RMark (version 3.0.0)

brownie: San Luis Valley mallard data

Description

A recovery data set for mallards in San Luis Valley Colorado

Format

A data frame with 108 observations on the following 5 variables.

ch

a character vector containing the encounter history of each bird

freq

frequency of that encounter history

ReleaseAge

the age of the bird when it was released

Details

This is a data set that accompanies program MARK as an example for Brownie and Seber recovery model. In those input files it is in a summarized format. Here it is in the LD encounter history format. The data can be stratified using ReleaseAge (Adult, Young) as a grouping variable.

Note that in the MARK example the variable is named Age. In the R code, the fields "age" and "Age" have specific meanings in the design data related to time since release. These will override the use of a field with the same name in the individual covariate data, so the names "time", "Time", "cohort", "Cohort", "age", and "Age" should not be used in the individual covariate data with possibly the exception of "cohort" which is not defined for models with "Square" PIMS such as POPAN and other Jolly-Seber type models.

Examples

# brownie=import.chdata("brownie.inp",field.types=c("n","f"))
# \donttest{
# This example is excluded from testing to reduce package check time
 data(brownie)
# default ordering of ReleaseAge is alphabetic so it is 
# Adult, Young which is why initial.ages=c(1,0)
# Seber Recovery
br=process.data(brownie,model="Recovery",groups="ReleaseAge",age.var=1,initial.ages=c(1,0))
br.ddl=make.design.data(br,parameters=list(S=list(age.bins=c(0,1,10)),
                                           r=list(age.bins=c(0,1,10))),right=FALSE)
mod=mark(br,br.ddl,model.parameters=list(S=list(formula=~-1+age:time,link="sin"),
                                           r=list(formula=~-1+age:time,link="sin")),delete=TRUE)
# Brownie Recovery
br=process.data(brownie,model="Brownie",groups="ReleaseAge",age.var=1,initial.ages=c(1,0))
br.ddl=make.design.data(br,parameters=list(S=list(age.bins=c(0,1,10)),
                               f=list(age.bins=c(0,1,10))),right=FALSE)
mod=mark(br,br.ddl,model.parameters=list(S=list(formula=~-1+age:time,link="sin"),
                               f=list(formula=~-1+age:time,link="sin")),delete=TRUE)
mod=mark(br,br.ddl,model.parameters=list(S=list(formula=~-1+age,link="sin"),
                               f=list(formula=~-1+age,link="sin")),delete=TRUE)
#Random effects Seber recovery (not run to save computation time)
#br=process.data(brownie,model="REDead",groups="ReleaseAge",age.var=1,initial.ages=c(1,0))
#br.ddl=make.design.data(br,parameters=list(S=list(age.bins=c(0,1,10)),
#                                       r=list(age.bins=c(0,1,10))),right=FALSE)
#mod=mark(br,br.ddl,model.parameters=list(S=list(formula=~age),r=list(formula=~age)),delete=TRUE)
#Pledger Mixture Seber recovery
br=process.data(brownie,model="PMDead",groups="ReleaseAge",
                           mixtures=3,age.var=1,initial.ages=c(1,0))
br.ddl=make.design.data(br,parameters=list(S=list(age.bins=c(0,1,10)),
                            r=list(age.bins=c(0,1,10))),right=FALSE)
mod=mark(br,br.ddl,model.parameters=list(pi=list(formula=~mixture),
                     S=list(formula=~age+mixture),r=list(formula=~age)),delete=TRUE)
br=process.data(brownie,model="PMDead",groups="ReleaseAge",
                     mixtures=2,age.var=1,initial.ages=c(1,0))
br.ddl=make.design.data(br,parameters=list(S=list(age.bins=c(0,1,10)),
                      r=list(age.bins=c(0,1,10))),right=FALSE)
mod=mark(br,br.ddl,model.parameters=list(pi=list(formula=~age),
                      S=list(formula=~age+mixture),r=list(formula=~age)),delete=TRUE)
# }