddl,input.links=input.links,delete=TRUE)
 summary(mymodel)

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