San Luis Valley mallard data
A recovery data set for mallards in San Luis Valley Colorado
A data frame with 108 observations on the following 5 variables.
a character vector containing the encounter history of each bird
frequency of that encounter history
the age of the bird when it was released
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.
# brownie=import.chdata("brownie.inp",field.types=c("n","f"))
# 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")))
# 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")))
mod=mark(br,br.ddl,model.parameters=list(S=list(formula=~-1+age,link="sin"),
f=list(formula=~-1+age,link="sin")))
#Random effects Seber recovery
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)))
#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)))
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)))Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.