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)
}