CJS age model with no new animals in last interval
Posted: Fri Apr 24, 2020 5:40 pm
Hi, I am working on CJS models where I have multiple groups. I also have 2 age classes. However, for this data set we continue trapping after we stop marking new individuals (we only mark juveniles for the first 2 sessions while we continue to trap them for another 2 sessions hence we have juveniles in interval 1 and 2 and adults in interval 2 and 3). We are interested in time as the age classes may differ as a result of not just age but time (trapping season). Despite having no new individuals trapped in the 3rd and 4th session, MARK still calculates an estimate for the juveniles in the 3rd interval. Any suggestions for how to deal with this? Should I set the 3rd interval equal to the 2nd interval? Or should I somehow (not sure how to do this in RMark but it can be done in MARK) set the juvenile survival (Phi) for the 3rd interval equal to the 2nd interval but allow the 3rd interval of adults differ for the 2nd and 3rd interval? Any other suggestions?
Thanks,
Amanda
Below is my basic code without constraining any parameters:
Thanks,
Amanda
Below is my basic code without constraining any parameters:
- Code: Select all
buck <- convert.inp("d:/allspec_4sites_nonew.inp",
covariates = c("sex","trt","species","site"))
# convert spec2, sex, and trt2 variables to factors so that we can treat them as
# grouping variables in the analysis to ease working with output later
buck$species <- factor(buck$species,
levels = c(0, 1,2),
labels = c("msp","nmex","pman"))
buck$sex <- factor(buck$sex,
levels = c(0, 1),
labels = c("fem", "male"))
buck$trt <- factor(buck$trt,
levels = c(0, 1),
labels = c("Pl", "Vac"))
buck$site <- factor(buck$site,
levels = c(0,1,2,3),
labels = c("PJ","fs131","fs127a","fs117"))
buck.process=process.data(buck,model="CJS", time.intervals=c(.858,.775,.833),groups=c("sex","trt","species","site"))
#add 2 age bins
buck.ddl=make.design.data(buck.process)
buck.ddl=add.design.data(buck.process,buck.ddl,parameter="Phi",type="age",
bins=c(0,.5,3),name="tages")
buck.ddl=add.design.data(buck.process,buck.ddl,parameter="p",type="age",
bins=c(0,1,4),name="tages")
buck.models=function()
{
Phi.time.adtrt.sex.adspecies.site=list(formula=~time+trt*sex+species*site)
Phi.site.adtime.adtrt.sex.adspecies.tages=list(formula=~site+time+trt*sex+species*tages)
Phi.time.adtrt.sex.adtrt.tages.adspecies.tages=list(formula=~time+trt*sex+trt*tages+species*tages)
Phi.site.adtime.adtrt.sex.adtrt.tages=list(formula=~site+time+trt*sex+trt*tages)
Phi.time.adtrt.sex.adspecies.sex.adspecies.tages=list(formula=~time+trt*sex+species*sex+species*tages)
Phi.time.adtages.sex.adtrt.sex.adspecies.tages=list(formula=~time+tages*sex+trt*sex+species*tages)
Phi.trt.sex.adspecies.tages.adtime.trt=list(formula=~trt*sex+species*tages+time*trt)
p.1=list(formula=~1)
p.site.time=list(formula=~site*time)
cml=create.model.list("CJS")
results=mark.wrapper(cml,data=buck.process,ddl=buck.ddl)
return(results)
}