Aging individuals in Known-fate

[mvh]

I'm analyzing an 8-year dataset based on telemetry monitoring of tree squirrels and have been using known-fate survival analysis in MARK. I'm hoping to apply the initial.age function in RMark to bring juveniles into the adult age class, enabling models that include age. Juveniles are marked July-December and enter the adult age class at the beginning of the following breeding season (March). Observations are monthly, so I was planning to "age" the juveniles 1/12 for each month they survive until they become adults. This results in individuals entering the data set at "ages" ranging from 0.33 (collared in July) to 0.75 (collared in December); adults enter and stay at 1. I was planning to bin the ages [0,0.99,10] to establish 2 age classes for analysis. The Problem: although adults and juveniles are represented each year, all “initial ages” are not represented for each cohort. Does this preclude having “year” as a variable in the analysis, or is there a way to code to have begin.time match the number of groups? The dataset is continuous for each animal (96 occasions) beginning with January of the year it enters the study (consistent with previous examples of multiple-year known-fate data in this Forum). A subset of the data and code are below. Any help would be appreciated!

000000000010101010101010100000000000000000 2004 1 1
000000000010101011000000000000000000000000 2004 1 0.5
000000000000101010000000000000000000000000 2004 0 1
000000101010101010100000000000000000000000 2004 0 1
000000000000101010101010100000000000000000 2005 1 0.333
000000000000101010101010100000000000000000 2005 1 0.333
000000000000000010101010100000000000000000 2005 1 0.5
000000101010101010000000000000000000000000 2005 1 1
000000101010101010000000000000000000000000 2005 0 1
000000000000101010000000000000000000000000 2005 0 0.33
000000000000001010100000000000000000000000 2005 0 0.41
000000000000000010101010110000000000000000 2005 0 0.5
000000101010101010101010101010101010000000 2005 0 1

#codes: SEX (female=1, male=0); age (adult=1, juvenile=0.33, etc.)##
KWA<-import.chdata("KWAall.txt",field.names=c("ch","cohort","sex","age"),header=FALSE)
KWA.proc=process.data(KWA,model="Known",groups=c("cohort","age"),age.var=3,initial.age=c(0.33,0.41,0.5,1),time.intervals=rep(1/12,96),begin.time=c(rep(c(1998,1999,2000,2001,2002,2003,2004,2005),2)))
KWA.ddl=make.design.data(KWA.proc,parameters=list(S=list(time.bins=c(0,1999,2000,2001,2002,2003,2004,2005,3000),age.bins=c(0,0.98,10),right=FALSE)))
mark(KWA.proc,KWA.ddl,model.parameters=list(S=list(formula=~age)))
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