I'm somewhat new to MARK and RMark and I have a question about the assumptions MARK makes in determining survival when ages are grouped.
I have two age classes of birds that are morphologically distinct (1yr, and 2+yrs). We regularly catch birds first when they are 2+year olds. I'm wondering if my analysis is assuming birds that were caught first as 2+ were 1 the previous year and using those birds to determine 1yr old survival, or if only birds caught first as 1yr old are used to determine 1yr old survival? I would prefer the latter as I am uncomfortable with the assumptions necessary for the former.
My RMark code is as follows:
- Code: Select all
tsprocess <-process.data(datMark_F2,model="CJS",
begin.time=1990,
groups= ("age"),
initial.ages =c(1, 2))
ts.ddl <- make.design.data(tsprocess, parameters=list(Phi=list(age.bins=c(1, 1.5, 29)),
p=list(age.bins=c(1,1.5, 29))))
levels(ts.ddl$Phi$age)<- c("SY", "ASY")
levels(ts.ddl$p$age)<- c("SY", "ASY")
p.dot <- list(formula= ~1)
p.time <- list(formula= ~time)
Phi.dot <- list(formula=~1)
Phi.age <- list(formula=~age)
cml <- create.model.list("CJS")
female.results <- mark.wrapper(cml, data=tsprocess, ddl=ts.ddl, output=F, adjust=F)
Thank you very much for any and all assistance!