########################################################################################################################## # # Source publication: Hassall, C., Watts, P.C., Sherratt, T.N., Thompson, D.J. (2015) Live fast, die old: no evidence of # reproductive senescence or costs of mating in a damselfly (Odonata: Zygoptera), Jounal of Animal Ecology. # # These R scripts contain the backbone of the code used in the analysis for the paper. The data are presented in a # simplified form elsewhere on Figshare, and so the code cannot be run directly. However, linking the methods in the # paper with the code here and the data on Figshare will enable the reader to replicate the analysis. # # There are four groups of analysis, as outlined in the published paper: # # 1) The first deals with a simplified "cohort" analysis, where capture histories are pooled for animals of particular # ages. We then calculate the numbers mating or not mating on each day and use a binomial mixed effects model to investigate # age-related patterns. The data for this analysis are available ready for analysis in R from Figshare. # # 2) A simple analysis using RMark to look for an effect of breeding stratum on survival, resighting, and transition # probability. This can be seen below. As with 1), some data processing is required to obtain the chdata format required # by RMark. Details can be found on the RMark website: http://www.phidot.org/software/mark/rmark/. # # 3) An extension of 2) demonstrating the best fit of time, age, and stratum in each of the models. # # 4) An extention of 3) adding climate (as time-varying covariates) and mites (as individual covariates) to the models. # ########################################################################################################################## ########################################################################################################################## # 1) Cohort analysis ########################################################################################################################## data<-read.table("Cohort data.txt",header=TRUE) attach(data) # Create subsets of data for each sex dataF<-subset(data,Sex=="f") dataM<-subset(data,Sex=="m") # GLMER library(lme4) library(LMERConvenienceFunctions) summary(glmer(cbind(NMate,NNonMate)~Sex*Age+(1|Year),family="binomial",data=data)) summary(glmer(cbind(NPresent,NAbsent)~Sex*Age+(1|Year),family="binomial",data=data)) # Analyse in more detail for sex-specific trends summary(glmer(cbind(NMate,NNonMate)~Age+(1|Year),family="binomial",data=dataF)) summary(glmer(cbind(NPresent,NAbsent)~Age+(1|Year),family="binomial",data=dataF)) summary(glmer(cbind(NMate,NNonMate)~Age+(1|Year),family="binomial",data=dataM)) summary(glmer(cbind(NPresent,NAbsent)~Age+(1|Year),family="binomial",data=dataM)) # Test for overdispersion, from http://glmm.wikidot.com/faq overdisp_fun <- function(model) { vpars <- function(m) { nrow(m)*(nrow(m)+1)/2 } model.df <- sum(sapply(VarCorr(model),vpars))+length(fixef(model)) rdf <- nrow(model.frame(model))-model.df rp <- residuals(model,type="pearson") Pearson.chisq <- sum(rp^2) prat <- Pearson.chisq/rdf pval <- pchisq(Pearson.chisq, df=rdf, lower.tail=FALSE) c(chisq=Pearson.chisq,ratio=prat,rdf=rdf,p=pval) } MatingModAll<-glmer(cbind(NMate,NNonMate)~Sex*Age+(1|Year),family="binomial",data=data) PresenceModAll<-glmer(cbind(NPresent,NAbsent)~Sex*Age+(1|Year),family="binomial",data=data) rdev <- sum(residuals(MMating)^2) mdf <- length(fixef(MMating)) rdf <- nrow(repsen2M)-mdf rdev/rdf # Analyse in more detail for sex-specific trends FMating<-glmer(cbind(NMate,NNonMate)~Age+(1|Year),family="binomial",data=dataF) FPresence<-glmer(cbind(NPresent,NAbsent)~Age+(1|Year),family="binomial",data=dataF) MMating<-glmer(cbind(NMate,NNonMate)~Age+(1|Year),family="binomial",data=dataM) MPresence<-glmer(cbind(NPresent,NAbsent)~Age+(1|Year),family="binomial",data=dataM) overdisp_fun(MatingModAll) overdisp_fun(PresenceModAll) overdisp_fun(FMating) overdisp_fun(FPresence) overdisp_fun(MMating) overdisp_fun(MPresence) # Overdispersion is present, so control with glmmPQL from MASS library(MASS) summary(glmmPQL(cbind(NMate,NNonMate)~Sex*Age,random=~1|Year,family=quasibinomial,data=subset(data,NMate>0 & NNonMate>0))) summary(glmmPQL(cbind(NPresent,NAbsent)~Sex*Age,random=~1|Year,family=binomial,data=data)) summary(glmmPQL(cbind(NMate,NNonMate)~Age,random=~1|Year,family=quasibinomial,data=subset(dataF,NMate>0 & NNonMate>0))) summary(glmmPQL(cbind(NPresent,NAbsent)~Age,random=~1|Year,family=binomial,data=dataF)) summary(glmmPQL(cbind(NMate,NNonMate)~Age,random=~1|Year,family=quasibinomial,data=subset(dataM,NMate>0 & NNonMate>0))) summary(glmmPQL(cbind(NPresent,NAbsent)~Age,random=~1|Year,family=binomial,data=dataM)) ################################################################################################################################################################################################ # 2) Testing for an effect of stratum (breeding state) on survivorship, resighting and transitions ################################################################################################################################################################################################ install.packages("RMark") library(RMark) ############################## ######## Males 2005 ######### ############################## # Here's the data, 0 = absent, N = present non-mating, B = present mating. library(RMark) setwd("...") multistrat_M_2005<-import.chdata("...", header = TRUE, field.names = NULL, field.types = NULL) # And actual parameters for the real models m_2005.process=process.data(multistrat_M_2005,model="Multistrata") m_2005.ddl=make.design.data(m_2005.process) # A "all dot" model is needed to calculate chat for the correction for overdispersion in the data: p.dot=list(formula=~1) S.dot=list(formula=~1) Psi.dot=list(formula=~1) p.strata=list(formula=~-1+stratum) S.strata=list(formula=~-1+stratum) Psi.strata=list(formula=~-1+stratum) # p(.),phi(.),psi(.) m_2005_p.dot_phi.dot_psi.dot=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p.dot,S=S.dot,Psi=Psi.dot),output=F,adjust=F,model.name="m_2005_p(.)_phi(.)_psi(.)") # p(stratum),phi(.),psi(.) m_2005_p.strat_phi.dot_psi.dot=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p.strata,S=S.dot,Psi=Psi.dot),output=F,adjust=F,model.name="m_2005_p(strat)_phi(.)_psi(.)") # p(.),phi(stratum),psi(.) m_2005_p.dot_phi.strat_psi.dot=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p.dot,S=S.strata,Psi=Psi.dot),output=F,adjust=F,model.name="m_2005_p(.)_phi(strat)_psi(.)") # p(.),phi(.),psi(stratum) m_2005_p.dot_phi.dot_psi.strat=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p.dot,S=S.dot,Psi=Psi.strata),output=F,adjust=F,model.name="m_2005_p(.)_phi(.)_psi(strat)") # p(stratum),phi(stratum),psi(.) m_2005_p.stratum_phi.stratum_psi.dot=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p.strata,S=S.strata,Psi=Psi.dot),output=F,adjust=F,model.name="m_2005_p(strat)_phi(strat)_psi(.)") # p(stratum),phi(.),psi(stratum) m_2005_p.stratum_phi.dot_psi.stratum=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p.strata,S=S.dot,Psi=Psi.strata),output=F,adjust=F,model.name="m_2005_p(strat)_phi(.)_psi(strat)") # p(.),phi(stratum),psi(stratum) m_2005_p.dot_phi.stratum_psi.stratum=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p.dot,S=S.strata,Psi=Psi.strata),output=F,adjust=F,model.name="m_2005_p(.)_phi(strat)_psi(strat)") # p(stratum),phi(stratum),psi(stratum) m_2005_p.stratum_phi.stratum_psi.stratum=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p.strata,S=S.strata,Psi=Psi.strata),output=F,adjust=F,model.name="m_2005_p(strat)_phi(strat)_psi(strat)") # Collect models m_2005_models<-collect.models(lx=c("m_2005_p.dot_phi.dot_psi.dot","m_2005_p.strat_phi.dot_psi.dot","m_2005_p.dot_phi.strat_psi.dot","m_2005_p.dot_phi.dot_psi.strat","m_2005_p.stratum_phi.stratum_psi.dot","m_2005_p.stratum_phi.dot_psi.stratum","m_2005_p.dot_phi.stratum_psi.stratum","m_2005_p.stratum_phi.stratum_psi.stratum")) write.table(m_2005_models[9],"...") # Saving the workspace so the models do not have to be run each time. save.image("...") # Getting the real parameter estimates is a little tough, but here is a method that works (for now) real_m_2005<-rbind(unique(summary(m_2005_p.stratum_phi.stratum_psi.stratum,show.fixed=T,showall=T,brief=F,se=T)$reals$S[,3:6]),unique(summary(m_2005_p.stratum_phi.stratum_psi.stratum,show.fixed=T,showall=T,brief=F,se=T)$reals$p[,3:6]),unique(summary(m_2005_p.stratum_phi.stratum_psi.stratum,show.fixed=T,showall=T,brief=F,se=T)$reals$Psi[,3:6])) write.table(real_m_2005,"...") ############################## ######## Males 2006 ######### ############################## multistrat_M_2006<-import.chdata("...", header = TRUE, field.names = NULL, field.types = NULL) m_2006.process=process.data(multistrat_M_2006,model="Multistrata") m_2006.ddl=make.design.data(m_2006.process) m_2006_p.dot_phi.dot_psi.dot=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p.dot,S=S.dot,Psi=Psi.dot),output=F,adjust=F,model.name="m_2006_p(.)_phi(.)_psi(.)") m_2006_p.strat_phi.dot_psi.dot=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p.strata,S=S.dot,Psi=Psi.dot),output=F,adjust=F,model.name="m_2006_p(strat)_phi(.)_psi(.)") m_2006_p.dot_phi.strat_psi.dot=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p.dot,S=S.strata,Psi=Psi.dot),output=F,adjust=F,model.name="m_2006_p(.)_phi(strat)_psi(.)") m_2006_p.dot_phi.dot_psi.strat=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p.dot,S=S.dot,Psi=Psi.strata),output=F,adjust=F,model.name="m_2006_p(.)_phi(.)_psi(strat)") m_2006_p.stratum_phi.stratum_psi.dot=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p.strata,S=S.strata,Psi=Psi.dot),output=F,adjust=F,model.name="m_2006_p(strat)_phi(strat)_psi(.)") m_2006_p.stratum_phi.dot_psi.stratum=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p.strata,S=S.dot,Psi=Psi.strata),output=F,adjust=F,model.name="m_2006_p(strat)_phi(.)_psi(strat)") m_2006_p.dot_phi.stratum_psi.stratum=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p.dot,S=S.strata,Psi=Psi.strata),output=F,adjust=F,model.name="m_2006_p(.)_phi(strat)_psi(strat)") m_2006_p.stratum_phi.stratum_psi.stratum=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p.strata,S=S.strata,Psi=Psi.strata),output=F,adjust=F,model.name="m_2006_p(strat)_phi(strat)_psi(strat)") m_2006_models<-collect.models(lx=c("m_2006_p.dot_phi.dot_psi.dot","m_2006_p.strat_phi.dot_psi.dot","m_2006_p.dot_phi.strat_psi.dot","m_2006_p.dot_phi.dot_psi.strat","m_2006_p.stratum_phi.stratum_psi.dot","m_2006_p.stratum_phi.dot_psi.stratum","m_2006_p.dot_phi.stratum_psi.stratum","m_2006_p.stratum_phi.stratum_psi.stratum")) write.table(m_2006_models[9],"...") real_m_2006<-rbind(unique(summary(m_2006_p.stratum_phi.stratum_psi.stratum,show.fixed=T,showall=T,brief=F,se=T)$reals$S[,3:6]),unique(summary(m_2006_p.stratum_phi.stratum_psi.stratum,show.fixed=T,showall=T,brief=F,se=T)$reals$p[,3:6]),unique(summary(m_2006_p.stratum_phi.stratum_psi.stratum,show.fixed=T,showall=T,brief=F,se=T)$reals$Psi[,3:6])) write.table(real_m_2006,"...") ############################## ######## Females 2005 ####### ############################## multistrat_F_2005<-import.chdata("...", header = TRUE, field.names = NULL, field.types = NULL) F_2005.process=process.data(multistrat_F_2005,model="Multistrata") F_2005.ddl=make.design.data(F_2005.process) F_2005_p.dot_phi.dot_psi.dot=mark(F_2005.process,F_2005.ddl,model.parameters=list(p=p.dot,S=S.dot,Psi=Psi.dot),output=F,adjust=F,model.name="F_2005_p(.)_phi(.)_psi(.)") F_2005_p.strat_phi.dot_psi.dot=mark(F_2005.process,F_2005.ddl,model.parameters=list(p=p.strata,S=S.dot,Psi=Psi.dot),output=F,adjust=F,model.name="F_2005_p(strat)_phi(.)_psi(.)") F_2005_p.dot_phi.strat_psi.dot=mark(F_2005.process,F_2005.ddl,model.parameters=list(p=p.dot,S=S.strata,Psi=Psi.dot),output=F,adjust=F,model.name="F_2005_p(.)_phi(strat)_psi(.)") F_2005_p.dot_phi.dot_psi.strat=mark(F_2005.process,F_2005.ddl,model.parameters=list(p=p.dot,S=S.dot,Psi=Psi.strata),output=F,adjust=F,model.name="F_2005_p(.)_phi(.)_psi(strat)") F_2005_p.stratum_phi.stratum_psi.dot=mark(F_2005.process,F_2005.ddl,model.parameters=list(p=p.strata,S=S.strata,Psi=Psi.dot),output=F,adjust=F,model.name="F_2005_p(strat)_phi(strat)_psi(.)") F_2005_p.stratum_phi.dot_psi.stratum=mark(F_2005.process,F_2005.ddl,model.parameters=list(p=p.strata,S=S.dot,Psi=Psi.strata),output=F,adjust=F,model.name="F_2005_p(strat)_phi(.)_psi(strat)") F_2005_p.dot_phi.stratum_psi.stratum=mark(F_2005.process,F_2005.ddl,model.parameters=list(p=p.dot,S=S.strata,Psi=Psi.strata),output=F,adjust=F,model.name="F_2005_p(.)_phi(strat)_psi(strat)") F_2005_p.stratum_phi.stratum_psi.stratum=mark(F_2005.process,F_2005.ddl,model.parameters=list(p=p.strata,S=S.strata,Psi=Psi.strata),output=F,adjust=F,model.name="F_2005_p(strat)_phi(strat)_psi(strat)") F_2005_models<-collect.models(lx=c("F_2005_p.dot_phi.dot_psi.dot","F_2005_p.strat_phi.dot_psi.dot","F_2005_p.dot_phi.strat_psi.dot","F_2005_p.dot_phi.dot_psi.strat","F_2005_p.stratum_phi.stratum_psi.dot","F_2005_p.stratum_phi.dot_psi.stratum","F_2005_p.dot_phi.stratum_psi.stratum","F_2005_p.stratum_phi.stratum_psi.stratum")) write.table(F_2005_models[9],"...") real_F_2005<-rbind(unique(summary(F_2005_p.stratum_phi.stratum_psi.stratum,show.fixed=T,showall=T,brief=F,se=T)$reals$S[,3:6]),unique(summary(F_2005_p.stratum_phi.stratum_psi.stratum,show.fixed=T,showall=T,brief=F,se=T)$reals$p[,3:6]),unique(summary(F_2005_p.stratum_phi.stratum_psi.stratum,show.fixed=T,showall=T,brief=F,se=T)$reals$Psi[,3:6])) write.table(real_F_2005,"...") ############################## ######## Females 2006 ####### ############################## multistrat_F_2006<-import.chdata("...", header = TRUE, field.names = NULL, field.types = NULL) F_2006.process=process.data(multistrat_F_2006,model="Multistrata") F_2006.ddl=make.design.data(F_2006.process) F_2006_p.dot_phi.dot_psi.dot=mark(F_2006.process,F_2006.ddl,model.parameters=list(p=p.dot,S=S.dot,Psi=Psi.dot),output=F,adjust=F,model.name="F_2006_p(.)_phi(.)_psi(.)") F_2006_p.strat_phi.dot_psi.dot=mark(F_2006.process,F_2006.ddl,model.parameters=list(p=p.strata,S=S.dot,Psi=Psi.dot),output=F,adjust=F,model.name="F_2006_p(strat)_phi(.)_psi(.)") F_2006_p.dot_phi.strat_psi.dot=mark(F_2006.process,F_2006.ddl,model.parameters=list(p=p.dot,S=S.strata,Psi=Psi.dot),output=F,adjust=F,model.name="F_2006_p(.)_phi(strat)_psi(.)") F_2006_p.dot_phi.dot_psi.strat=mark(F_2006.process,F_2006.ddl,model.parameters=list(p=p.dot,S=S.dot,Psi=Psi.strata),output=F,adjust=F,model.name="F_2006_p(.)_phi(.)_psi(strat)") F_2006_p.stratum_phi.stratum_psi.dot=mark(F_2006.process,F_2006.ddl,model.parameters=list(p=p.strata,S=S.strata,Psi=Psi.dot),output=F,adjust=F,model.name="F_2006_p(strat)_phi(strat)_psi(.)") F_2006_p.stratum_phi.dot_psi.stratum=mark(F_2006.process,F_2006.ddl,model.parameters=list(p=p.strata,S=S.dot,Psi=Psi.strata),output=F,adjust=F,model.name="F_2006_p(strat)_phi(.)_psi(strat)") F_2006_p.dot_phi.stratum_psi.stratum=mark(F_2006.process,F_2006.ddl,model.parameters=list(p=p.dot,S=S.strata,Psi=Psi.strata),output=F,adjust=F,model.name="F_2006_p(.)_phi(strat)_psi(strat)") F_2006_p.stratum_phi.stratum_psi.stratum=mark(F_2006.process,F_2006.ddl,model.parameters=list(p=p.strata,S=S.strata,Psi=Psi.strata),output=F,adjust=F,model.name="F_2006_p(strat)_phi(strat)_psi(strat)") F_2006_models<-collect.models(lx=c("F_2006_p.dot_phi.dot_psi.dot","F_2006_p.strat_phi.dot_psi.dot","F_2006_p.dot_phi.strat_psi.dot","F_2006_p.dot_phi.dot_psi.strat","F_2006_p.stratum_phi.stratum_psi.dot","F_2006_p.stratum_phi.dot_psi.stratum","F_2006_p.dot_phi.stratum_psi.stratum","F_2006_p.stratum_phi.stratum_psi.stratum")) write.table(F_2006_models[9],"...") real_F_2006<-rbind(unique(summary(F_2006_p.stratum_phi.stratum_psi.stratum,show.fixed=T,showall=T,brief=F,se=T)$reals$S[,3:6]),unique(summary(F_2006_p.stratum_phi.stratum_psi.stratum,show.fixed=T,showall=T,brief=F,se=T)$reals$p[,3:6]),unique(summary(F_2006_p.stratum_phi.stratum_psi.stratum,show.fixed=T,showall=T,brief=F,se=T)$reals$Psi[,3:6])) write.table(real_F_2006,"...") ################################################################################################################################################################################################ # 3) Full models with age, stratum and time ################################################################################################################################################################################################ ############## # Males 2005 # ############## # Enter the data, 0 = absent, N = present non-mating, B = present mating. library(RMark) setwd("...") multistrat_M_2005<-import.chdata("...", header = TRUE, field.names = NULL, field.types = NULL) # And actual parameters for the real models m_2005.process=process.data(multistrat_M_2005,model="Multistrata") m_2005.ddl=make.design.data(m_2005.process) # All the models for the different parameters p.t=list(formula=~time) p.t.plus.strat=list(formula=~-1+stratum+time) p.t.by.strat=list(formula=~-1+stratum*time) S.age=list(formula=~Age) S.dot=list(formula=~1) S.strat=list(formula=~Age) S.age.plus.strat=list(formula=~-1+stratum+Age) S.age.by.strat=list(formula=~-1+stratum*Age) Psi.dot=list(formula=~1) Psi.age=list(formula=~Age) Psi.strat=list(formula=~-1+stratum) Psi.age.plus.strat=list(formula=~-1+stratum+Age) p.dot=list(formula=~1) S.dot=list(formula=~1) Psi.dot=list(formula=~1) p.strata=list(formula=~-1+stratum) S.strata=list(formula=~-1+stratum) Psi.strata=list(formula=~-1+stratum) #p(t),Phi(X),Psi(.) m_2005_p.t_phi.X_psi.dot=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p.t,S=S.age,Psi=Psi.dot),output=F,adjust=F,model.name="m_2005_p.t_Phi.X_Psi.dot") #p(t),Phi(X),Psi(X) m_2005_p.t_phi.X_psi.X=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p.t,S=S.age,Psi=Psi.age),output=F,adjust=F,model.name="m_2005_p.t_Phi.X_Psi.age") #p(t),Phi(X),Psi(stratum) m_2005_p.t_phi.X_psi.strat=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p.t,S=S.age,Psi=Psi.strat),output=F,adjust=F,model.name="m_2005_p.t_Phi.X_Psi.stratum") #p(t),Phi(X),Psi(X + stratum) m_2005_p.t_phi.X_psi.X.plus.strat=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p.t,S=S.age,Psi=Psi.age.plus.strat),output=F,adjust=F,model.name="m_2005_p.t_Phi.X_Psi.X.plus.stratum") #p(t),Phi(X + stratum),Psi(.) m_2005_p.t_phi.X.plus.strat_psi.dot=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p.t,S=S.age.plus.strat,Psi=Psi.dot),output=F,adjust=F,model.name="m_2005_p.t_Phi.X.plus.stratum_Psi.dot") #p(t),Phi(X + stratum),Psi(X) m_2005_p.t_phi.X.plus.strat_psi.X=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p.t,S=S.age.plus.strat,Psi=Psi.age),output=F,adjust=F,model.name="m_2005_p.t_Phi.X.plus.stratum_Psi.age") #p(t),Phi(X + stratum),Psi(stratum) m_2005_p.t_phi.X.plus.strat_psi.strat=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p.t,S=S.age.plus.strat,Psi=Psi.strat),output=F,adjust=F,model.name="m_2005_p.t_Phi.X.plus.stratum_Psi.stratum") #p(t),Phi(X + stratum),Psi(X + stratum) m_2005_p.t_phi.X.plus.strat_psi.X.plus.strat=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p.t,S=S.age.plus.strat,Psi=Psi.age.plus.strat),output=F,adjust=F,model.name="m_2005_p.t_Phi.X.plus.stratum_Psi.X.plus.stratum") #p(t + stratum),Phi(X),Psi(.) m_2005_p.t.plus.strat_phi.X_psi.dot=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p.t.plus.strat,S=S.age,Psi=Psi.dot),output=F,adjust=F,model.name="m_2005_p.t.plus.stratum_Phi.X_Psi.dot") #p(t + stratum),Phi(X),Psi(X) m_2005_p.t.plus.strat_phi.X_psi.X=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p.t.plus.strat,S=S.age,Psi=Psi.age),output=F,adjust=F,model.name="m_2005_p.t.plus.stratum_Phi.X_Psi.age") #p(t + stratum),Phi(X),Psi(stratum) m_2005_p.t.plus.strat_phi.X_psi.strat=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p.t.plus.strat,S=S.age,Psi=Psi.strat),output=F,adjust=F,model.name="m_2005_p.t.plus.stratum_Phi.X_Psi.stratum") #p(t + stratum),Phi(X),Psi(X + stratum) m_2005_p.t.plus.strat_phi.X_psi.X.plus.strat=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p.t.plus.strat,S=S.age,Psi=Psi.age.plus.strat),output=F,adjust=F,model.name="m_2005_p.t.plus.stratum_Phi.X_Psi.X.plus.stratum") #p(t + stratum),Phi(X + stratum),Psi(.) m_2005_p.t.plus.strat_phi.X.plus.strat_psi.dot=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p.t.plus.strat,S=S.age.plus.strat,Psi=Psi.dot),output=F,adjust=F,model.name="m_2005_p.t.plus.stratum_Phi.X.plus.stratum_Psi.dot") #p(t + stratum),Phi(X + stratum),Psi(X) m_2005_p.t.plus.strat_phi.X.plus.strat_psi.X=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p.t.plus.strat,S=S.age.plus.strat,Psi=Psi.age),output=F,adjust=F,model.name="m_2005_p.t.plus.stratum_Phi.X.plus.stratum_Psi.age") #p(t + stratum),Phi(X + stratum),Psi(stratum) m_2005_p.t.plus.strat_phi.X.plus.strat_psi.strat=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p.t.plus.strat,S=S.age.plus.strat,Psi=Psi.strat),output=F,adjust=F,model.name="m_2005_p.t.plus.stratum_Phi.X.plus.stratum_Psi.stratum") #p(t + stratum),Phi(X + stratum),Psi(X + stratum) m_2005_p.t.plus.strat_phi.X.plus.strat_psi.X.plus.strat=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p.t.plus.strat,S=S.age.plus.strat,Psi=Psi.age.plus.strat),output=F,adjust=F,model.name="m_2005_p.t.plus.stratum_Phi.X.plus.stratum_Psi.X.plus.stratum") #p(t * stratum),Phi(X),Psi(.) m_2005_p.t.by.strat_phi.X_psi.dot=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p.t.by.strat,S=S.age,Psi=Psi.dot),output=F,adjust=F,model.name="m_2005_p.t.by.stratum_Phi.X_Psi.dot") #p(t * stratum),Phi(X),Psi(X) m_2005_p.t.by.strat_phi.X_psi.X=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p.t.by.strat,S=S.age,Psi=Psi.age),output=F,adjust=F,model.name="m_2005_p.t.by.stratum_Phi.X_Psi.X") #p(t * stratum),Phi(X),Psi(stratum) m_2005_p.t.by.strat_phi.X_psi.strat=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p.t.by.strat,S=S.age,Psi=Psi.strat),output=F,adjust=F,model.name="m_2005_p.t.by.stratum_Phi.X_Psi.stratum") #p(t * stratum),Phi(X),Psi(X + stratum) m_2005_p.t.by.strat_phi.X_psi.X.plus.strat=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p.t.by.strat,S=S.age,Psi=Psi.age.plus.strat),output=F,adjust=F,model.name="m_2005_p.t.by.stratum_Phi.X_Psi.X.plus.stratum") #p(t * stratum),Phi(X + stratum),Psi(.) m_2005_p.t.by.strat_phi.X.plus.strat_psi.dot=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p.t.by.strat,S=S.age.plus.strat,Psi=Psi.dot),output=F,adjust=F,model.name="m_2005_p.t.by.stratum_Phi.X.plus.stratum_Psi.dot") #p(t * stratum),Phi(X + stratum),Psi(X) m_2005_p.t.by.strat_phi.X.plus.strat_psi.X=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p.t.by.strat,S=S.age.plus.strat,Psi=Psi.age),output=F,adjust=F,model.name="m_2005_p.t.by.stratum_Phi.X.plus.stratum_Psi.age") #p(t * stratum),Phi(X + stratum),Psi(stratum) m_2005_p.t.by.strat_phi.X.plus.strat_psi.strat=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p.t.by.strat,S=S.age.plus.strat,Psi=Psi.strat),output=F,adjust=F,model.name="m_2005_p.t.by.stratum_Phi.X.plus.stratum_Psi.stratum") #p(t * stratum),Phi(X + stratum),Psi(X + stratum) m_2005_p.t.by.strat_phi.X.plus.strat_psi.X.plus.strat=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p.t.by.strat,S=S.age.plus.strat,Psi=Psi.age.plus.strat),output=F,adjust=F,model.name="m_2005_p.t.by.stratum_Phi.X.plus.stratum_Psi.X.plus.stratum") #p(t),Phi(X + stratum),Psi(.) m_2005_p.t_phi.X.by.strat_psi.dot=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p.t,S=S.age.by.strat,Psi=Psi.dot),output=F,adjust=F,model.name="m_2005_p.t_Phi.X.by.stratum_Psi.dot") #p(t),Phi(X + stratum),Psi(X) m_2005_p.t_phi.X.by.strat_psi.X=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p.t,S=S.age.by.strat,Psi=Psi.age),output=F,adjust=F,model.name="m_2005_p.t_Phi.X.by.stratum_Psi.age") #p(t),Phi(X + stratum),Psi(stratum) m_2005_p.t_phi.X.by.strat_psi.strat=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p.t,S=S.age.by.strat,Psi=Psi.strat),output=F,adjust=F,model.name="m_2005_p.t_Phi.X.by.stratum_Psi.stratum") #p(t),Phi(X + stratum),Psi(X + stratum) m_2005_p.t_phi.X.by.strat_psi.X.plus.strat=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p.t,S=S.age.by.strat,Psi=Psi.age.plus.strat),output=F,adjust=F,model.name="m_2005_p.t_Phi.X.by.stratum_Psi.X.plus.stratum") #p(t + stratum),Phi(X + stratum),Psi(.) m_2005_p.t.plus.strat_phi.X.by.strat_psi.dot=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p.t.plus.strat,S=S.age.by.strat,Psi=Psi.dot),output=F,adjust=F,model.name="m_2005_p.t.plus.stratum_Phi.X.by.stratum_Psi.dot") #p(t + stratum),Phi(X + stratum),Psi(X) m_2005_p.t.plus.strat_phi.X.by.strat_psi.X=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p.t.plus.strat,S=S.age.by.strat,Psi=Psi.age),output=F,adjust=F,model.name="m_2005_p.t.plus.stratum_Phi.X.by.stratum_Psi.age") #p(t + stratum),Phi(X + stratum),Psi(stratum) m_2005_p.t.plus.strat_phi.X.by.strat_psi.strat=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p.t.plus.strat,S=S.age.by.strat,Psi=Psi.strat),output=F,adjust=F,model.name="m_2005_p.t.plus.stratum_Phi.X.by.stratum_Psi.stratum") #p(t + stratum),Phi(X + stratum),Psi(X + stratum) m_2005_p.t.plus.strat_phi.X.by.strat_psi.X.plus.strat=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p.t.plus.strat,S=S.age.by.strat,Psi=Psi.age.plus.strat),output=F,adjust=F,model.name="m_2005_p.t.plus.stratum_Phi.X.by.stratum_Psi.X.plus.stratum") #p(t * stratum),Phi(X + stratum),Psi(.) m_2005_p.t.by.strat_phi.X.by.strat_psi.dot=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p.t.by.strat,S=S.age.by.strat,Psi=Psi.dot),output=F,adjust=F,model.name="m_2005_p.t.by.stratum_Phi.X.by.stratum_Psi.dot") #p(t * stratum),Phi(X + stratum),Psi(X) m_2005_p.t.by.strat_phi.X.by.strat_psi.X=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p.t.by.strat,S=S.age.by.strat,Psi=Psi.age),output=F,adjust=F,model.name="m_2005_p.t.by.stratum_Phi.X.by.stratum_Psi.age") #p(t * stratum),Phi(X + stratum),Psi(stratum) m_2005_p.t.by.strat_phi.X.by.strat_psi.strat=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p.t.by.strat,S=S.age.by.strat,Psi=Psi.strat),output=F,adjust=F,model.name="m_2005_p.t.by.stratum_Phi.X.by.stratum_Psi.stratum") #p(t * stratum),Phi(X + stratum),Psi(X + stratum) m_2005_p.t.by.strat_phi.X.by.strat_psi.X.plus.strat=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p.t.by.strat,S=S.age.by.strat,Psi=Psi.age.plus.strat),output=F,adjust=F,model.name="m_2005_p.t.by.stratum_Phi.X.by.stratum_Psi.X.plus.stratum") # And here are all the models without the age term being constrained in the phi() model. #p(t),Phi(dot),Psi(.) m_2005_p.t_phi.dot_psi.dot=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p.t,S=S.dot,Psi=Psi.dot),output=F,adjust=F,model.name="m_2005_p.t_Phi.dot_psi.dot") #p(t),Phi(dot),Psi(X) m_2005_p.t_phi.dot_psi.X=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p.t,S=S.dot,Psi=Psi.age),output=F,adjust=F,model.name="m_2005_p.t_Phi.dot_psi.age") #p(t),Phi(dot),Psi(stratum) m_2005_p.t_phi.dot_psi.strat=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p.t,S=S.dot,Psi=Psi.strat),output=F,adjust=F,model.name="m_2005_p.t_Phi.dot_psi.stratum") #p(t),Phi(dot),Psi(X + stratum) m_2005_p.t_phi.dot_psi.X.plus.strat=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p.t,S=S.dot,Psi=Psi.age.plus.strat),output=F,adjust=F,model.name="m_2005_p.t_Phi.dot_psi.X.plus.stratum") #p(t),Phi(X + stratum),Psi(.) m_2005_p.t_phi.strat_psi.dot=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p.t,S=S.strat,Psi=Psi.dot),output=F,adjust=F,model.name="m_2005_p.t_Phi.stratum_Psi.dot") #p(t),Phi(X + stratum),Psi(X) m_2005_p.t_phi.strat_psi.X=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p.t,S=S.strat,Psi=Psi.age),output=F,adjust=F,model.name="m_2005_p.t_Phi.stratum_Psi.age") #p(t),Phi(X + stratum),Psi(stratum) m_2005_p.t_phi.strat_psi.strat=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p.t,S=S.strat,Psi=Psi.strat),output=F,adjust=F,model.name="m_2005_p.t_Phi.stratum_Psi.stratum") #p(t),Phi(X + stratum),Psi(X + stratum) m_2005_p.t_phi.strat_psi.X.plus.strat=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p.t,S=S.strat,Psi=Psi.age.plus.strat),output=F,adjust=F,model.name="m_2005_p.t_Phi.stratum_Psi.X.plus.stratum") #p(t + stratum),Phi(.),Psi(.) m_2005_p.t.plus.strat_phi.X_psi.dot=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p.t.plus.strat,S=S.dot,Psi=Psi.dot),output=F,adjust=F,model.name="m_2005_p.t.plus.stratum_Phi.dot_Psi.dot") #p(t + stratum),Phi(.),Psi(X) m_2005_p.t.plus.strat_phi.X_psi.X=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p.t.plus.strat,S=S.dot,Psi=Psi.age),output=F,adjust=F,model.name="m_2005_p.t.plus.stratum_Phi.dot_Psi.age") #p(t + stratum),Phi(.),Psi(stratum) m_2005_p.t.plus.strat_phi.X_psi.strat=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p.t.plus.strat,S=S.dot,Psi=Psi.strat),output=F,adjust=F,model.name="m_2005_p.t.plus.stratum_Phi.dot_Psi.stratum") #p(t + stratum),Phi(.),Psi(X + stratum) m_2005_p.t.plus.strat_phi.X_psi.X.plus.strat=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p.t.plus.strat,S=S.dot,Psi=Psi.age.plus.strat),output=F,adjust=F,model.name="m_2005_p.t.plus.stratum_Phi.dot_Psi.X.plus.stratum") #p(t + stratum),Phi(stratum),Psi(.) m_2005_p.t.plus.strat_phi.strat_psi.dot=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p.t.plus.strat,S=S.strat,Psi=Psi.dot),output=F,adjust=F,model.name="m_2005_p.t.plus.stratum_Phi.stratum_Psi.dot") #p(t + stratum),Phi(stratum),Psi(X) m_2005_p.t.plus.strat_phi.strat_psi.X=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p.t.plus.strat,S=S.strat,Psi=Psi.age),output=F,adjust=F,model.name="m_2005_p.t.plus.stratum_Phi.stratum_Psi.age") #p(t + stratum),Phi(stratum),Psi(stratum) m_2005_p.t.plus.strat_phi.strat_psi.strat=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p.t.plus.strat,S=S.strat,Psi=Psi.strat),output=F,adjust=F,model.name="m_2005_p.t.plus.stratum_Phi.stratum_Psi.stratum") #p(t + stratum),Phi(stratum),Psi(X + stratum) m_2005_p.t.plus.strat_phi.strat_psi.X.plus.strat=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p.t.plus.strat,S=S.strat,Psi=Psi.age.plus.strat),output=F,adjust=F,model.name="m_2005_p.t.plus.stratum_Phi.stratum_Psi.X.plus.stratum") #p(t * stratum),Phi(.),Psi(.) m_2005_p.t.by.strat_phi.dot_psi.dot=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p.t.by.strat,S=S.dot,Psi=Psi.dot),output=F,adjust=F,model.name="m_2005_p.t.by.stratum_Phi.dot_psi.dot") #p(t * stratum),Phi(.),Psi(X) m_2005_p.t.by.strat_phi.dot_psi.X=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p.t.by.strat,S=S.dot,Psi=Psi.age),output=F,adjust=F,model.name="m_2005_p.t.by.stratum_Phi.dot_psi.X") #p(t * stratum),Phi(.),Psi(stratum) m_2005_p.t.by.strat_phi.dot_psi.strat=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p.t.by.strat,S=S.dot,Psi=Psi.strat),output=F,adjust=F,model.name="m_2005_p.t.by.stratum_Phi.dot_psi.stratum") #p(t * stratum),Phi(.),Psi(X + stratum) m_2005_p.t.by.strat_phi.dot_psi.X.plus.strat=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p.t.by.strat,S=S.dot,Psi=Psi.age.plus.strat),output=F,adjust=F,model.name="m_2005_p.t.by.stratum_Phi.dot_psi.X.plus.stratum") #p(t * stratum),Phi(stratum),Psi(.) m_2005_p.t.by.strat_phi.strat_psi.dot=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p.t.by.strat,S=S.strat,Psi=Psi.dot),output=F,adjust=F,model.name="m_2005_p.t.by.stratum_Phi.stratum_Psi.dot") #p(t * stratum),Phi(stratum),Psi(X) m_2005_p.t.by.strat_phi.strat_psi.X=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p.t.by.strat,S=S.strat,Psi=Psi.age),output=F,adjust=F,model.name="m_2005_p.t.by.stratum_Phi.stratum_Psi.age") #p(t * stratum),Phi(stratum),Psi(stratum) m_2005_p.t.by.strat_phi.strat_psi.strat=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p.t.by.strat,S=S.strat,Psi=Psi.strat),output=F,adjust=F,model.name="m_2005_p.t.by.stratum_Phi.stratum_Psi.stratum") #p(t * stratum),Phi(stratum),Psi(X + stratum) m_2005_p.t.by.strat_phi.strat_psi.X.plus.strat=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p.t.by.strat,S=S.strat,Psi=Psi.age.plus.strat),output=F,adjust=F,model.name="m_2005_p.t.by.stratum_Phi.stratum_Psi.X.plus.stratum") # Collect models m_2005_models<-collect.models(lx=c("m_2005_p.t_phi.X_psi.dot","m_2005_p.t_phi.X_psi.X","m_2005_p.t_phi.X_psi.strat","m_2005_p.t_phi.X_psi.X.plus.strat","m_2005_p.t_phi.X.plus.strat_psi.dot","m_2005_p.t_phi.X.plus.strat_psi.X","m_2005_p.t_phi.X.plus.strat_psi.strat","m_2005_p.t_phi.X.plus.strat_psi.X.plus.strat","m_2005_p.t.plus.strat_phi.X_psi.dot","m_2005_p.t.plus.strat_phi.X_psi.X","m_2005_p.t.plus.strat_phi.X_psi.strat","m_2005_p.t.plus.strat_phi.X_psi.X.plus.strat","m_2005_p.t.plus.strat_phi.X.plus.strat_psi.dot","m_2005_p.t.plus.strat_phi.X.plus.strat_psi.X","m_2005_p.t.plus.strat_phi.X.plus.strat_psi.strat","m_2005_p.t.plus.strat_phi.X.plus.strat_psi.X.plus.strat","m_2005_p.t.by.strat_phi.X_psi.dot","m_2005_p.t.by.strat_phi.X_psi.X","m_2005_p.t.by.strat_phi.X_psi.strat","m_2005_p.t.by.strat_phi.X_psi.X.plus.strat","m_2005_p.t.by.strat_phi.X.plus.strat_psi.dot","m_2005_p.t.by.strat_phi.X.plus.strat_psi.X","m_2005_p.t.by.strat_phi.X.plus.strat_psi.strat","m_2005_p.t.by.strat_phi.X.plus.strat_psi.X.plus.strat","m_2005_p.t_phi.X.by.strat_psi.dot","m_2005_p.t_phi.X.by.strat_psi.X","m_2005_p.t_phi.X.by.strat_psi.strat","m_2005_p.t_phi.X.by.strat_psi.X.plus.strat","m_2005_p.t.plus.strat_phi.X.by.strat_psi.dot","m_2005_p.t.plus.strat_phi.X.by.strat_psi.X","m_2005_p.t.plus.strat_phi.X.by.strat_psi.strat","m_2005_p.t.plus.strat_phi.X.by.strat_psi.X.plus.strat","m_2005_p.t.by.strat_phi.X.by.strat_psi.dot","m_2005_p.t.by.strat_phi.X.by.strat_psi.X","m_2005_p.t.by.strat_phi.X.by.strat_psi.strat","m_2005_p.t.by.strat_phi.X.by.strat_psi.X.plus.strat","m_2005_p.t_phi.dot_psi.dot","m_2005_p.t_phi.dot_psi.X","m_2005_p.t_phi.dot_psi.strat","m_2005_p.t_phi.dot_psi.X.plus.strat","m_2005_p.t_phi.strat_psi.dot","m_2005_p.t_phi.strat_psi.X","m_2005_p.t_phi.strat_psi.strat","m_2005_p.t_phi.strat_psi.X.plus.strat","m_2005_p.t.plus.strat_phi.X_psi.dot","m_2005_p.t.plus.strat_phi.X_psi.X","m_2005_p.t.plus.strat_phi.X_psi.strat","m_2005_p.t.plus.strat_phi.X_psi.X.plus.strat","m_2005_p.t.plus.strat_phi.strat_psi.dot","m_2005_p.t.plus.strat_phi.strat_psi.X","m_2005_p.t.plus.strat_phi.strat_psi.strat","m_2005_p.t.plus.strat_phi.strat_psi.X.plus.strat","m_2005_p.t.by.strat_phi.dot_psi.dot","m_2005_p.t.by.strat_phi.dot_psi.X","m_2005_p.t.by.strat_phi.dot_psi.strat","m_2005_p.t.by.strat_phi.dot_psi.X.plus.strat","m_2005_p.t.by.strat_phi.strat_psi.dot","m_2005_p.t.by.strat_phi.strat_psi.X","m_2005_p.t.by.strat_phi.strat_psi.strat","m_2005_p.t.by.strat_phi.strat_psi.X.plus.strat")) write.table(m_2005_models[61],"...") # Saving the workspace so the models do not have to be repeated each time save.image("...") # Getting the real parameter estimates is a little tough, but here is a method that works (for now) real_m_2005<-rbind(unique(summary(m_2005_p.stratum_phi.stratum_psi.stratum,show.fixed=T,showall=T,brief=F,se=T)$reals$S[,3:6]),unique(summary(m_2005_p.stratum_phi.stratum_psi.stratum,show.fixed=T,showall=T,brief=F,se=T)$reals$p[,3:6]),unique(summary(m_2005_p.stratum_phi.stratum_psi.stratum,show.fixed=T,showall=T,brief=F,se=T)$reals$Psi[,3:6])) write.table(real_m_2005,"...") ############## # Males 2006 # ############## multistrat_M_2006<-import.chdata("...", header = TRUE, field.names = NULL, field.types = NULL) m_2006.process=process.data(multistrat_M_2006,model="Multistrata") m_2006.ddl=make.design.data(m_2006.process) #p(t),Phi(X),Psi(.) m_2006_p.t_phi.X_psi.dot=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p.t,S=S.age,Psi=Psi.dot),output=F,adjust=F,model.name="m_2006_p.t_Phi.X_Psi.dot") #p(t),Phi(X),Psi(X) m_2006_p.t_phi.X_psi.X=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p.t,S=S.age,Psi=Psi.age),output=F,adjust=F,model.name="m_2006_p.t_Phi.X_Psi.age") #p(t),Phi(X),Psi(stratum) m_2006_p.t_phi.X_psi.strat=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p.t,S=S.age,Psi=Psi.strat),output=F,adjust=F,model.name="m_2006_p.t_Phi.X_Psi.stratum") #p(t),Phi(X),Psi(X + stratum) m_2006_p.t_phi.X_psi.X.plus.strat=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p.t,S=S.age,Psi=Psi.age.plus.strat),output=F,adjust=F,model.name="m_2006_p.t_Phi.X_Psi.X.plus.stratum") #p(t),Phi(X + stratum),Psi(.) m_2006_p.t_phi.X.plus.strat_psi.dot=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p.t,S=S.age.plus.strat,Psi=Psi.dot),output=F,adjust=F,model.name="m_2006_p.t_Phi.X.plus.stratum_Psi.dot") #p(t),Phi(X + stratum),Psi(X) m_2006_p.t_phi.X.plus.strat_psi.X=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p.t,S=S.age.plus.strat,Psi=Psi.age),output=F,adjust=F,model.name="m_2006_p.t_Phi.X.plus.stratum_Psi.age") #p(t),Phi(X + stratum),Psi(stratum) m_2006_p.t_phi.X.plus.strat_psi.strat=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p.t,S=S.age.plus.strat,Psi=Psi.strat),output=F,adjust=F,model.name="m_2006_p.t_Phi.X.plus.stratum_Psi.stratum") #p(t),Phi(X + stratum),Psi(X + stratum) m_2006_p.t_phi.X.plus.strat_psi.X.plus.strat=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p.t,S=S.age.plus.strat,Psi=Psi.age.plus.strat),output=F,adjust=F,model.name="m_2006_p.t_Phi.X.plus.stratum_Psi.X.plus.stratum") #p(t + stratum),Phi(X),Psi(.) m_2006_p.t.plus.strat_phi.X_psi.dot=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p.t.plus.strat,S=S.age,Psi=Psi.dot),output=F,adjust=F,model.name="m_2006_p.t.plus.stratum_Phi.X_Psi.dot") #p(t + stratum),Phi(X),Psi(X) m_2006_p.t.plus.strat_phi.X_psi.X=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p.t.plus.strat,S=S.age,Psi=Psi.age),output=F,adjust=F,model.name="m_2006_p.t.plus.stratum_Phi.X_Psi.age") #p(t + stratum),Phi(X),Psi(stratum) m_2006_p.t.plus.strat_phi.X_psi.strat=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p.t.plus.strat,S=S.age,Psi=Psi.strat),output=F,adjust=F,model.name="m_2006_p.t.plus.stratum_Phi.X_Psi.stratum") #p(t + stratum),Phi(X),Psi(X + stratum) m_2006_p.t.plus.strat_phi.X_psi.X.plus.strat=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p.t.plus.strat,S=S.age,Psi=Psi.age.plus.strat),output=F,adjust=F,model.name="m_2006_p.t.plus.stratum_Phi.X_Psi.X.plus.stratum") #p(t + stratum),Phi(X + stratum),Psi(.) m_2006_p.t.plus.strat_phi.X.plus.strat_psi.dot=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p.t.plus.strat,S=S.age.plus.strat,Psi=Psi.dot),output=F,adjust=F,model.name="m_2006_p.t.plus.stratum_Phi.X.plus.stratum_Psi.dot") #p(t + stratum),Phi(X + stratum),Psi(X) m_2006_p.t.plus.strat_phi.X.plus.strat_psi.X=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p.t.plus.strat,S=S.age.plus.strat,Psi=Psi.age),output=F,adjust=F,model.name="m_2006_p.t.plus.stratum_Phi.X.plus.stratum_Psi.age") #p(t + stratum),Phi(X + stratum),Psi(stratum) m_2006_p.t.plus.strat_phi.X.plus.strat_psi.strat=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p.t.plus.strat,S=S.age.plus.strat,Psi=Psi.strat),output=F,adjust=F,model.name="m_2006_p.t.plus.stratum_Phi.X.plus.stratum_Psi.stratum") #p(t + stratum),Phi(X + stratum),Psi(X + stratum) m_2006_p.t.plus.strat_phi.X.plus.strat_psi.X.plus.strat=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p.t.plus.strat,S=S.age.plus.strat,Psi=Psi.age.plus.strat),output=F,adjust=F,model.name="m_2006_p.t.plus.stratum_Phi.X.plus.stratum_Psi.X.plus.stratum") #p(t * stratum),Phi(X),Psi(.) m_2006_p.t.by.strat_phi.X_psi.dot=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p.t.by.strat,S=S.age,Psi=Psi.dot),output=F,adjust=F,model.name="m_2006_p.t.by.stratum_Phi.X_Psi.dot") #p(t * stratum),Phi(X),Psi(X) m_2006_p.t.by.strat_phi.X_psi.X=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p.t.by.strat,S=S.age,Psi=Psi.age),output=F,adjust=F,model.name="m_2006_p.t.by.stratum_Phi.X_Psi.X") #p(t * stratum),Phi(X),Psi(stratum) m_2006_p.t.by.strat_phi.X_psi.strat=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p.t.by.strat,S=S.age,Psi=Psi.strat),output=F,adjust=F,model.name="m_2006_p.t.by.stratum_Phi.X_Psi.stratum") #p(t * stratum),Phi(X),Psi(X + stratum) m_2006_p.t.by.strat_phi.X_psi.X.plus.strat=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p.t.by.strat,S=S.age,Psi=Psi.age.plus.strat),output=F,adjust=F,model.name="m_2006_p.t.by.stratum_Phi.X_Psi.X.plus.stratum") #p(t * stratum),Phi(X + stratum),Psi(.) m_2006_p.t.by.strat_phi.X.plus.strat_psi.dot=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p.t.by.strat,S=S.age.plus.strat,Psi=Psi.dot),output=F,adjust=F,model.name="m_2006_p.t.by.stratum_Phi.X.plus.stratum_Psi.dot") #p(t * stratum),Phi(X + stratum),Psi(X) m_2006_p.t.by.strat_phi.X.plus.strat_psi.X=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p.t.by.strat,S=S.age.plus.strat,Psi=Psi.age),output=F,adjust=F,model.name="m_2006_p.t.by.stratum_Phi.X.plus.stratum_Psi.age") #p(t * stratum),Phi(X + stratum),Psi(stratum) m_2006_p.t.by.strat_phi.X.plus.strat_psi.strat=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p.t.by.strat,S=S.age.plus.strat,Psi=Psi.strat),output=F,adjust=F,model.name="m_2006_p.t.by.stratum_Phi.X.plus.stratum_Psi.stratum") #p(t * stratum),Phi(X + stratum),Psi(X + stratum) m_2006_p.t.by.strat_phi.X.plus.strat_psi.X.plus.strat=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p.t.by.strat,S=S.age.plus.strat,Psi=Psi.age.plus.strat),output=F,adjust=F,model.name="m_2006_p.t.by.stratum_Phi.X.plus.stratum_Psi.X.plus.stratum") #p(t),Phi(X + stratum),Psi(.) m_2006_p.t_phi.X.by.strat_psi.dot=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p.t,S=S.age.by.strat,Psi=Psi.dot),output=F,adjust=F,model.name="m_2006_p.t_Phi.X.by.stratum_Psi.dot") #p(t),Phi(X + stratum),Psi(X) m_2006_p.t_phi.X.by.strat_psi.X=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p.t,S=S.age.by.strat,Psi=Psi.age),output=F,adjust=F,model.name="m_2006_p.t_Phi.X.by.stratum_Psi.age") #p(t),Phi(X + stratum),Psi(stratum) m_2006_p.t_phi.X.by.strat_psi.strat=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p.t,S=S.age.by.strat,Psi=Psi.strat),output=F,adjust=F,model.name="m_2006_p.t_Phi.X.by.stratum_Psi.stratum") #p(t),Phi(X + stratum),Psi(X + stratum) m_2006_p.t_phi.X.by.strat_psi.X.plus.strat=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p.t,S=S.age.by.strat,Psi=Psi.age.plus.strat),output=F,adjust=F,model.name="m_2006_p.t_Phi.X.by.stratum_Psi.X.plus.stratum") #p(t + stratum),Phi(X + stratum),Psi(.) m_2006_p.t.plus.strat_phi.X.by.strat_psi.dot=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p.t.plus.strat,S=S.age.by.strat,Psi=Psi.dot),output=F,adjust=F,model.name="m_2006_p.t.plus.stratum_Phi.X.by.stratum_Psi.dot") #p(t + stratum),Phi(X + stratum),Psi(X) m_2006_p.t.plus.strat_phi.X.by.strat_psi.X=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p.t.plus.strat,S=S.age.by.strat,Psi=Psi.age),output=F,adjust=F,model.name="m_2006_p.t.plus.stratum_Phi.X.by.stratum_Psi.age") #p(t + stratum),Phi(X + stratum),Psi(stratum) m_2006_p.t.plus.strat_phi.X.by.strat_psi.strat=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p.t.plus.strat,S=S.age.by.strat,Psi=Psi.strat),output=F,adjust=F,model.name="m_2006_p.t.plus.stratum_Phi.X.by.stratum_Psi.stratum") #p(t + stratum),Phi(X + stratum),Psi(X + stratum) m_2006_p.t.plus.strat_phi.X.by.strat_psi.X.plus.strat=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p.t.plus.strat,S=S.age.by.strat,Psi=Psi.age.plus.strat),output=F,adjust=F,model.name="m_2006_p.t.plus.stratum_Phi.X.by.stratum_Psi.X.plus.stratum") #p(t * stratum),Phi(X + stratum),Psi(.) m_2006_p.t.by.strat_phi.X.by.strat_psi.dot=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p.t.by.strat,S=S.age.by.strat,Psi=Psi.dot),output=F,adjust=F,model.name="m_2006_p.t.by.stratum_Phi.X.by.stratum_Psi.dot") #p(t * stratum),Phi(X + stratum),Psi(X) m_2006_p.t.by.strat_phi.X.by.strat_psi.X=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p.t.by.strat,S=S.age.by.strat,Psi=Psi.age),output=F,adjust=F,model.name="m_2006_p.t.by.stratum_Phi.X.by.stratum_Psi.age") #p(t * stratum),Phi(X + stratum),Psi(stratum) m_2006_p.t.by.strat_phi.X.by.strat_psi.strat=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p.t.by.strat,S=S.age.by.strat,Psi=Psi.strat),output=F,adjust=F,model.name="m_2006_p.t.by.stratum_Phi.X.by.stratum_Psi.stratum") #p(t * stratum),Phi(X + stratum),Psi(X + stratum) m_2006_p.t.by.strat_phi.X.by.strat_psi.X.plus.strat=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p.t.by.strat,S=S.age.by.strat,Psi=Psi.age.plus.strat),output=F,adjust=F,model.name="m_2006_p.t.by.stratum_Phi.X.by.stratum_Psi.X.plus.stratum") # And here are all the models without the age term being constrained in the phi() model. #p(t),Phi(dot),Psi(.) m_2006_p.t_phi.dot_psi.dot=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p.t,S=S.dot,Psi=Psi.dot),output=F,adjust=F,model.name="m_2006_p.t_Phi.dot_psi.dot") #p(t),Phi(dot),Psi(X) m_2006_p.t_phi.dot_psi.X=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p.t,S=S.dot,Psi=Psi.age),output=F,adjust=F,model.name="m_2006_p.t_Phi.dot_psi.age") #p(t),Phi(dot),Psi(stratum) m_2006_p.t_phi.dot_psi.strat=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p.t,S=S.dot,Psi=Psi.strat),output=F,adjust=F,model.name="m_2006_p.t_Phi.dot_psi.stratum") #p(t),Phi(dot),Psi(X + stratum) m_2006_p.t_phi.dot_psi.X.plus.strat=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p.t,S=S.dot,Psi=Psi.age.plus.strat),output=F,adjust=F,model.name="m_2006_p.t_Phi.dot_psi.X.plus.stratum") #p(t),Phi(X + stratum),Psi(.) m_2006_p.t_phi.strat_psi.dot=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p.t,S=S.strat,Psi=Psi.dot),output=F,adjust=F,model.name="m_2006_p.t_Phi.stratum_Psi.dot") #p(t),Phi(X + stratum),Psi(X) m_2006_p.t_phi.strat_psi.X=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p.t,S=S.strat,Psi=Psi.age),output=F,adjust=F,model.name="m_2006_p.t_Phi.stratum_Psi.age") #p(t),Phi(X + stratum),Psi(stratum) m_2006_p.t_phi.strat_psi.strat=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p.t,S=S.strat,Psi=Psi.strat),output=F,adjust=F,model.name="m_2006_p.t_Phi.stratum_Psi.stratum") #p(t),Phi(X + stratum),Psi(X + stratum) m_2006_p.t_phi.strat_psi.X.plus.strat=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p.t,S=S.strat,Psi=Psi.age.plus.strat),output=F,adjust=F,model.name="m_2006_p.t_Phi.stratum_Psi.X.plus.stratum") #p(t + stratum),Phi(.),Psi(.) m_2006_p.t.plus.strat_phi.X_psi.dot=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p.t.plus.strat,S=S.dot,Psi=Psi.dot),output=F,adjust=F,model.name="m_2006_p.t.plus.stratum_Phi.dot_Psi.dot") #p(t + stratum),Phi(.),Psi(X) m_2006_p.t.plus.strat_phi.X_psi.X=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p.t.plus.strat,S=S.dot,Psi=Psi.age),output=F,adjust=F,model.name="m_2006_p.t.plus.stratum_Phi.dot_Psi.age") #p(t + stratum),Phi(.),Psi(stratum) m_2006_p.t.plus.strat_phi.X_psi.strat=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p.t.plus.strat,S=S.dot,Psi=Psi.strat),output=F,adjust=F,model.name="m_2006_p.t.plus.stratum_Phi.dot_Psi.stratum") #p(t + stratum),Phi(.),Psi(X + stratum) m_2006_p.t.plus.strat_phi.X_psi.X.plus.strat=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p.t.plus.strat,S=S.dot,Psi=Psi.age.plus.strat),output=F,adjust=F,model.name="m_2006_p.t.plus.stratum_Phi.dot_Psi.X.plus.stratum") #p(t + stratum),Phi(stratum),Psi(.) m_2006_p.t.plus.strat_phi.strat_psi.dot=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p.t.plus.strat,S=S.strat,Psi=Psi.dot),output=F,adjust=F,model.name="m_2006_p.t.plus.stratum_Phi.stratum_Psi.dot") #p(t + stratum),Phi(stratum),Psi(X) m_2006_p.t.plus.strat_phi.strat_psi.X=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p.t.plus.strat,S=S.strat,Psi=Psi.age),output=F,adjust=F,model.name="m_2006_p.t.plus.stratum_Phi.stratum_Psi.age") #p(t + stratum),Phi(stratum),Psi(stratum) m_2006_p.t.plus.strat_phi.strat_psi.strat=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p.t.plus.strat,S=S.strat,Psi=Psi.strat),output=F,adjust=F,model.name="m_2006_p.t.plus.stratum_Phi.stratum_Psi.stratum") #p(t + stratum),Phi(stratum),Psi(X + stratum) m_2006_p.t.plus.strat_phi.strat_psi.X.plus.strat=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p.t.plus.strat,S=S.strat,Psi=Psi.age.plus.strat),output=F,adjust=F,model.name="m_2006_p.t.plus.stratum_Phi.stratum_Psi.X.plus.stratum") #p(t * stratum),Phi(.),Psi(.) m_2006_p.t.by.strat_phi.dot_psi.dot=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p.t.by.strat,S=S.dot,Psi=Psi.dot),output=F,adjust=F,model.name="m_2006_p.t.by.stratum_Phi.dot_psi.dot") #p(t * stratum),Phi(.),Psi(X) m_2006_p.t.by.strat_phi.dot_psi.X=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p.t.by.strat,S=S.dot,Psi=Psi.age),output=F,adjust=F,model.name="m_2006_p.t.by.stratum_Phi.dot_psi.X") #p(t * stratum),Phi(.),Psi(stratum) m_2006_p.t.by.strat_phi.dot_psi.strat=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p.t.by.strat,S=S.dot,Psi=Psi.strat),output=F,adjust=F,model.name="m_2006_p.t.by.stratum_Phi.dot_psi.stratum") #p(t * stratum),Phi(.),Psi(X + stratum) m_2006_p.t.by.strat_phi.dot_psi.X.plus.strat=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p.t.by.strat,S=S.dot,Psi=Psi.age.plus.strat),output=F,adjust=F,model.name="m_2006_p.t.by.stratum_Phi.dot_psi.X.plus.stratum") #p(t * stratum),Phi(stratum),Psi(.) m_2006_p.t.by.strat_phi.strat_psi.dot=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p.t.by.strat,S=S.strat,Psi=Psi.dot),output=F,adjust=F,model.name="m_2006_p.t.by.stratum_Phi.stratum_Psi.dot") #p(t * stratum),Phi(stratum),Psi(X) m_2006_p.t.by.strat_phi.strat_psi.X=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p.t.by.strat,S=S.strat,Psi=Psi.age),output=F,adjust=F,model.name="m_2006_p.t.by.stratum_Phi.stratum_Psi.age") #p(t * stratum),Phi(stratum),Psi(stratum) m_2006_p.t.by.strat_phi.strat_psi.strat=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p.t.by.strat,S=S.strat,Psi=Psi.strat),output=F,adjust=F,model.name="m_2006_p.t.by.stratum_Phi.stratum_Psi.stratum") #p(t * stratum),Phi(stratum),Psi(X + stratum) m_2006_p.t.by.strat_phi.strat_psi.X.plus.strat=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p.t.by.strat,S=S.strat,Psi=Psi.age.plus.strat),output=F,adjust=F,model.name="m_2006_p.t.by.stratum_Phi.stratum_Psi.X.plus.stratum") # Collect models m_2006_models<-collect.models(lx=c("m_2006_p.t_phi.X_psi.dot","m_2006_p.t_phi.X_psi.X","m_2006_p.t_phi.X_psi.strat","m_2006_p.t_phi.X_psi.X.plus.strat","m_2006_p.t_phi.X.plus.strat_psi.dot","m_2006_p.t_phi.X.plus.strat_psi.X","m_2006_p.t_phi.X.plus.strat_psi.strat","m_2006_p.t_phi.X.plus.strat_psi.X.plus.strat","m_2006_p.t.plus.strat_phi.X_psi.dot","m_2006_p.t.plus.strat_phi.X_psi.X","m_2006_p.t.plus.strat_phi.X_psi.strat","m_2006_p.t.plus.strat_phi.X_psi.X.plus.strat","m_2006_p.t.plus.strat_phi.X.plus.strat_psi.dot","m_2006_p.t.plus.strat_phi.X.plus.strat_psi.X","m_2006_p.t.plus.strat_phi.X.plus.strat_psi.strat","m_2006_p.t.plus.strat_phi.X.plus.strat_psi.X.plus.strat","m_2006_p.t.by.strat_phi.X_psi.dot","m_2006_p.t.by.strat_phi.X_psi.X","m_2006_p.t.by.strat_phi.X_psi.strat","m_2006_p.t.by.strat_phi.X_psi.X.plus.strat","m_2006_p.t.by.strat_phi.X.plus.strat_psi.dot","m_2006_p.t.by.strat_phi.X.plus.strat_psi.X","m_2006_p.t.by.strat_phi.X.plus.strat_psi.strat","m_2006_p.t.by.strat_phi.X.plus.strat_psi.X.plus.strat","m_2006_p.t_phi.X.by.strat_psi.dot","m_2006_p.t_phi.X.by.strat_psi.X","m_2006_p.t_phi.X.by.strat_psi.strat","m_2006_p.t_phi.X.by.strat_psi.X.plus.strat","m_2006_p.t.plus.strat_phi.X.by.strat_psi.dot","m_2006_p.t.plus.strat_phi.X.by.strat_psi.X","m_2006_p.t.plus.strat_phi.X.by.strat_psi.strat","m_2006_p.t.plus.strat_phi.X.by.strat_psi.X.plus.strat","m_2006_p.t.by.strat_phi.X.by.strat_psi.dot","m_2006_p.t.by.strat_phi.X.by.strat_psi.X","m_2006_p.t.by.strat_phi.X.by.strat_psi.strat","m_2006_p.t.by.strat_phi.X.by.strat_psi.X.plus.strat","m_2006_p.t_phi.dot_psi.dot","m_2006_p.t_phi.dot_psi.X","m_2006_p.t_phi.dot_psi.strat","m_2006_p.t_phi.dot_psi.X.plus.strat","m_2006_p.t_phi.strat_psi.dot","m_2006_p.t_phi.strat_psi.X","m_2006_p.t_phi.strat_psi.strat","m_2006_p.t_phi.strat_psi.X.plus.strat","m_2006_p.t.plus.strat_phi.X_psi.dot","m_2006_p.t.plus.strat_phi.X_psi.X","m_2006_p.t.plus.strat_phi.X_psi.strat","m_2006_p.t.plus.strat_phi.X_psi.X.plus.strat","m_2006_p.t.plus.strat_phi.strat_psi.dot","m_2006_p.t.plus.strat_phi.strat_psi.X","m_2006_p.t.plus.strat_phi.strat_psi.strat","m_2006_p.t.plus.strat_phi.strat_psi.X.plus.strat","m_2006_p.t.by.strat_phi.dot_psi.dot","m_2006_p.t.by.strat_phi.dot_psi.X","m_2006_p.t.by.strat_phi.dot_psi.strat","m_2006_p.t.by.strat_phi.dot_psi.X.plus.strat","m_2006_p.t.by.strat_phi.strat_psi.dot","m_2006_p.t.by.strat_phi.strat_psi.X","m_2006_p.t.by.strat_phi.strat_psi.strat","m_2006_p.t.by.strat_phi.strat_psi.X.plus.strat")) write.table(m_2006_models[61],"...") # Saving the workspace so the models do not have to be repeated each time #save.image("...") ################ # Females 2005 # ################ multistrat_f_2005<-import.chdata("...", header = TRUE, field.names = NULL, field.types = NULL) f_2005.process=process.data(multistrat_f_2005,model="Multistrata") f_2005.ddl=make.design.data(f_2005.process) #p(t),Phi(X),Psi(.) f_2005_p.t_phi.X_psi.dot=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p.t,S=S.age,Psi=Psi.dot),output=F,adjust=F,model.name="f_2005_p.t_Phi.X_Psi.dot") #p(t),Phi(X),Psi(X) f_2005_p.t_phi.X_psi.X=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p.t,S=S.age,Psi=Psi.age),output=F,adjust=F,model.name="f_2005_p.t_Phi.X_Psi.age") #p(t),Phi(X),Psi(stratum) f_2005_p.t_phi.X_psi.strat=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p.t,S=S.age,Psi=Psi.strat),output=F,adjust=F,model.name="f_2005_p.t_Phi.X_Psi.stratum") #p(t),Phi(X),Psi(X + stratum) f_2005_p.t_phi.X_psi.X.plus.strat=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p.t,S=S.age,Psi=Psi.age.plus.strat),output=F,adjust=F,model.name="f_2005_p.t_Phi.X_Psi.X.plus.stratum") #p(t),Phi(X + stratum),Psi(.) f_2005_p.t_phi.X.plus.strat_psi.dot=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p.t,S=S.age.plus.strat,Psi=Psi.dot),output=F,adjust=F,model.name="f_2005_p.t_Phi.X.plus.stratum_Psi.dot") #p(t),Phi(X + stratum),Psi(X) f_2005_p.t_phi.X.plus.strat_psi.X=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p.t,S=S.age.plus.strat,Psi=Psi.age),output=F,adjust=F,model.name="f_2005_p.t_Phi.X.plus.stratum_Psi.age") #p(t),Phi(X + stratum),Psi(stratum) f_2005_p.t_phi.X.plus.strat_psi.strat=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p.t,S=S.age.plus.strat,Psi=Psi.strat),output=F,adjust=F,model.name="f_2005_p.t_Phi.X.plus.stratum_Psi.stratum") #p(t),Phi(X + stratum),Psi(X + stratum) f_2005_p.t_phi.X.plus.strat_psi.X.plus.strat=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p.t,S=S.age.plus.strat,Psi=Psi.age.plus.strat),output=F,adjust=F,model.name="f_2005_p.t_Phi.X.plus.stratum_Psi.X.plus.stratum") #p(t + stratum),Phi(X),Psi(.) f_2005_p.t.plus.strat_phi.X_psi.dot=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p.t.plus.strat,S=S.age,Psi=Psi.dot),output=F,adjust=F,model.name="f_2005_p.t.plus.stratum_Phi.X_Psi.dot") #p(t + stratum),Phi(X),Psi(X) f_2005_p.t.plus.strat_phi.X_psi.X=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p.t.plus.strat,S=S.age,Psi=Psi.age),output=F,adjust=F,model.name="f_2005_p.t.plus.stratum_Phi.X_Psi.age") #p(t + stratum),Phi(X),Psi(stratum) f_2005_p.t.plus.strat_phi.X_psi.strat=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p.t.plus.strat,S=S.age,Psi=Psi.strat),output=F,adjust=F,model.name="f_2005_p.t.plus.stratum_Phi.X_Psi.stratum") #p(t + stratum),Phi(X),Psi(X + stratum) f_2005_p.t.plus.strat_phi.X_psi.X.plus.strat=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p.t.plus.strat,S=S.age,Psi=Psi.age.plus.strat),output=F,adjust=F,model.name="f_2005_p.t.plus.stratum_Phi.X_Psi.X.plus.stratum") #p(t + stratum),Phi(X + stratum),Psi(.) f_2005_p.t.plus.strat_phi.X.plus.strat_psi.dot=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p.t.plus.strat,S=S.age.plus.strat,Psi=Psi.dot),output=F,adjust=F,model.name="f_2005_p.t.plus.stratum_Phi.X.plus.stratum_Psi.dot") #p(t + stratum),Phi(X + stratum),Psi(X) f_2005_p.t.plus.strat_phi.X.plus.strat_psi.X=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p.t.plus.strat,S=S.age.plus.strat,Psi=Psi.age),output=F,adjust=F,model.name="f_2005_p.t.plus.stratum_Phi.X.plus.stratum_Psi.age") #p(t + stratum),Phi(X + stratum),Psi(stratum) f_2005_p.t.plus.strat_phi.X.plus.strat_psi.strat=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p.t.plus.strat,S=S.age.plus.strat,Psi=Psi.strat),output=F,adjust=F,model.name="f_2005_p.t.plus.stratum_Phi.X.plus.stratum_Psi.stratum") #p(t + stratum),Phi(X + stratum),Psi(X + stratum) f_2005_p.t.plus.strat_phi.X.plus.strat_psi.X.plus.strat=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p.t.plus.strat,S=S.age.plus.strat,Psi=Psi.age.plus.strat),output=F,adjust=F,model.name="f_2005_p.t.plus.stratum_Phi.X.plus.stratum_Psi.X.plus.stratum") #p(t * stratum),Phi(X),Psi(.) f_2005_p.t.by.strat_phi.X_psi.dot=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p.t.by.strat,S=S.age,Psi=Psi.dot),output=F,adjust=F,model.name="f_2005_p.t.by.stratum_Phi.X_Psi.dot") #p(t * stratum),Phi(X),Psi(X) f_2005_p.t.by.strat_phi.X_psi.X=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p.t.by.strat,S=S.age,Psi=Psi.age),output=F,adjust=F,model.name="f_2005_p.t.by.stratum_Phi.X_Psi.X") #p(t * stratum),Phi(X),Psi(stratum) f_2005_p.t.by.strat_phi.X_psi.strat=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p.t.by.strat,S=S.age,Psi=Psi.strat),output=F,adjust=F,model.name="f_2005_p.t.by.stratum_Phi.X_Psi.stratum") #p(t * stratum),Phi(X),Psi(X + stratum) f_2005_p.t.by.strat_phi.X_psi.X.plus.strat=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p.t.by.strat,S=S.age,Psi=Psi.age.plus.strat),output=F,adjust=F,model.name="f_2005_p.t.by.stratum_Phi.X_Psi.X.plus.stratum") #p(t * stratum),Phi(X + stratum),Psi(.) f_2005_p.t.by.strat_phi.X.plus.strat_psi.dot=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p.t.by.strat,S=S.age.plus.strat,Psi=Psi.dot),output=F,adjust=F,model.name="f_2005_p.t.by.stratum_Phi.X.plus.stratum_Psi.dot") #p(t * stratum),Phi(X + stratum),Psi(X) f_2005_p.t.by.strat_phi.X.plus.strat_psi.X=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p.t.by.strat,S=S.age.plus.strat,Psi=Psi.age),output=F,adjust=F,model.name="f_2005_p.t.by.stratum_Phi.X.plus.stratum_Psi.age") #p(t * stratum),Phi(X + stratum),Psi(stratum) f_2005_p.t.by.strat_phi.X.plus.strat_psi.strat=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p.t.by.strat,S=S.age.plus.strat,Psi=Psi.strat),output=F,adjust=F,model.name="f_2005_p.t.by.stratum_Phi.X.plus.stratum_Psi.stratum") #p(t * stratum),Phi(X + stratum),Psi(X + stratum) f_2005_p.t.by.strat_phi.X.plus.strat_psi.X.plus.strat=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p.t.by.strat,S=S.age.plus.strat,Psi=Psi.age.plus.strat),output=F,adjust=F,model.name="f_2005_p.t.by.stratum_Phi.X.plus.stratum_Psi.X.plus.stratum") #p(t),Phi(X + stratum),Psi(.) f_2005_p.t_phi.X.by.strat_psi.dot=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p.t,S=S.age.by.strat,Psi=Psi.dot),output=F,adjust=F,model.name="f_2005_p.t_Phi.X.by.stratum_Psi.dot") #p(t),Phi(X + stratum),Psi(X) f_2005_p.t_phi.X.by.strat_psi.X=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p.t,S=S.age.by.strat,Psi=Psi.age),output=F,adjust=F,model.name="f_2005_p.t_Phi.X.by.stratum_Psi.age") #p(t),Phi(X + stratum),Psi(stratum) f_2005_p.t_phi.X.by.strat_psi.strat=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p.t,S=S.age.by.strat,Psi=Psi.strat),output=F,adjust=F,model.name="f_2005_p.t_Phi.X.by.stratum_Psi.stratum") #p(t),Phi(X + stratum),Psi(X + stratum) f_2005_p.t_phi.X.by.strat_psi.X.plus.strat=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p.t,S=S.age.by.strat,Psi=Psi.age.plus.strat),output=F,adjust=F,model.name="f_2005_p.t_Phi.X.by.stratum_Psi.X.plus.stratum") #p(t + stratum),Phi(X + stratum),Psi(.) f_2005_p.t.plus.strat_phi.X.by.strat_psi.dot=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p.t.plus.strat,S=S.age.by.strat,Psi=Psi.dot),output=F,adjust=F,model.name="f_2005_p.t.plus.stratum_Phi.X.by.stratum_Psi.dot") #p(t + stratum),Phi(X + stratum),Psi(X) f_2005_p.t.plus.strat_phi.X.by.strat_psi.X=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p.t.plus.strat,S=S.age.by.strat,Psi=Psi.age),output=F,adjust=F,model.name="f_2005_p.t.plus.stratum_Phi.X.by.stratum_Psi.age") #p(t + stratum),Phi(X + stratum),Psi(stratum) f_2005_p.t.plus.strat_phi.X.by.strat_psi.strat=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p.t.plus.strat,S=S.age.by.strat,Psi=Psi.strat),output=F,adjust=F,model.name="f_2005_p.t.plus.stratum_Phi.X.by.stratum_Psi.stratum") #p(t + stratum),Phi(X + stratum),Psi(X + stratum) f_2005_p.t.plus.strat_phi.X.by.strat_psi.X.plus.strat=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p.t.plus.strat,S=S.age.by.strat,Psi=Psi.age.plus.strat),output=F,adjust=F,model.name="f_2005_p.t.plus.stratum_Phi.X.by.stratum_Psi.X.plus.stratum") #p(t * stratum),Phi(X + stratum),Psi(.) f_2005_p.t.by.strat_phi.X.by.strat_psi.dot=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p.t.by.strat,S=S.age.by.strat,Psi=Psi.dot),output=F,adjust=F,model.name="f_2005_p.t.by.stratum_Phi.X.by.stratum_Psi.dot") #p(t * stratum),Phi(X + stratum),Psi(X) f_2005_p.t.by.strat_phi.X.by.strat_psi.X=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p.t.by.strat,S=S.age.by.strat,Psi=Psi.age),output=F,adjust=F,model.name="f_2005_p.t.by.stratum_Phi.X.by.stratum_Psi.age") #p(t * stratum),Phi(X + stratum),Psi(stratum) f_2005_p.t.by.strat_phi.X.by.strat_psi.strat=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p.t.by.strat,S=S.age.by.strat,Psi=Psi.strat),output=F,adjust=F,model.name="f_2005_p.t.by.stratum_Phi.X.by.stratum_Psi.stratum") #p(t * stratum),Phi(X + stratum),Psi(X + stratum) f_2005_p.t.by.strat_phi.X.by.strat_psi.X.plus.strat=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p.t.by.strat,S=S.age.by.strat,Psi=Psi.age.plus.strat),output=F,adjust=F,model.name="f_2005_p.t.by.stratum_Phi.X.by.stratum_Psi.X.plus.stratum") # And here are all the models without the age term being constrained in the phi() model. #p(t),Phi(dot),Psi(.) f_2005_p.t_phi.dot_psi.dot=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p.t,S=S.dot,Psi=Psi.dot),output=F,adjust=F,model.name="f_2005_p.t_Phi.dot_psi.dot") #p(t),Phi(dot),Psi(X) f_2005_p.t_phi.dot_psi.X=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p.t,S=S.dot,Psi=Psi.age),output=F,adjust=F,model.name="f_2005_p.t_Phi.dot_psi.age") #p(t),Phi(dot),Psi(stratum) f_2005_p.t_phi.dot_psi.strat=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p.t,S=S.dot,Psi=Psi.strat),output=F,adjust=F,model.name="f_2005_p.t_Phi.dot_psi.stratum") #p(t),Phi(dot),Psi(X + stratum) f_2005_p.t_phi.dot_psi.X.plus.strat=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p.t,S=S.dot,Psi=Psi.age.plus.strat),output=F,adjust=F,model.name="f_2005_p.t_Phi.dot_psi.X.plus.stratum") #p(t),Phi(X + stratum),Psi(.) f_2005_p.t_phi.strat_psi.dot=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p.t,S=S.strat,Psi=Psi.dot),output=F,adjust=F,model.name="f_2005_p.t_Phi.stratum_Psi.dot") #p(t),Phi(X + stratum),Psi(X) f_2005_p.t_phi.strat_psi.X=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p.t,S=S.strat,Psi=Psi.age),output=F,adjust=F,model.name="f_2005_p.t_Phi.stratum_Psi.age") #p(t),Phi(X + stratum),Psi(stratum) f_2005_p.t_phi.strat_psi.strat=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p.t,S=S.strat,Psi=Psi.strat),output=F,adjust=F,model.name="f_2005_p.t_Phi.stratum_Psi.stratum") #p(t),Phi(X + stratum),Psi(X + stratum) f_2005_p.t_phi.strat_psi.X.plus.strat=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p.t,S=S.strat,Psi=Psi.age.plus.strat),output=F,adjust=F,model.name="f_2005_p.t_Phi.stratum_Psi.X.plus.stratum") #p(t + stratum),Phi(.),Psi(.) f_2005_p.t.plus.strat_phi.X_psi.dot=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p.t.plus.strat,S=S.dot,Psi=Psi.dot),output=F,adjust=F,model.name="f_2005_p.t.plus.stratum_Phi.dot_Psi.dot") #p(t + stratum),Phi(.),Psi(X) f_2005_p.t.plus.strat_phi.X_psi.X=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p.t.plus.strat,S=S.dot,Psi=Psi.age),output=F,adjust=F,model.name="f_2005_p.t.plus.stratum_Phi.dot_Psi.age") #p(t + stratum),Phi(.),Psi(stratum) f_2005_p.t.plus.strat_phi.X_psi.strat=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p.t.plus.strat,S=S.dot,Psi=Psi.strat),output=F,adjust=F,model.name="f_2005_p.t.plus.stratum_Phi.dot_Psi.stratum") #p(t + stratum),Phi(.),Psi(X + stratum) f_2005_p.t.plus.strat_phi.X_psi.X.plus.strat=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p.t.plus.strat,S=S.dot,Psi=Psi.age.plus.strat),output=F,adjust=F,model.name="f_2005_p.t.plus.stratum_Phi.dot_Psi.X.plus.stratum") #p(t + stratum),Phi(stratum),Psi(.) f_2005_p.t.plus.strat_phi.strat_psi.dot=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p.t.plus.strat,S=S.strat,Psi=Psi.dot),output=F,adjust=F,model.name="f_2005_p.t.plus.stratum_Phi.stratum_Psi.dot") #p(t + stratum),Phi(stratum),Psi(X) f_2005_p.t.plus.strat_phi.strat_psi.X=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p.t.plus.strat,S=S.strat,Psi=Psi.age),output=F,adjust=F,model.name="f_2005_p.t.plus.stratum_Phi.stratum_Psi.age") #p(t + stratum),Phi(stratum),Psi(stratum) f_2005_p.t.plus.strat_phi.strat_psi.strat=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p.t.plus.strat,S=S.strat,Psi=Psi.strat),output=F,adjust=F,model.name="f_2005_p.t.plus.stratum_Phi.stratum_Psi.stratum") #p(t + stratum),Phi(stratum),Psi(X + stratum) f_2005_p.t.plus.strat_phi.strat_psi.X.plus.strat=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p.t.plus.strat,S=S.strat,Psi=Psi.age.plus.strat),output=F,adjust=F,model.name="f_2005_p.t.plus.stratum_Phi.stratum_Psi.X.plus.stratum") #p(t * stratum),Phi(.),Psi(.) f_2005_p.t.by.strat_phi.dot_psi.dot=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p.t.by.strat,S=S.dot,Psi=Psi.dot),output=F,adjust=F,model.name="f_2005_p.t.by.stratum_Phi.dot_psi.dot") #p(t * stratum),Phi(.),Psi(X) f_2005_p.t.by.strat_phi.dot_psi.X=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p.t.by.strat,S=S.dot,Psi=Psi.age),output=F,adjust=F,model.name="f_2005_p.t.by.stratum_Phi.dot_psi.X") #p(t * stratum),Phi(.),Psi(stratum) f_2005_p.t.by.strat_phi.dot_psi.strat=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p.t.by.strat,S=S.dot,Psi=Psi.strat),output=F,adjust=F,model.name="f_2005_p.t.by.stratum_Phi.dot_psi.stratum") #p(t * stratum),Phi(.),Psi(X + stratum) f_2005_p.t.by.strat_phi.dot_psi.X.plus.strat=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p.t.by.strat,S=S.dot,Psi=Psi.age.plus.strat),output=F,adjust=F,model.name="f_2005_p.t.by.stratum_Phi.dot_psi.X.plus.stratum") #p(t * stratum),Phi(stratum),Psi(.) f_2005_p.t.by.strat_phi.strat_psi.dot=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p.t.by.strat,S=S.strat,Psi=Psi.dot),output=F,adjust=F,model.name="f_2005_p.t.by.stratum_Phi.stratum_Psi.dot") #p(t * stratum),Phi(stratum),Psi(X) f_2005_p.t.by.strat_phi.strat_psi.X=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p.t.by.strat,S=S.strat,Psi=Psi.age),output=F,adjust=F,model.name="f_2005_p.t.by.stratum_Phi.stratum_Psi.age") #p(t * stratum),Phi(stratum),Psi(stratum) f_2005_p.t.by.strat_phi.strat_psi.strat=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p.t.by.strat,S=S.strat,Psi=Psi.strat),output=F,adjust=F,model.name="f_2005_p.t.by.stratum_Phi.stratum_Psi.stratum") #p(t * stratum),Phi(stratum),Psi(X + stratum) f_2005_p.t.by.strat_phi.strat_psi.X.plus.strat=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p.t.by.strat,S=S.strat,Psi=Psi.age.plus.strat),output=F,adjust=F,model.name="f_2005_p.t.by.stratum_Phi.stratum_Psi.X.plus.stratum") # Collect models f_2005_models<-collect.models(lx=c("f_2005_p.t_phi.X_psi.dot","f_2005_p.t_phi.X_psi.X","f_2005_p.t_phi.X_psi.strat","f_2005_p.t_phi.X_psi.X.plus.strat","f_2005_p.t_phi.X.plus.strat_psi.dot","f_2005_p.t_phi.X.plus.strat_psi.X","f_2005_p.t_phi.X.plus.strat_psi.strat","f_2005_p.t_phi.X.plus.strat_psi.X.plus.strat","f_2005_p.t.plus.strat_phi.X_psi.dot","f_2005_p.t.plus.strat_phi.X_psi.X","f_2005_p.t.plus.strat_phi.X_psi.strat","f_2005_p.t.plus.strat_phi.X_psi.X.plus.strat","f_2005_p.t.plus.strat_phi.X.plus.strat_psi.dot","f_2005_p.t.plus.strat_phi.X.plus.strat_psi.X","f_2005_p.t.plus.strat_phi.X.plus.strat_psi.strat","f_2005_p.t.plus.strat_phi.X.plus.strat_psi.X.plus.strat","f_2005_p.t.by.strat_phi.X_psi.dot","f_2005_p.t.by.strat_phi.X_psi.X","f_2005_p.t.by.strat_phi.X_psi.strat","f_2005_p.t.by.strat_phi.X_psi.X.plus.strat","f_2005_p.t.by.strat_phi.X.plus.strat_psi.dot","f_2005_p.t.by.strat_phi.X.plus.strat_psi.X","f_2005_p.t.by.strat_phi.X.plus.strat_psi.strat","f_2005_p.t.by.strat_phi.X.plus.strat_psi.X.plus.strat","f_2005_p.t_phi.X.by.strat_psi.dot","f_2005_p.t_phi.X.by.strat_psi.X","f_2005_p.t_phi.X.by.strat_psi.strat","f_2005_p.t_phi.X.by.strat_psi.X.plus.strat","f_2005_p.t.plus.strat_phi.X.by.strat_psi.dot","f_2005_p.t.plus.strat_phi.X.by.strat_psi.X","f_2005_p.t.plus.strat_phi.X.by.strat_psi.strat","f_2005_p.t.plus.strat_phi.X.by.strat_psi.X.plus.strat","f_2005_p.t.by.strat_phi.X.by.strat_psi.dot","f_2005_p.t.by.strat_phi.X.by.strat_psi.X","f_2005_p.t.by.strat_phi.X.by.strat_psi.strat","f_2005_p.t.by.strat_phi.X.by.strat_psi.X.plus.strat","f_2005_p.t_phi.dot_psi.dot","f_2005_p.t_phi.dot_psi.X","f_2005_p.t_phi.dot_psi.strat","f_2005_p.t_phi.dot_psi.X.plus.strat","f_2005_p.t_phi.strat_psi.dot","f_2005_p.t_phi.strat_psi.X","f_2005_p.t_phi.strat_psi.strat","f_2005_p.t_phi.strat_psi.X.plus.strat","f_2005_p.t.plus.strat_phi.X_psi.dot","f_2005_p.t.plus.strat_phi.X_psi.X","f_2005_p.t.plus.strat_phi.X_psi.strat","f_2005_p.t.plus.strat_phi.X_psi.X.plus.strat","f_2005_p.t.plus.strat_phi.strat_psi.dot","f_2005_p.t.plus.strat_phi.strat_psi.X","f_2005_p.t.plus.strat_phi.strat_psi.strat","f_2005_p.t.plus.strat_phi.strat_psi.X.plus.strat","f_2005_p.t.by.strat_phi.dot_psi.dot","f_2005_p.t.by.strat_phi.dot_psi.X","f_2005_p.t.by.strat_phi.dot_psi.strat","f_2005_p.t.by.strat_phi.dot_psi.X.plus.strat","f_2005_p.t.by.strat_phi.strat_psi.dot","f_2005_p.t.by.strat_phi.strat_psi.X","f_2005_p.t.by.strat_phi.strat_psi.strat","f_2005_p.t.by.strat_phi.strat_psi.X.plus.strat")) write.table(f_2005_models[61],"...") # Saving the workspace so the models do not have to be repeated each time save.image("...") ################ # Females 2006 # ################ multistrat_f_2006<-import.chdata("...", header = TRUE, field.names = NULL, field.types = NULL) f_2006.process=process.data(multistrat_f_2006,model="Multistrata") f_2006.ddl=make.design.data(f_2006.process) #p(t),Phi(X),Psi(.) f_2006_p.t_phi.X_psi.dot=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p.t,S=S.age,Psi=Psi.dot),output=F,adjust=F,model.name="f_2006_p.t_Phi.X_Psi.dot") #p(t),Phi(X),Psi(X) f_2006_p.t_phi.X_psi.X=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p.t,S=S.age,Psi=Psi.age),output=F,adjust=F,model.name="f_2006_p.t_Phi.X_Psi.age") #p(t),Phi(X),Psi(stratum) f_2006_p.t_phi.X_psi.strat=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p.t,S=S.age,Psi=Psi.strat),output=F,adjust=F,model.name="f_2006_p.t_Phi.X_Psi.stratum") #p(t),Phi(X),Psi(X + stratum) f_2006_p.t_phi.X_psi.X.plus.strat=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p.t,S=S.age,Psi=Psi.age.plus.strat),output=F,adjust=F,model.name="f_2006_p.t_Phi.X_Psi.X.plus.stratum") #p(t),Phi(X + stratum),Psi(.) f_2006_p.t_phi.X.plus.strat_psi.dot=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p.t,S=S.age.plus.strat,Psi=Psi.dot),output=F,adjust=F,model.name="f_2006_p.t_Phi.X.plus.stratum_Psi.dot") #p(t),Phi(X + stratum),Psi(X) f_2006_p.t_phi.X.plus.strat_psi.X=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p.t,S=S.age.plus.strat,Psi=Psi.age),output=F,adjust=F,model.name="f_2006_p.t_Phi.X.plus.stratum_Psi.age") #p(t),Phi(X + stratum),Psi(stratum) f_2006_p.t_phi.X.plus.strat_psi.strat=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p.t,S=S.age.plus.strat,Psi=Psi.strat),output=F,adjust=F,model.name="f_2006_p.t_Phi.X.plus.stratum_Psi.stratum") #p(t),Phi(X + stratum),Psi(X + stratum) f_2006_p.t_phi.X.plus.strat_psi.X.plus.strat=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p.t,S=S.age.plus.strat,Psi=Psi.age.plus.strat),output=F,adjust=F,model.name="f_2006_p.t_Phi.X.plus.stratum_Psi.X.plus.stratum") #p(t + stratum),Phi(X),Psi(.) f_2006_p.t.plus.strat_phi.X_psi.dot=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p.t.plus.strat,S=S.age,Psi=Psi.dot),output=F,adjust=F,model.name="f_2006_p.t.plus.stratum_Phi.X_Psi.dot") #p(t + stratum),Phi(X),Psi(X) f_2006_p.t.plus.strat_phi.X_psi.X=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p.t.plus.strat,S=S.age,Psi=Psi.age),output=F,adjust=F,model.name="f_2006_p.t.plus.stratum_Phi.X_Psi.age") #p(t + stratum),Phi(X),Psi(stratum) f_2006_p.t.plus.strat_phi.X_psi.strat=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p.t.plus.strat,S=S.age,Psi=Psi.strat),output=F,adjust=F,model.name="f_2006_p.t.plus.stratum_Phi.X_Psi.stratum") #p(t + stratum),Phi(X),Psi(X + stratum) f_2006_p.t.plus.strat_phi.X_psi.X.plus.strat=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p.t.plus.strat,S=S.age,Psi=Psi.age.plus.strat),output=F,adjust=F,model.name="f_2006_p.t.plus.stratum_Phi.X_Psi.X.plus.stratum") #p(t + stratum),Phi(X + stratum),Psi(.) f_2006_p.t.plus.strat_phi.X.plus.strat_psi.dot=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p.t.plus.strat,S=S.age.plus.strat,Psi=Psi.dot),output=F,adjust=F,model.name="f_2006_p.t.plus.stratum_Phi.X.plus.stratum_Psi.dot") #p(t + stratum),Phi(X + stratum),Psi(X) f_2006_p.t.plus.strat_phi.X.plus.strat_psi.X=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p.t.plus.strat,S=S.age.plus.strat,Psi=Psi.age),output=F,adjust=F,model.name="f_2006_p.t.plus.stratum_Phi.X.plus.stratum_Psi.age") #p(t + stratum),Phi(X + stratum),Psi(stratum) f_2006_p.t.plus.strat_phi.X.plus.strat_psi.strat=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p.t.plus.strat,S=S.age.plus.strat,Psi=Psi.strat),output=F,adjust=F,model.name="f_2006_p.t.plus.stratum_Phi.X.plus.stratum_Psi.stratum") #p(t + stratum),Phi(X + stratum),Psi(X + stratum) f_2006_p.t.plus.strat_phi.X.plus.strat_psi.X.plus.strat=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p.t.plus.strat,S=S.age.plus.strat,Psi=Psi.age.plus.strat),output=F,adjust=F,model.name="f_2006_p.t.plus.stratum_Phi.X.plus.stratum_Psi.X.plus.stratum") #p(t * stratum),Phi(X),Psi(.) f_2006_p.t.by.strat_phi.X_psi.dot=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p.t.by.strat,S=S.age,Psi=Psi.dot),output=F,adjust=F,model.name="f_2006_p.t.by.stratum_Phi.X_Psi.dot") #p(t * stratum),Phi(X),Psi(X) f_2006_p.t.by.strat_phi.X_psi.X=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p.t.by.strat,S=S.age,Psi=Psi.age),output=F,adjust=F,model.name="f_2006_p.t.by.stratum_Phi.X_Psi.X") #p(t * stratum),Phi(X),Psi(stratum) f_2006_p.t.by.strat_phi.X_psi.strat=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p.t.by.strat,S=S.age,Psi=Psi.strat),output=F,adjust=F,model.name="f_2006_p.t.by.stratum_Phi.X_Psi.stratum") #p(t * stratum),Phi(X),Psi(X + stratum) f_2006_p.t.by.strat_phi.X_psi.X.plus.strat=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p.t.by.strat,S=S.age,Psi=Psi.age.plus.strat),output=F,adjust=F,model.name="f_2006_p.t.by.stratum_Phi.X_Psi.X.plus.stratum") #p(t * stratum),Phi(X + stratum),Psi(.) f_2006_p.t.by.strat_phi.X.plus.strat_psi.dot=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p.t.by.strat,S=S.age.plus.strat,Psi=Psi.dot),output=F,adjust=F,model.name="f_2006_p.t.by.stratum_Phi.X.plus.stratum_Psi.dot") #p(t * stratum),Phi(X + stratum),Psi(X) f_2006_p.t.by.strat_phi.X.plus.strat_psi.X=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p.t.by.strat,S=S.age.plus.strat,Psi=Psi.age),output=F,adjust=F,model.name="f_2006_p.t.by.stratum_Phi.X.plus.stratum_Psi.age") #p(t * stratum),Phi(X + stratum),Psi(stratum) f_2006_p.t.by.strat_phi.X.plus.strat_psi.strat=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p.t.by.strat,S=S.age.plus.strat,Psi=Psi.strat),output=F,adjust=F,model.name="f_2006_p.t.by.stratum_Phi.X.plus.stratum_Psi.stratum") #p(t * stratum),Phi(X + stratum),Psi(X + stratum) f_2006_p.t.by.strat_phi.X.plus.strat_psi.X.plus.strat=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p.t.by.strat,S=S.age.plus.strat,Psi=Psi.age.plus.strat),output=F,adjust=F,model.name="f_2006_p.t.by.stratum_Phi.X.plus.stratum_Psi.X.plus.stratum") #p(t),Phi(X + stratum),Psi(.) f_2006_p.t_phi.X.by.strat_psi.dot=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p.t,S=S.age.by.strat,Psi=Psi.dot),output=F,adjust=F,model.name="f_2006_p.t_Phi.X.by.stratum_Psi.dot") #p(t),Phi(X + stratum),Psi(X) f_2006_p.t_phi.X.by.strat_psi.X=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p.t,S=S.age.by.strat,Psi=Psi.age),output=F,adjust=F,model.name="f_2006_p.t_Phi.X.by.stratum_Psi.age") #p(t),Phi(X + stratum),Psi(stratum) f_2006_p.t_phi.X.by.strat_psi.strat=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p.t,S=S.age.by.strat,Psi=Psi.strat),output=F,adjust=F,model.name="f_2006_p.t_Phi.X.by.stratum_Psi.stratum") #p(t),Phi(X + stratum),Psi(X + stratum) f_2006_p.t_phi.X.by.strat_psi.X.plus.strat=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p.t,S=S.age.by.strat,Psi=Psi.age.plus.strat),output=F,adjust=F,model.name="f_2006_p.t_Phi.X.by.stratum_Psi.X.plus.stratum") #p(t + stratum),Phi(X + stratum),Psi(.) f_2006_p.t.plus.strat_phi.X.by.strat_psi.dot=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p.t.plus.strat,S=S.age.by.strat,Psi=Psi.dot),output=F,adjust=F,model.name="f_2006_p.t.plus.stratum_Phi.X.by.stratum_Psi.dot") #p(t + stratum),Phi(X + stratum),Psi(X) f_2006_p.t.plus.strat_phi.X.by.strat_psi.X=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p.t.plus.strat,S=S.age.by.strat,Psi=Psi.age),output=F,adjust=F,model.name="f_2006_p.t.plus.stratum_Phi.X.by.stratum_Psi.age") #p(t + stratum),Phi(X + stratum),Psi(stratum) f_2006_p.t.plus.strat_phi.X.by.strat_psi.strat=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p.t.plus.strat,S=S.age.by.strat,Psi=Psi.strat),output=F,adjust=F,model.name="f_2006_p.t.plus.stratum_Phi.X.by.stratum_Psi.stratum") #p(t + stratum),Phi(X + stratum),Psi(X + stratum) f_2006_p.t.plus.strat_phi.X.by.strat_psi.X.plus.strat=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p.t.plus.strat,S=S.age.by.strat,Psi=Psi.age.plus.strat),output=F,adjust=F,model.name="f_2006_p.t.plus.stratum_Phi.X.by.stratum_Psi.X.plus.stratum") #p(t * stratum),Phi(X + stratum),Psi(.) f_2006_p.t.by.strat_phi.X.by.strat_psi.dot=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p.t.by.strat,S=S.age.by.strat,Psi=Psi.dot),output=F,adjust=F,model.name="f_2006_p.t.by.stratum_Phi.X.by.stratum_Psi.dot") #p(t * stratum),Phi(X + stratum),Psi(X) f_2006_p.t.by.strat_phi.X.by.strat_psi.X=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p.t.by.strat,S=S.age.by.strat,Psi=Psi.age),output=F,adjust=F,model.name="f_2006_p.t.by.stratum_Phi.X.by.stratum_Psi.age") #p(t * stratum),Phi(X + stratum),Psi(stratum) f_2006_p.t.by.strat_phi.X.by.strat_psi.strat=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p.t.by.strat,S=S.age.by.strat,Psi=Psi.strat),output=F,adjust=F,model.name="f_2006_p.t.by.stratum_Phi.X.by.stratum_Psi.stratum") #p(t * stratum),Phi(X + stratum),Psi(X + stratum) f_2006_p.t.by.strat_phi.X.by.strat_psi.X.plus.strat=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p.t.by.strat,S=S.age.by.strat,Psi=Psi.age.plus.strat),output=F,adjust=F,model.name="f_2006_p.t.by.stratum_Phi.X.by.stratum_Psi.X.plus.stratum") # And here are all the models without the age term being constrained in the phi() model. #p(t),Phi(dot),Psi(.) f_2006_p.t_phi.dot_psi.dot=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p.t,S=S.dot,Psi=Psi.dot),output=F,adjust=F,model.name="f_2006_p.t_Phi.dot_psi.dot") #p(t),Phi(dot),Psi(X) f_2006_p.t_phi.dot_psi.X=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p.t,S=S.dot,Psi=Psi.age),output=F,adjust=F,model.name="f_2006_p.t_Phi.dot_psi.age") #p(t),Phi(dot),Psi(stratum) f_2006_p.t_phi.dot_psi.strat=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p.t,S=S.dot,Psi=Psi.strat),output=F,adjust=F,model.name="f_2006_p.t_Phi.dot_psi.stratum") #p(t),Phi(dot),Psi(X + stratum) f_2006_p.t_phi.dot_psi.X.plus.strat=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p.t,S=S.dot,Psi=Psi.age.plus.strat),output=F,adjust=F,model.name="f_2006_p.t_Phi.dot_psi.X.plus.stratum") #p(t),Phi(X + stratum),Psi(.) f_2006_p.t_phi.strat_psi.dot=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p.t,S=S.strat,Psi=Psi.dot),output=F,adjust=F,model.name="f_2006_p.t_Phi.stratum_Psi.dot") #p(t),Phi(X + stratum),Psi(X) f_2006_p.t_phi.strat_psi.X=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p.t,S=S.strat,Psi=Psi.age),output=F,adjust=F,model.name="f_2006_p.t_Phi.stratum_Psi.age") #p(t),Phi(X + stratum),Psi(stratum) f_2006_p.t_phi.strat_psi.strat=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p.t,S=S.strat,Psi=Psi.strat),output=F,adjust=F,model.name="f_2006_p.t_Phi.stratum_Psi.stratum") #p(t),Phi(X + stratum),Psi(X + stratum) f_2006_p.t_phi.strat_psi.X.plus.strat=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p.t,S=S.strat,Psi=Psi.age.plus.strat),output=F,adjust=F,model.name="f_2006_p.t_Phi.stratum_Psi.X.plus.stratum") #p(t + stratum),Phi(.),Psi(.) f_2006_p.t.plus.strat_phi.X_psi.dot=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p.t.plus.strat,S=S.dot,Psi=Psi.dot),output=F,adjust=F,model.name="f_2006_p.t.plus.stratum_Phi.dot_Psi.dot") #p(t + stratum),Phi(.),Psi(X) f_2006_p.t.plus.strat_phi.X_psi.X=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p.t.plus.strat,S=S.dot,Psi=Psi.age),output=F,adjust=F,model.name="f_2006_p.t.plus.stratum_Phi.dot_Psi.age") #p(t + stratum),Phi(.),Psi(stratum) f_2006_p.t.plus.strat_phi.X_psi.strat=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p.t.plus.strat,S=S.dot,Psi=Psi.strat),output=F,adjust=F,model.name="f_2006_p.t.plus.stratum_Phi.dot_Psi.stratum") #p(t + stratum),Phi(.),Psi(X + stratum) f_2006_p.t.plus.strat_phi.X_psi.X.plus.strat=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p.t.plus.strat,S=S.dot,Psi=Psi.age.plus.strat),output=F,adjust=F,model.name="f_2006_p.t.plus.stratum_Phi.dot_Psi.X.plus.stratum") #p(t + stratum),Phi(stratum),Psi(.) f_2006_p.t.plus.strat_phi.strat_psi.dot=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p.t.plus.strat,S=S.strat,Psi=Psi.dot),output=F,adjust=F,model.name="f_2006_p.t.plus.stratum_Phi.stratum_Psi.dot") #p(t + stratum),Phi(stratum),Psi(X) f_2006_p.t.plus.strat_phi.strat_psi.X=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p.t.plus.strat,S=S.strat,Psi=Psi.age),output=F,adjust=F,model.name="f_2006_p.t.plus.stratum_Phi.stratum_Psi.age") #p(t + stratum),Phi(stratum),Psi(stratum) f_2006_p.t.plus.strat_phi.strat_psi.strat=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p.t.plus.strat,S=S.strat,Psi=Psi.strat),output=F,adjust=F,model.name="f_2006_p.t.plus.stratum_Phi.stratum_Psi.stratum") #p(t + stratum),Phi(stratum),Psi(X + stratum) f_2006_p.t.plus.strat_phi.strat_psi.X.plus.strat=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p.t.plus.strat,S=S.strat,Psi=Psi.age.plus.strat),output=F,adjust=F,model.name="f_2006_p.t.plus.stratum_Phi.stratum_Psi.X.plus.stratum") #p(t * stratum),Phi(.),Psi(.) f_2006_p.t.by.strat_phi.dot_psi.dot=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p.t.by.strat,S=S.dot,Psi=Psi.dot),output=F,adjust=F,model.name="f_2006_p.t.by.stratum_Phi.dot_psi.dot") #p(t * stratum),Phi(.),Psi(X) f_2006_p.t.by.strat_phi.dot_psi.X=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p.t.by.strat,S=S.dot,Psi=Psi.age),output=F,adjust=F,model.name="f_2006_p.t.by.stratum_Phi.dot_psi.X") #p(t * stratum),Phi(.),Psi(stratum) f_2006_p.t.by.strat_phi.dot_psi.strat=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p.t.by.strat,S=S.dot,Psi=Psi.strat),output=F,adjust=F,model.name="f_2006_p.t.by.stratum_Phi.dot_psi.stratum") #p(t * stratum),Phi(.),Psi(X + stratum) f_2006_p.t.by.strat_phi.dot_psi.X.plus.strat=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p.t.by.strat,S=S.dot,Psi=Psi.age.plus.strat),output=F,adjust=F,model.name="f_2006_p.t.by.stratum_Phi.dot_psi.X.plus.stratum") #p(t * stratum),Phi(stratum),Psi(.) f_2006_p.t.by.strat_phi.strat_psi.dot=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p.t.by.strat,S=S.strat,Psi=Psi.dot),output=F,adjust=F,model.name="f_2006_p.t.by.stratum_Phi.stratum_Psi.dot") #p(t * stratum),Phi(stratum),Psi(X) f_2006_p.t.by.strat_phi.strat_psi.X=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p.t.by.strat,S=S.strat,Psi=Psi.age),output=F,adjust=F,model.name="f_2006_p.t.by.stratum_Phi.stratum_Psi.age") #p(t * stratum),Phi(stratum),Psi(stratum) f_2006_p.t.by.strat_phi.strat_psi.strat=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p.t.by.strat,S=S.strat,Psi=Psi.strat),output=F,adjust=F,model.name="f_2006_p.t.by.stratum_Phi.stratum_Psi.stratum") #p(t * stratum),Phi(stratum),Psi(X + stratum) f_2006_p.t.by.strat_phi.strat_psi.X.plus.strat=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p.t.by.strat,S=S.strat,Psi=Psi.age.plus.strat),output=F,adjust=F,model.name="f_2006_p.t.by.stratum_Phi.stratum_Psi.X.plus.stratum") # Collect models f_2006_models<-collect.models(lx=c("f_2006_p.t_phi.X_psi.dot","f_2006_p.t_phi.X_psi.X","f_2006_p.t_phi.X_psi.strat","f_2006_p.t_phi.X_psi.X.plus.strat","f_2006_p.t_phi.X.plus.strat_psi.dot","f_2006_p.t_phi.X.plus.strat_psi.X","f_2006_p.t_phi.X.plus.strat_psi.strat","f_2006_p.t_phi.X.plus.strat_psi.X.plus.strat","f_2006_p.t.plus.strat_phi.X_psi.dot","f_2006_p.t.plus.strat_phi.X_psi.X","f_2006_p.t.plus.strat_phi.X_psi.strat","f_2006_p.t.plus.strat_phi.X_psi.X.plus.strat","f_2006_p.t.plus.strat_phi.X.plus.strat_psi.dot","f_2006_p.t.plus.strat_phi.X.plus.strat_psi.X","f_2006_p.t.plus.strat_phi.X.plus.strat_psi.strat","f_2006_p.t.plus.strat_phi.X.plus.strat_psi.X.plus.strat","f_2006_p.t.by.strat_phi.X_psi.dot","f_2006_p.t.by.strat_phi.X_psi.X","f_2006_p.t.by.strat_phi.X_psi.strat","f_2006_p.t.by.strat_phi.X_psi.X.plus.strat","f_2006_p.t.by.strat_phi.X.plus.strat_psi.dot","f_2006_p.t.by.strat_phi.X.plus.strat_psi.X","f_2006_p.t.by.strat_phi.X.plus.strat_psi.strat","f_2006_p.t.by.strat_phi.X.plus.strat_psi.X.plus.strat","f_2006_p.t_phi.X.by.strat_psi.dot","f_2006_p.t_phi.X.by.strat_psi.X","f_2006_p.t_phi.X.by.strat_psi.strat","f_2006_p.t_phi.X.by.strat_psi.X.plus.strat","f_2006_p.t.plus.strat_phi.X.by.strat_psi.dot","f_2006_p.t.plus.strat_phi.X.by.strat_psi.X","f_2006_p.t.plus.strat_phi.X.by.strat_psi.strat","f_2006_p.t.plus.strat_phi.X.by.strat_psi.X.plus.strat","f_2006_p.t.by.strat_phi.X.by.strat_psi.dot","f_2006_p.t.by.strat_phi.X.by.strat_psi.X","f_2006_p.t.by.strat_phi.X.by.strat_psi.strat","f_2006_p.t.by.strat_phi.X.by.strat_psi.X.plus.strat","f_2006_p.t_phi.dot_psi.dot","f_2006_p.t_phi.dot_psi.X","f_2006_p.t_phi.dot_psi.strat","f_2006_p.t_phi.dot_psi.X.plus.strat","f_2006_p.t_phi.strat_psi.dot","f_2006_p.t_phi.strat_psi.X","f_2006_p.t_phi.strat_psi.strat","f_2006_p.t_phi.strat_psi.X.plus.strat","f_2006_p.t.plus.strat_phi.X_psi.dot","f_2006_p.t.plus.strat_phi.X_psi.X","f_2006_p.t.plus.strat_phi.X_psi.strat","f_2006_p.t.plus.strat_phi.X_psi.X.plus.strat","f_2006_p.t.plus.strat_phi.strat_psi.dot","f_2006_p.t.plus.strat_phi.strat_psi.X","f_2006_p.t.plus.strat_phi.strat_psi.strat","f_2006_p.t.plus.strat_phi.strat_psi.X.plus.strat","f_2006_p.t.by.strat_phi.dot_psi.dot","f_2006_p.t.by.strat_phi.dot_psi.X","f_2006_p.t.by.strat_phi.dot_psi.strat","f_2006_p.t.by.strat_phi.dot_psi.X.plus.strat","f_2006_p.t.by.strat_phi.strat_psi.dot","f_2006_p.t.by.strat_phi.strat_psi.X","f_2006_p.t.by.strat_phi.strat_psi.strat","f_2006_p.t.by.strat_phi.strat_psi.X.plus.strat")) write.table(f_2006_models[61],"...") # Saving the workspace so the models do not have to be repeated each time save.image("...") ################################################################################################################################################################################################ # 4) Best models from (2) with age, stratum and time along with additional covariates (climate and mites) ################################################################################################################################################################################################ ############## # Males 2005 # ############## # Input the data, 0 = absent, N = present non-mating, B = present mating. library(RMark) setwd("...") multistrat_M_2005<-import.chdata("...", header = TRUE, field.names = NULL, field.types = NULL) climate_2005<-read.table("...", header = TRUE) climate_2006<-read.table("...", header = TRUE) attach(climate_2005) attach(climate_2006) climate05=data.frame(time=climate_2005[,1],mean_temp_C_2005,prec_mm_2005,sun_hrs_2005) climate06=data.frame(time=climate_2006[,1],mean_temp_C_2006,prec_mm_2006,sun_hrs_2006) # Mite data mites_m_2005<-read.table("...", header = TRUE) mites_m_2006<-read.table("...", header = TRUE) mites_f_2005<-read.table("...", header = TRUE) mites_f_2006<-read.table("...", header = TRUE) attach(mites_m_2005) attach(mites_m_2006) attach(mites_f_2005) attach(mites_f_2006) # And actual parameters for the real models multistrat_M_2005$Mite_M_05<-Mite_M_05 multistrat_M_2005$Mite_M_05_sq<-Mite_M_05^2 multistrat_M_2005$WL<-M_05_Winglength multistrat_M_2005$WL_sq<-M_05_Winglength_sq multistrat_M_2005<-na.omit(multistrat_M_2005) m_2005.process=process.data(multistrat_M_2005,model="Multistrata") m_2005.ddl=make.design.data(m_2005.process) m_2005.ddl$p<-merge_design.covariates(m_2005.ddl$p,climate05) m_2005.ddl$S<-merge_design.covariates(m_2005.ddl$S,climate05) m_2005.ddl$Psi<-merge_design.covariates(m_2005.ddl$Psi,climate05) # All the models for the different parameters p=list(formula=~prec_mm_2005+sun_hrs_2005+mean_temp_C_2005+Mite_M_05+Mite_M_05_sq+stratum) S=list(formula=~Age:stratum+I(Age^2):stratum+Mite_M_05+Mite_M_05_sq+stratum) Psi.c=list(formula=~prec_mm_2005+sun_hrs_2005+mean_temp_C_2005+stratum) Psi.m=list(formula=~Mite_M_05+Mite_M_05_sq+stratum) Psi.s=list(formula=~WL+WL_sq+stratum) Psi.x=list(formula=~Age:stratum+I(Age^2):stratum+stratum) Psi.c.m=list(formula=~prec_mm_2005+sun_hrs_2005+mean_temp_C_2005+Mite_M_05+Mite_M_05_sq+stratum) Psi.c.s=list(formula=~prec_mm_2005+sun_hrs_2005+mean_temp_C_2005+WL+WL_sq+stratum) Psi.c.x=list(formula=~prec_mm_2005+sun_hrs_2005+mean_temp_C_2005+Age:stratum+I(Age^2):stratum+stratum) Psi.m.s=list(formula=~Mite_M_05+Mite_M_05_sq+WL+WL_sq+stratum) Psi.m.x=list(formula=~Age:stratum+I(Age^2):stratum+Mite_M_05+Mite_M_05_sq+stratum) Psi.s.x=list(formula=~Age:stratum+I(Age^2):stratum+WL+WL_sq+stratum) Psi.c.m.s=list(formula=~prec_mm_2005+sun_hrs_2005+mean_temp_C_2005+Mite_M_05+Mite_M_05_sq+WL+WL_sq+stratum) Psi.c.m.x=list(formula=~prec_mm_2005+sun_hrs_2005+mean_temp_C_2005+Mite_M_05+Mite_M_05_sq+Age:stratum+I(Age^2):stratum+stratum) Psi.c.s.x=list(formula=~prec_mm_2005+sun_hrs_2005+mean_temp_C_2005+Age:stratum+I(Age^2):stratum+stratum+WL+WL_sq) Psi.m.s.x=list(formula=~Age:stratum+I(Age^2):stratum+Mite_M_05+Mite_M_05_sq+WL+WL_sq+stratum) Psi.c.m.s.x=list(formula=~prec_mm_2005+sun_hrs_2005+mean_temp_C_2005+Mite_M_05+Mite_M_05_sq+Age:stratum+I(Age^2):stratum+WL+WL_sq+stratum) #p(c+m+strat),Phi(x+m+strat),Psi(strat+c) m_2005_p.c.m.strat_phi.X.m.strat_psi.strat.c=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p,S=S,Psi=Psi.c),output=F,adjust=F,model.name="m_2005_p.c.m.strat_phi.X.m.strat_psi.strat.c") #p(c+m+strat),Phi(x+m+strat),Psi(strat+m) m_2005_p.c.m.strat_phi.X.m.strat_psi.strat.m=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p,S=S,Psi=Psi.m),output=F,adjust=F,model.name="m_2005_p.c.m.strat_phi.X.m.strat_psi.strat.m") #p(c+m+strat),Phi(x+m+strat),Psi(strat+s) m_2005_p.c.m.strat_phi.X.m.strat_psi.strat.s=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p,S=S,Psi=Psi.s),output=F,adjust=F,model.name="m_2005_p.c.m.strat_phi.X.m.strat_psi.strat.s") #p(c+m+strat),Phi(x+m+strat),Psi(strat+x) m_2005_p.c.m.strat_phi.X.m.strat_psi.strat.x=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p,S=S,Psi=Psi.x),output=F,adjust=F,model.name="m_2005_p.c.m.strat_phi.X.m.strat_psi.strat.x") #p(c+m+strat),Phi(x+m+strat),Psi(strat+c+m) m_2005_p.c.m.strat_phi.X.m.strat_psi.strat.c.m=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p,S=S,Psi=Psi.c.m),output=F,adjust=F,model.name="m_2005_p.c.m.strat_phi.X.m.strat_psi.strat.c.m") #p(c+m+strat),Phi(x+m+strat),Psi(strat+c+s) m_2005_p.c.m.strat_phi.X.m.strat_psi.strat.c.s=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p,S=S,Psi=Psi.c.s),output=F,adjust=F,model.name="m_2005_p.c.m.strat_phi.X.m.strat_psi.strat.c.s") #p(c+m+strat),Phi(x+m+strat),Psi(strat+c+x) m_2005_p.c.m.strat_phi.X.m.strat_psi.strat.c.x=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p,S=S,Psi=Psi.c.x),output=F,adjust=F,model.name="m_2005_p.c.m.strat_phi.X.m.strat_psi.strat.c.x") #p(c+m+strat),Phi(x+m+strat),Psi(strat+m+s) m_2005_p.c.m.strat_phi.X.m.strat_psi.strat.m.s=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p,S=S,Psi=Psi.m.s),output=F,adjust=F,model.name="m_2005_p.c.m.strat_phi.X.m.strat_psi.strat.m.s") #p(c+m+strat),Phi(x+m+strat),Psi(strat+m+x) m_2005_p.c.m.strat_phi.X.m.strat_psi.strat.m.x=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p,S=S,Psi=Psi.m.x),output=F,adjust=F,model.name="m_2005_p.c.m.strat_phi.X.m.strat_psi.strat.m.x") #p(c+m+strat),Phi(x+m+strat),Psi(strat+s+x) m_2005_p.c.m.strat_phi.X.m.strat_psi.strat.s.x=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p,S=S,Psi=Psi.s.x),output=F,adjust=F,model.name="m_2005_p.c.m.strat_phi.X.m.strat_psi.strat.s.x") #p(c+m+strat),Phi(x+m+strat),Psi(strat+c+m+s) m_2005_p.c.m.strat_phi.X.m.strat_psi.strat.c.m.s=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p,S=S,Psi=Psi.c.m.s),output=F,adjust=F,model.name="m_2005_p.c.m.strat_phi.X.m.strat_psi.strat.c.m.s") #p(c+m+strat),Phi(x+m+strat),Psi(strat+c+m+x) m_2005_p.c.m.strat_phi.X.m.strat_psi.strat.c.m.x=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p,S=S,Psi=Psi.c.m.x),output=F,adjust=F,model.name="m_2005_p.c.m.strat_phi.X.m.strat_psi.strat.c.m.x") #p(c+m+strat),Phi(x+m+strat),Psi(strat+c+s+x) m_2005_p.c.m.strat_phi.X.m.strat_psi.strat.c.s.x=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p,S=S,Psi=Psi.c.s.x),output=F,adjust=F,model.name="m_2005_p.c.m.strat_phi.X.m.strat_psi.strat.c.s.x") #p(c+m+strat),Phi(x+m+strat),Psi(strat+m+s+x) m_2005_p.c.m.strat_phi.X.m.strat_psi.strat.m.s.x=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p,S=S,Psi=Psi.m.s.x),output=F,adjust=F,model.name="m_2005_p.c.m.strat_phi.X.m.strat_psi.strat.m.s.x") #p(c+m+strat),Phi(x+m+strat),Psi(strat+c+m+s+x) m_2005_p.c.m.strat_phi.X.m.strat_psi.strat.c.m.s.x=mark(m_2005.process,m_2005.ddl,model.parameters=list(p=p,S=S,Psi=Psi.c.m.s.x),output=F,adjust=F,model.name="m_2005_p.c.m.strat_phi.X.m.strat_psi.strat.c.m.s.x") # Collect models m_2005_new_model_set<-collect.models(lx=c("m_2005_p.c.m.strat_phi.X.m.strat_psi.strat.c","m_2005_p.c.m.strat_phi.X.m.strat_psi.strat.m","m_2005_p.c.m.strat_phi.X.m.strat_psi.strat.s","m_2005_p.c.m.strat_phi.X.m.strat_psi.strat.x","m_2005_p.c.m.strat_phi.X.m.strat_psi.strat.c.m","m_2005_p.c.m.strat_phi.X.m.strat_psi.strat.c.s","m_2005_p.c.m.strat_phi.X.m.strat_psi.strat.c.x","m_2005_p.c.m.strat_phi.X.m.strat_psi.strat.m.s","m_2005_p.c.m.strat_phi.X.m.strat_psi.strat.m.x","m_2005_p.c.m.strat_phi.X.m.strat_psi.strat.s.x","m_2005_p.c.m.strat_phi.X.m.strat_psi.strat.c.m.s","m_2005_p.c.m.strat_phi.X.m.strat_psi.strat.c.m.x","m_2005_p.c.m.strat_phi.X.m.strat_psi.strat.c.s.x","m_2005_p.c.m.strat_phi.X.m.strat_psi.strat.m.s.x","m_2005_p.c.m.strat_phi.X.m.strat_psi.strat.c.m.s.x")) write.table(m_2005_new_model_set[16],"...") save.image("...") # List of models: m_2005_models<-list(m_2005_p.c.m.strat_phi.X.m.strat_psi.strat.c,m_2005_p.c.m.strat_phi.X.m.strat_psi.strat.m,m_2005_p.c.m.strat_phi.X.m.strat_psi.strat.s,m_2005_p.c.m.strat_phi.X.m.strat_psi.strat.x,m_2005_p.c.m.strat_phi.X.m.strat_psi.strat.c.m,m_2005_p.c.m.strat_phi.X.m.strat_psi.strat.c.s,m_2005_p.c.m.strat_phi.X.m.strat_psi.strat.c.x,m_2005_p.c.m.strat_phi.X.m.strat_psi.strat.m.s,m_2005_p.c.m.strat_phi.X.m.strat_psi.strat.m.x,m_2005_p.c.m.strat_phi.X.m.strat_psi.strat.s.x,m_2005_p.c.m.strat_phi.X.m.strat_psi.strat.c.m.s,m_2005_p.c.m.strat_phi.X.m.strat_psi.strat.c.m.x,m_2005_p.c.m.strat_phi.X.m.strat_psi.strat.c.s.x,m_2005_p.c.m.strat_phi.X.m.strat_psi.strat.m.s.x,m_2005_p.c.m.strat_phi.X.m.strat_psi.strat.c.m.s.x) # Model selection table library(MuMIn) m05_model.table<-model.sel(m_2005_models) write.table(m05_model.table,"...") # Model averaging of those models with delta-AIC <2 model.avg(m_2005_models, subset = delta<2) # Calculation of the importance of different variables importance(m_2005_models) # Extracting parameters from the models S.parameters<-get.real(m_2005_p.c.m.strat_phi.X.m.strat_psi.strat.c.s.x,parameter="S",se=TRUE) p.parameters<-get.real(m_2005_p.c.m.strat_phi.X.m.strat_psi.strat.c.s.x,parameter="p",se=TRUE) Psi.parameters<-get.real(m_2005_p.c.m.strat_phi.X.m.strat_psi.strat.c.s.x,parameter="Psi",se=TRUE) # Now use those parameters to average across ages and give mean esimates LCLs and UCLs M_2005_age.ests<-matrix(ncol=10,nrow=77) colnames(M_2005_age.ests)<-c("Age","S.Estimate","S.LCL","S.UCL","p.Estimate","p.LCL","p.UCL","Psi.Estimate","Psi.LCL","Psi.UCL") for(x in 1:77){ S.age.subset<-as.numeric(subset(S.parameters$estimate,S.parameters$Age==x)) M_2005_age.ests[x,1]<-x M_2005_age.ests[x,2]<-mean(S.age.subset) M_2005_age.ests[x,3]<-mean(S.age.subset)-1.96*(sd(S.age.subset)/sqrt(length(S.age.subset))) M_2005_age.ests[x,4]<-mean(S.age.subset)+1.96*(sd(S.age.subset)/sqrt(length(S.age.subset))) p.age.subset<-as.numeric(subset(p.parameters$estimate,p.parameters$Age==x)) M_2005_age.ests[x,5]<-mean(p.age.subset) M_2005_age.ests[x,6]<-mean(p.age.subset)-1.96*(sd(p.age.subset)/sqrt(length(p.age.subset))) M_2005_age.ests[x,7]<-mean(p.age.subset)+1.96*(sd(p.age.subset)/sqrt(length(p.age.subset))) Psi.age.subset<-as.numeric(subset(Psi.parameters$estimate,Psi.parameters$Age==x)) M_2005_age.ests[x,8]<-mean(Psi.age.subset) M_2005_age.ests[x,9]<-mean(Psi.age.subset)-1.96*(sd(Psi.age.subset)/sqrt(length(Psi.age.subset))) M_2005_age.ests[x,10]<-mean(Psi.age.subset)+1.96*(sd(Psi.age.subset)/sqrt(length(Psi.age.subset))) } # Plot with error bars plot(M_2005_age.ests[,1],M_2005_age.ests[,2]) polygon(c(rev(M_2005_age.ests[,1]),M_2005_age.ests[,1]),c(rev(M_2005_age.ests[,3]),M_2005_age.ests[,4]),col = "grey75", border = FALSE) lines(M_2005_age.ests[,1], M_2005_age.ests[,2], lwd = 2) lines(M_2005_age.ests[,1], M_2005_age.ests[,3], col="red",lty=2) lines(M_2005_age.ests[,1], M_2005_age.ests[,4], col="red",lty=2) write.table(M_2005_age.ests,"...") m_2005_age.ests<-matrix(ncol=13,nrow=76) colnames(m_2005_age.ests)<-c("Age","B.S.mean","B.S.LCL","B.S.UCL","NB.S.mean","NB.S.LCL","NB.S.UCL","B.Psi.mean","B.Psi.LCL","B.Psi.UCL","NB.Psi.mean","NB.Psi.LCL","NB.Psi.UCL") # Note that in this case there is only one estimate for the survival parameter so just extract the LCL and UCL associated with that for(x in 1:76){ B.S.age.subset<-as.numeric(subset(S.parameters$estimate,S.parameters$Age==x & S.parameters$stratum=="B")) B.S.lcl.subset<-as.numeric(subset(S.parameters$lcl,S.parameters$Age==x & S.parameters$stratum=="B")) B.S.ucl.subset<-as.numeric(subset(S.parameters$ucl,S.parameters$Age==x & S.parameters$stratum=="B")) m_2005_age.ests[x,1]<-x m_2005_age.ests[x,2]<-mean(B.S.age.subset) m_2005_age.ests[x,3]<-mean(B.S.lcl.subset) m_2005_age.ests[x,4]<-mean(B.S.ucl.subset) NB.S.age.subset<-as.numeric(subset(S.parameters$estimate,S.parameters$Age==x & S.parameters$stratum=="N")) NB.S.lcl.subset<-as.numeric(subset(S.parameters$lcl,S.parameters$Age==x & S.parameters$stratum=="N")) NB.S.ucl.subset<-as.numeric(subset(S.parameters$ucl,S.parameters$Age==x & S.parameters$stratum=="N")) m_2005_age.ests[x,5]<-mean(NB.S.age.subset) m_2005_age.ests[x,6]<-mean(NB.S.lcl.subset) m_2005_age.ests[x,7]<-mean(NB.S.ucl.subset) B.Psi.age.subset<-as.numeric(subset(Psi.parameters$estimate,Psi.parameters$Age==x & Psi.parameters$stratum=="B")) B.Psi.lcl.subset<-as.numeric(subset(Psi.parameters$lcl,Psi.parameters$Age==x & Psi.parameters$stratum=="B")) B.Psi.ucl.subset<-as.numeric(subset(Psi.parameters$ucl,Psi.parameters$Age==x & Psi.parameters$stratum=="B")) m_2005_age.ests[x,8]<-mean(B.Psi.age.subset) m_2005_age.ests[x,9]<-mean(B.Psi.lcl.subset) m_2005_age.ests[x,10]<-mean(B.Psi.ucl.subset) NB.Psi.age.subset<-as.numeric(subset(Psi.parameters$estimate,Psi.parameters$Age==x & Psi.parameters$stratum=="N")) NB.Psi.lcl.subset<-as.numeric(subset(Psi.parameters$lcl,Psi.parameters$Age==x & Psi.parameters$stratum=="N")) NB.Psi.ucl.subset<-as.numeric(subset(Psi.parameters$ucl,Psi.parameters$Age==x & Psi.parameters$stratum=="N")) m_2005_age.ests[x,11]<-mean(NB.Psi.age.subset) m_2005_age.ests[x,12]<-mean(NB.Psi.lcl.subset) m_2005_age.ests[x,13]<-mean(NB.Psi.ucl.subset) } write.table(m_2005_age.ests,"...") ######################################################################################################################################################################################################################## ######################################################################################################################################################################################################################## ############## # Males 2006 # ############## library(RMark) setwd("...") multistrat_M_2006<-import.chdata("...", header = TRUE, field.names = NULL, field.types = NULL) # Climate change climate_2006<-read.table("...", header = TRUE) attach(climate_2006) climate06=data.frame(time=climate_2006[,1],mean_temp_C_2006,prec_mm_2006,sun_hrs_2006) # Mite data mites_m_2006<-read.table("...", header = TRUE) attach(mites_m_2006) # And actual parameters for the real models multistrat_M_2006$Mite_M_06<-Mite_M_06 multistrat_M_2006$Mite_M_06_sq<-Mite_M_06^2 multistrat_M_2006$WL<-M_06_Winglength multistrat_M_2006$WL_sq<-M_06_Winglength_sq multistrat_M_2006<-na.omit(multistrat_M_2006) m_2006.process=process.data(multistrat_M_2006,model="Multistrata") m_2006.ddl=make.design.data(m_2006.process) m_2006.ddl$p<-merge_design.covariates(m_2006.ddl$p,climate06) m_2006.ddl$S<-merge_design.covariates(m_2006.ddl$S,climate06) m_2006.ddl$Psi<-merge_design.covariates(m_2006.ddl$Psi,climate06) # All the models for the different parameters p=list(formula=~prec_mm_2006+sun_hrs_2006+mean_temp_C_2006+Mite_M_06+Mite_M_06_sq+stratum) S=list(formula=~Age:stratum+I(Age^2):stratum+Mite_M_06+Mite_M_06_sq+stratum) Psi.c=list(formula=~prec_mm_2006+sun_hrs_2006+mean_temp_C_2006+stratum) Psi.m=list(formula=~Mite_M_06+Mite_M_06_sq+stratum) Psi.s=list(formula=~WL+WL_sq+stratum) Psi.x=list(formula=~Age:stratum+I(Age^2):stratum+stratum) Psi.c.m=list(formula=~prec_mm_2006+sun_hrs_2006+mean_temp_C_2006+Mite_M_06+Mite_M_06_sq+stratum) Psi.c.s=list(formula=~prec_mm_2006+sun_hrs_2006+mean_temp_C_2006+WL+WL_sq+stratum) Psi.c.x=list(formula=~prec_mm_2006+sun_hrs_2006+mean_temp_C_2006+Age:stratum+I(Age^2):stratum+stratum) Psi.m.s=list(formula=~Mite_M_06+Mite_M_06_sq+WL+WL_sq+stratum) Psi.m.x=list(formula=~Age:stratum+I(Age^2):stratum+Mite_M_06+Mite_M_06_sq+stratum) Psi.s.x=list(formula=~Age:stratum+I(Age^2):stratum+WL+WL_sq+stratum) Psi.c.m.s=list(formula=~prec_mm_2006+sun_hrs_2006+mean_temp_C_2006+Mite_M_06+Mite_M_06_sq+WL+WL_sq+stratum) Psi.c.m.x=list(formula=~prec_mm_2006+sun_hrs_2006+mean_temp_C_2006+Mite_M_06+Mite_M_06_sq+Age:stratum+I(Age^2):stratum+stratum) Psi.c.s.x=list(formula=~prec_mm_2006+sun_hrs_2006+mean_temp_C_2006+Age:stratum+I(Age^2):stratum+stratum+WL+WL_sq) Psi.m.s.x=list(formula=~Age:stratum+I(Age^2):stratum+Mite_M_06+Mite_M_06_sq+WL+WL_sq+stratum) Psi.c.m.s.x=list(formula=~prec_mm_2006+sun_hrs_2006+mean_temp_C_2006+Mite_M_06+Mite_M_06_sq+Age:stratum+I(Age^2):stratum+WL+WL_sq+stratum) #p(c+m+strat),Phi(x+m+strat),Psi(strat+c) m_2006_p.c.m.strat_phi.X.m.strat_psi.strat.c=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p,S=S,Psi=Psi.c),output=F,adjust=F,model.name="m_2006_p.c.m.strat_phi.X.m.strat_psi.strat.c") #p(c+m+strat),Phi(x+m+strat),Psi(strat+m) m_2006_p.c.m.strat_phi.X.m.strat_psi.strat.m=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p,S=S,Psi=Psi.m),output=F,adjust=F,model.name="m_2006_p.c.m.strat_phi.X.m.strat_psi.strat.m") #p(c+m+strat),Phi(x+m+strat),Psi(strat+s) m_2006_p.c.m.strat_phi.X.m.strat_psi.strat.s=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p,S=S,Psi=Psi.s),output=F,adjust=F,model.name="m_2006_p.c.m.strat_phi.X.m.strat_psi.strat.s") #p(c+m+strat),Phi(x+m+strat),Psi(strat+x) m_2006_p.c.m.strat_phi.X.m.strat_psi.strat.x=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p,S=S,Psi=Psi.x),output=F,adjust=F,model.name="m_2006_p.c.m.strat_phi.X.m.strat_psi.strat.x") #p(c+m+strat),Phi(x+m+strat),Psi(strat+c+m) m_2006_p.c.m.strat_phi.X.m.strat_psi.strat.c.m=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p,S=S,Psi=Psi.c.m),output=F,adjust=F,model.name="m_2006_p.c.m.strat_phi.X.m.strat_psi.strat.c.m") #p(c+m+strat),Phi(x+m+strat),Psi(strat+c+s) m_2006_p.c.m.strat_phi.X.m.strat_psi.strat.c.s=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p,S=S,Psi=Psi.c.s),output=F,adjust=F,model.name="m_2006_p.c.m.strat_phi.X.m.strat_psi.strat.c.s") #p(c+m+strat),Phi(x+m+strat),Psi(strat+c+x) m_2006_p.c.m.strat_phi.X.m.strat_psi.strat.c.x=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p,S=S,Psi=Psi.c.x),output=F,adjust=F,model.name="m_2006_p.c.m.strat_phi.X.m.strat_psi.strat.c.x") #p(c+m+strat),Phi(x+m+strat),Psi(strat+m+s) m_2006_p.c.m.strat_phi.X.m.strat_psi.strat.m.s=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p,S=S,Psi=Psi.m.s),output=F,adjust=F,model.name="m_2006_p.c.m.strat_phi.X.m.strat_psi.strat.m.s") #p(c+m+strat),Phi(x+m+strat),Psi(strat+m+x) m_2006_p.c.m.strat_phi.X.m.strat_psi.strat.m.x=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p,S=S,Psi=Psi.m.x),output=F,adjust=F,model.name="m_2006_p.c.m.strat_phi.X.m.strat_psi.strat.m.x") #p(c+m+strat),Phi(x+m+strat),Psi(strat+s+x) m_2006_p.c.m.strat_phi.X.m.strat_psi.strat.s.x=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p,S=S,Psi=Psi.s.x),output=F,adjust=F,model.name="m_2006_p.c.m.strat_phi.X.m.strat_psi.strat.s.x") #p(c+m+strat),Phi(x+m+strat),Psi(strat+c+m+s) m_2006_p.c.m.strat_phi.X.m.strat_psi.strat.c.m.s=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p,S=S,Psi=Psi.c.m.s),output=F,adjust=F,model.name="m_2006_p.c.m.strat_phi.X.m.strat_psi.strat.c.m.s") #p(c+m+strat),Phi(x+m+strat),Psi(strat+c+m+x) m_2006_p.c.m.strat_phi.X.m.strat_psi.strat.c.m.x=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p,S=S,Psi=Psi.c.m.x),output=F,adjust=F,model.name="m_2006_p.c.m.strat_phi.X.m.strat_psi.strat.c.m.x") #p(c+m+strat),Phi(x+m+strat),Psi(strat+c+s+x) m_2006_p.c.m.strat_phi.X.m.strat_psi.strat.c.s.x=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p,S=S,Psi=Psi.c.s.x),output=F,adjust=F,model.name="m_2006_p.c.m.strat_phi.X.m.strat_psi.strat.c.s.x") #p(c+m+strat),Phi(x+m+strat),Psi(strat+m+s+x) m_2006_p.c.m.strat_phi.X.m.strat_psi.strat.m.s.x=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p,S=S,Psi=Psi.m.s.x),output=F,adjust=F,model.name="m_2006_p.c.m.strat_phi.X.m.strat_psi.strat.m.s.x") #p(c+m+strat),Phi(x+m+strat),Psi(strat+c+m+s+x) m_2006_p.c.m.strat_phi.X.m.strat_psi.strat.c.m.s.x=mark(m_2006.process,m_2006.ddl,model.parameters=list(p=p,S=S,Psi=Psi.c.m.s.x),output=F,adjust=F,model.name="m_2006_p.c.m.strat_phi.X.m.strat_psi.strat.c.m.s.x") # Collect models m_2006_new_model_set<-collect.models(lx=c("m_2006_p.c.m.strat_phi.X.m.strat_psi.strat.c","m_2006_p.c.m.strat_phi.X.m.strat_psi.strat.m","m_2006_p.c.m.strat_phi.X.m.strat_psi.strat.s","m_2006_p.c.m.strat_phi.X.m.strat_psi.strat.x","m_2006_p.c.m.strat_phi.X.m.strat_psi.strat.c.m","m_2006_p.c.m.strat_phi.X.m.strat_psi.strat.c.s","m_2006_p.c.m.strat_phi.X.m.strat_psi.strat.c.x","m_2006_p.c.m.strat_phi.X.m.strat_psi.strat.m.s","m_2006_p.c.m.strat_phi.X.m.strat_psi.strat.m.x","m_2006_p.c.m.strat_phi.X.m.strat_psi.strat.s.x","m_2006_p.c.m.strat_phi.X.m.strat_psi.strat.c.m.s","m_2006_p.c.m.strat_phi.X.m.strat_psi.strat.c.m.x","m_2006_p.c.m.strat_phi.X.m.strat_psi.strat.c.s.x","m_2006_p.c.m.strat_phi.X.m.strat_psi.strat.m.s.x","m_2006_p.c.m.strat_phi.X.m.strat_psi.strat.c.m.s.x")) write.table(m_2006_new_model_set[16],"...") # List of models: m_2006_models<-list(m_2006_p.c.m.strat_phi.X.m.strat_psi.strat.c,m_2006_p.c.m.strat_phi.X.m.strat_psi.strat.m,m_2006_p.c.m.strat_phi.X.m.strat_psi.strat.s,m_2006_p.c.m.strat_phi.X.m.strat_psi.strat.x,m_2006_p.c.m.strat_phi.X.m.strat_psi.strat.c.m,m_2006_p.c.m.strat_phi.X.m.strat_psi.strat.c.s,m_2006_p.c.m.strat_phi.X.m.strat_psi.strat.c.x,m_2006_p.c.m.strat_phi.X.m.strat_psi.strat.m.s,m_2006_p.c.m.strat_phi.X.m.strat_psi.strat.m.x,m_2006_p.c.m.strat_phi.X.m.strat_psi.strat.s.x,m_2006_p.c.m.strat_phi.X.m.strat_psi.strat.c.m.s,m_2006_p.c.m.strat_phi.X.m.strat_psi.strat.c.m.x,m_2006_p.c.m.strat_phi.X.m.strat_psi.strat.c.s.x,m_2006_p.c.m.strat_phi.X.m.strat_psi.strat.m.s.x,m_2006_p.c.m.strat_phi.X.m.strat_psi.strat.c.m.s.x) # Model selection table library(MuMIn) m06_model.table<-model.sel(m_2006_models) write.table(m06_model.table,"...") # Model averaging of those models with delta-AIC <2 model.avg(m_2006_models, subset = delta<2) # Calculation of the importance of different variables importance(m_2006_models) save.image("...") # Extracting parameters from the models S.parameters<-get.real(m_2006_p.c.m.strat_phi.X.m.strat_psi.strat.c.m.s.x,parameter="S",se=TRUE) p.parameters<-get.real(m_2006_p.c.m.strat_phi.X.m.strat_psi.strat.c.m.s.x,parameter="p",se=TRUE) Psi.parameters<-get.real(m_2006_p.c.m.strat_phi.X.m.strat_psi.strat.c.m.s.x,parameter="Psi",se=TRUE) # Now use those parameters to average across ages and give mean esimates LCLs and UCLs M_2006_age.ests<-matrix(ncol=10,nrow=56) colnames(M_2006_age.ests)<-c("Age","S.Estimate","S.LCL","S.UCL","p.Estimate","p.LCL","p.UCL","Psi.Estimate","Psi.LCL","Psi.UCL") for(x in 1:56){ S.age.subset<-as.numeric(subset(S.parameters$estimate,S.parameters$Age==x)) M_2006_age.ests[x,1]<-x M_2006_age.ests[x,2]<-mean(S.age.subset) M_2006_age.ests[x,3]<-mean(S.age.subset)-1.96*(sd(S.age.subset)/sqrt(length(S.age.subset))) M_2006_age.ests[x,4]<-mean(S.age.subset)+1.96*(sd(S.age.subset)/sqrt(length(S.age.subset))) p.age.subset<-as.numeric(subset(p.parameters$estimate,p.parameters$Age==x)) M_2006_age.ests[x,5]<-mean(p.age.subset) M_2006_age.ests[x,6]<-mean(p.age.subset)-1.96*(sd(p.age.subset)/sqrt(length(p.age.subset))) M_2006_age.ests[x,7]<-mean(p.age.subset)+1.96*(sd(p.age.subset)/sqrt(length(p.age.subset))) Psi.age.subset<-as.numeric(subset(Psi.parameters$estimate,Psi.parameters$Age==x)) M_2006_age.ests[x,8]<-mean(Psi.age.subset) M_2006_age.ests[x,9]<-mean(Psi.age.subset)-1.96*(sd(Psi.age.subset)/sqrt(length(Psi.age.subset))) M_2006_age.ests[x,10]<-mean(Psi.age.subset)+1.96*(sd(Psi.age.subset)/sqrt(length(Psi.age.subset))) } # Plot with error bars plot(M_2006_age.ests[,1],M_2006_age.ests[,2]) polygon(c(rev(M_2006_age.ests[,1]),M_2006_age.ests[,1]),c(rev(M_2006_age.ests[,3]),M_2006_age.ests[,4]),col = "grey75", border = FALSE) lines(M_2006_age.ests[,1], M_2006_age.ests[,2], lwd = 2) lines(M_2006_age.ests[,1], M_2006_age.ests[,3], col="red",lty=2) lines(M_2006_age.ests[,1], M_2006_age.ests[,4], col="red",lty=2) write.table(M_2006_age.ests,"...") save.image("...") m_2006_age.ests<-matrix(ncol=13,nrow=56) colnames(m_2006_age.ests)<-c("Age","B.S.mean","B.S.LCL","B.S.UCL","NB.S.mean","NB.S.LCL","NB.S.UCL","B.Psi.mean","B.Psi.LCL","B.Psi.UCL","NB.Psi.mean","NB.Psi.LCL","NB.Psi.UCL") for(x in 1:56){ B.S.age.subset<-as.numeric(subset(S.parameters$estimate,S.parameters$Age==x & S.parameters$stratum=="B")) B.S.lcl.subset<-as.numeric(subset(S.parameters$lcl,S.parameters$Age==x & S.parameters$stratum=="B")) B.S.ucl.subset<-as.numeric(subset(S.parameters$ucl,S.parameters$Age==x & S.parameters$stratum=="B")) m_2006_age.ests[x,1]<-x m_2006_age.ests[x,2]<-mean(B.S.age.subset) m_2006_age.ests[x,3]<-mean(B.S.lcl.subset) m_2006_age.ests[x,4]<-mean(B.S.ucl.subset) NB.S.age.subset<-as.numeric(subset(S.parameters$estimate,S.parameters$Age==x & S.parameters$stratum=="N")) NB.S.lcl.subset<-as.numeric(subset(S.parameters$lcl,S.parameters$Age==x & S.parameters$stratum=="N")) NB.S.ucl.subset<-as.numeric(subset(S.parameters$ucl,S.parameters$Age==x & S.parameters$stratum=="N")) m_2006_age.ests[x,5]<-mean(NB.S.age.subset) m_2006_age.ests[x,6]<-mean(NB.S.lcl.subset) m_2006_age.ests[x,7]<-mean(NB.S.ucl.subset) B.Psi.age.subset<-as.numeric(subset(Psi.parameters$estimate,Psi.parameters$Age==x & Psi.parameters$stratum=="B")) B.Psi.lcl.subset<-as.numeric(subset(Psi.parameters$lcl,Psi.parameters$Age==x & Psi.parameters$stratum=="B")) B.Psi.ucl.subset<-as.numeric(subset(Psi.parameters$ucl,Psi.parameters$Age==x & Psi.parameters$stratum=="B")) m_2006_age.ests[x,8]<-mean(B.Psi.age.subset) m_2006_age.ests[x,9]<-mean(B.Psi.lcl.subset) m_2006_age.ests[x,10]<-mean(B.Psi.ucl.subset) NB.Psi.age.subset<-as.numeric(subset(Psi.parameters$estimate,Psi.parameters$Age==x & Psi.parameters$stratum=="N")) NB.Psi.lcl.subset<-as.numeric(subset(Psi.parameters$lcl,Psi.parameters$Age==x & Psi.parameters$stratum=="N")) NB.Psi.ucl.subset<-as.numeric(subset(Psi.parameters$ucl,Psi.parameters$Age==x & Psi.parameters$stratum=="N")) m_2006_age.ests[x,11]<-mean(NB.Psi.age.subset) m_2006_age.ests[x,12]<-mean(NB.Psi.lcl.subset) m_2006_age.ests[x,13]<-mean(NB.Psi.ucl.subset) } write.table(m_2006_age.ests,"...") ######################################################################################################################################################################################################################## ######################################################################################################################################################################################################################## ################ # Females 2005 # ################ library(RMark) setwd("...") climate_2005<-read.table("...", header = TRUE) attach(climate_2005) climate05=data.frame(time=climate_2005[,1],mean_temp_C_2005,prec_mm_2005,sun_hrs_2005) # Mite data mites_f_2005<-read.table("...", header = TRUE) attach(mites_f_2005) multistrat_f_2005<-import.chdata("...", header = TRUE, field.names = NULL, field.types = NULL) multistrat_f_2005$Mite_f_05<-Mite_F_05 multistrat_f_2005$Mite_f_05_sq<-Mite_F_05^2 multistrat_f_2005$WL<-F_05_Winglength multistrat_f_2005$WL_sq<-F_05_Winglength_sq multistrat_f_2005<-na.omit(multistrat_f_2005) # And actual parameters for the real models f_2005.process=process.data(multistrat_f_2005,model="Multistrata") f_2005.ddl=make.design.data(f_2005.process) f_2005.ddl$p<-merge_design.covariates(f_2005.ddl$p,climate05) f_2005.ddl$S<-merge_design.covariates(f_2005.ddl$S,climate05) f_2005.ddl$Psi<-merge_design.covariates(f_2005.ddl$Psi,climate05) # All the models for the different parameters p=list(formula=~prec_mm_2005+sun_hrs_2005+mean_temp_C_2005+Mite_f_05+Mite_f_05_sq+stratum) S=list(formula=~Age:stratum+I(Age^2):stratum+Mite_f_05+Mite_f_05_sq+stratum) Psi.c=list(formula=~prec_mm_2005+sun_hrs_2005+mean_temp_C_2005+stratum) Psi.m=list(formula=~Mite_f_05+Mite_f_05_sq+stratum) Psi.s=list(formula=~WL+WL_sq+stratum) Psi.x=list(formula=~Age:stratum+I(Age^2):stratum+stratum) Psi.c.m=list(formula=~prec_mm_2005+sun_hrs_2005+mean_temp_C_2005+Mite_f_05+Mite_f_05_sq+stratum) Psi.c.s=list(formula=~prec_mm_2005+sun_hrs_2005+mean_temp_C_2005+WL+WL_sq+stratum) Psi.c.x=list(formula=~prec_mm_2005+sun_hrs_2005+mean_temp_C_2005+Age:stratum+I(Age^2):stratum+stratum) Psi.m.s=list(formula=~Mite_f_05+Mite_f_05_sq+WL+WL_sq+stratum) Psi.m.x=list(formula=~Age:stratum+I(Age^2):stratum+Mite_f_05+Mite_f_05_sq+stratum) Psi.s.x=list(formula=~Age:stratum+I(Age^2):stratum+WL+WL_sq+stratum) Psi.c.m.s=list(formula=~prec_mm_2005+sun_hrs_2005+mean_temp_C_2005+Mite_f_05+Mite_f_05_sq+WL+WL_sq+stratum) Psi.c.m.x=list(formula=~prec_mm_2005+sun_hrs_2005+mean_temp_C_2005+Mite_f_05+Mite_f_05_sq+Age:stratum+I(Age^2):stratum+stratum) Psi.c.s.x=list(formula=~prec_mm_2005+sun_hrs_2005+mean_temp_C_2005+Age:stratum+I(Age^2):stratum+stratum+WL+WL_sq) Psi.m.s.x=list(formula=~Age:stratum+I(Age^2):stratum+Mite_f_05+Mite_f_05_sq+WL+WL_sq+stratum) Psi.c.m.s.x=list(formula=~prec_mm_2005+sun_hrs_2005+mean_temp_C_2005+Mite_f_05+Mite_f_05_sq+Age:stratum+I(Age^2):stratum+WL+WL_sq+stratum) #p(c+m+strat),Phi(x+m+strat),Psi(strat+c) f_2005_p.c.m.strat_phi.X.m.strat_psi.strat.c=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p,S=S,Psi=Psi.c),output=F,adjust=F,model.name="f_2005_p.c.m.strat_phi.X.m.strat_psi.strat.c") #p(c+m+strat),Phi(x+m+strat),Psi(strat+m) f_2005_p.c.m.strat_phi.X.m.strat_psi.strat.m=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p,S=S,Psi=Psi.m),output=F,adjust=F,model.name="f_2005_p.c.m.strat_phi.X.m.strat_psi.strat.m") #p(c+m+strat),Phi(x+m+strat),Psi(strat+s) f_2005_p.c.m.strat_phi.X.m.strat_psi.strat.s=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p,S=S,Psi=Psi.s),output=F,adjust=F,model.name="f_2005_p.c.m.strat_phi.X.m.strat_psi.strat.s") #p(c+m+strat),Phi(x+m+strat),Psi(strat+x) f_2005_p.c.m.strat_phi.X.m.strat_psi.strat.x=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p,S=S,Psi=Psi.x),output=F,adjust=F,model.name="f_2005_p.c.m.strat_phi.X.m.strat_psi.strat.x") #p(c+m+strat),Phi(x+m+strat),Psi(strat+c+m) f_2005_p.c.m.strat_phi.X.m.strat_psi.strat.c.m=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p,S=S,Psi=Psi.c.m),output=F,adjust=F,model.name="f_2005_p.c.m.strat_phi.X.m.strat_psi.strat.c.m") #p(c+m+strat),Phi(x+m+strat),Psi(strat+c+s) f_2005_p.c.m.strat_phi.X.m.strat_psi.strat.c.s=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p,S=S,Psi=Psi.c.s),output=F,adjust=F,model.name="f_2005_p.c.m.strat_phi.X.m.strat_psi.strat.c.s") #p(c+m+strat),Phi(x+m+strat),Psi(strat+c+x) f_2005_p.c.m.strat_phi.X.m.strat_psi.strat.c.x=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p,S=S,Psi=Psi.c.x),output=F,adjust=F,model.name="f_2005_p.c.m.strat_phi.X.m.strat_psi.strat.c.x") #p(c+m+strat),Phi(x+m+strat),Psi(strat+m+s) f_2005_p.c.m.strat_phi.X.m.strat_psi.strat.m.s=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p,S=S,Psi=Psi.m.s),output=F,adjust=F,model.name="f_2005_p.c.m.strat_phi.X.m.strat_psi.strat.m.s") #p(c+m+strat),Phi(x+m+strat),Psi(strat+m+x) f_2005_p.c.m.strat_phi.X.m.strat_psi.strat.m.x=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p,S=S,Psi=Psi.m.x),output=F,adjust=F,model.name="f_2005_p.c.m.strat_phi.X.m.strat_psi.strat.m.x") #p(c+m+strat),Phi(x+m+strat),Psi(strat+s+x) f_2005_p.c.m.strat_phi.X.m.strat_psi.strat.s.x=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p,S=S,Psi=Psi.s.x),output=F,adjust=F,model.name="f_2005_p.c.m.strat_phi.X.m.strat_psi.strat.s.x") #p(c+m+strat),Phi(x+m+strat),Psi(strat+c+m+s) f_2005_p.c.m.strat_phi.X.m.strat_psi.strat.c.m.s=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p,S=S,Psi=Psi.c.m.s),output=F,adjust=F,model.name="f_2005_p.c.m.strat_phi.X.m.strat_psi.strat.c.m.s") #p(c+m+strat),Phi(x+m+strat),Psi(strat+c+m+x) f_2005_p.c.m.strat_phi.X.m.strat_psi.strat.c.m.x=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p,S=S,Psi=Psi.c.m.x),output=F,adjust=F,model.name="f_2005_p.c.m.strat_phi.X.m.strat_psi.strat.c.m.x") #p(c+m+strat),Phi(x+m+strat),Psi(strat+c+s+x) f_2005_p.c.m.strat_phi.X.m.strat_psi.strat.c.s.x=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p,S=S,Psi=Psi.c.s.x),output=F,adjust=F,model.name="f_2005_p.c.m.strat_phi.X.m.strat_psi.strat.c.s.x") #p(c+m+strat),Phi(x+m+strat),Psi(strat+m+s+x) f_2005_p.c.m.strat_phi.X.m.strat_psi.strat.m.s.x=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p,S=S,Psi=Psi.m.s.x),output=F,adjust=F,model.name="f_2005_p.c.m.strat_phi.X.m.strat_psi.strat.m.s.x") #p(c+m+strat),Phi(x+m+strat),Psi(strat+c+m+s+x) f_2005_p.c.m.strat_phi.X.m.strat_psi.strat.c.m.s.x=mark(f_2005.process,f_2005.ddl,model.parameters=list(p=p,S=S,Psi=Psi.c.m.s.x),output=F,adjust=F,model.name="f_2005_p.c.m.strat_phi.X.m.strat_psi.strat.c.m.s.x") # Collect models f_2005_new_model_set<-collect.models(lx=c("f_2005_p.c.m.strat_phi.X.m.strat_psi.strat.c","f_2005_p.c.m.strat_phi.X.m.strat_psi.strat.m","f_2005_p.c.m.strat_phi.X.m.strat_psi.strat.s","f_2005_p.c.m.strat_phi.X.m.strat_psi.strat.x","f_2005_p.c.m.strat_phi.X.m.strat_psi.strat.c.m","f_2005_p.c.m.strat_phi.X.m.strat_psi.strat.c.s","f_2005_p.c.m.strat_phi.X.m.strat_psi.strat.c.x","f_2005_p.c.m.strat_phi.X.m.strat_psi.strat.m.s","f_2005_p.c.m.strat_phi.X.m.strat_psi.strat.m.x","f_2005_p.c.m.strat_phi.X.m.strat_psi.strat.s.x","f_2005_p.c.m.strat_phi.X.m.strat_psi.strat.c.m.s","f_2005_p.c.m.strat_phi.X.m.strat_psi.strat.c.m.x","f_2005_p.c.m.strat_phi.X.m.strat_psi.strat.c.s.x","f_2005_p.c.m.strat_phi.X.m.strat_psi.strat.m.s.x","f_2005_p.c.m.strat_phi.X.m.strat_psi.strat.c.m.s.x")) write.table(f_2005_new_model_set[16],"...") # List of models: f_2005_models<-list(f_2005_p.c.m.strat_phi.X.m.strat_psi.strat.c,f_2005_p.c.m.strat_phi.X.m.strat_psi.strat.m,f_2005_p.c.m.strat_phi.X.m.strat_psi.strat.s,f_2005_p.c.m.strat_phi.X.m.strat_psi.strat.x,f_2005_p.c.m.strat_phi.X.m.strat_psi.strat.c.m,f_2005_p.c.m.strat_phi.X.m.strat_psi.strat.c.s,f_2005_p.c.m.strat_phi.X.m.strat_psi.strat.c.x,f_2005_p.c.m.strat_phi.X.m.strat_psi.strat.m.s,f_2005_p.c.m.strat_phi.X.m.strat_psi.strat.m.x,f_2005_p.c.m.strat_phi.X.m.strat_psi.strat.s.x,f_2005_p.c.m.strat_phi.X.m.strat_psi.strat.c.m.s,f_2005_p.c.m.strat_phi.X.m.strat_psi.strat.c.m.x,f_2005_p.c.m.strat_phi.X.m.strat_psi.strat.c.s.x,f_2005_p.c.m.strat_phi.X.m.strat_psi.strat.m.s.x,f_2005_p.c.m.strat_phi.X.m.strat_psi.strat.c.m.s.x) # Model selection table library(MuMIn) f05_model.table<-model.sel(f_2005_models) write.table(f05_model.table,"...") # Model averaging of those models with delta-AIC <2 model.avg(f_2005_models, subset = delta<2) # Calculation of the importance of different variables importance(f_2005_models) # Extracting parameters from the models S.parameters<-get.real(f_2005_p.c.m.strat_phi.X.m.strat_psi.strat.m,parameter="S",se=TRUE) p.parameters<-get.real(f_2005_p.c.m.strat_phi.X.m.strat_psi.strat.m,parameter="p",se=TRUE) Psi.parameters<-get.real(f_2005_p.c.m.strat_phi.X.m.strat_psi.strat.m,parameter="Psi",se=TRUE) # Now use those parameters to average across ages and give mean esimates LCLs and UCLs f_2005_age.ests<-matrix(ncol=10,nrow=56) colnames(f_2005_age.ests)<-c("Age","S.Estimate","S.LCL","S.UCL","p.Estimate","p.LCL","p.UCL","Psi.Estimate","Psi.LCL","Psi.UCL") for(x in 1:56){ S.age.subset<-as.numeric(subset(S.parameters$estimate,S.parameters$Age==x)) f_2005_age.ests[x,1]<-x f_2005_age.ests[x,2]<-mean(S.age.subset) f_2005_age.ests[x,3]<-mean(S.age.subset)-1.96*(sd(S.age.subset)/sqrt(length(S.age.subset))) f_2005_age.ests[x,4]<-mean(S.age.subset)+1.96*(sd(S.age.subset)/sqrt(length(S.age.subset))) p.age.subset<-as.numeric(subset(p.parameters$estimate,p.parameters$Age==x)) f_2005_age.ests[x,5]<-mean(p.age.subset) f_2005_age.ests[x,6]<-mean(p.age.subset)-1.96*(sd(p.age.subset)/sqrt(length(p.age.subset))) f_2005_age.ests[x,7]<-mean(p.age.subset)+1.96*(sd(p.age.subset)/sqrt(length(p.age.subset))) Psi.age.subset<-as.numeric(subset(Psi.parameters$estimate,Psi.parameters$Age==x)) f_2005_age.ests[x,8]<-mean(Psi.age.subset) f_2005_age.ests[x,9]<-mean(Psi.age.subset)-1.96*(sd(Psi.age.subset)/sqrt(length(Psi.age.subset))) f_2005_age.ests[x,10]<-mean(Psi.age.subset)+1.96*(sd(Psi.age.subset)/sqrt(length(Psi.age.subset))) } # Plot with error bars plot(f_2005_age.ests[,1],f_2005_age.ests[,2]) polygon(c(rev(f_2005_age.ests[,1]),f_2005_age.ests[,1]),c(rev(f_2005_age.ests[,3]),f_2005_age.ests[,4]),col = "grey75", border = FALSE) lines(f_2005_age.ests[,1], f_2005_age.ests[,2], lwd = 2) lines(f_2005_age.ests[,1], f_2005_age.ests[,3], col="red",lty=2) lines(f_2005_age.ests[,1], f_2005_age.ests[,4], col="red",lty=2) write.table(f_2005_age.ests,"...") save.image("...") # Now use those parameters to average across ages and give mean esimates LCLs and UCLs f_2005_age.ests<-matrix(ncol=13,nrow=76) colnames(f_2005_age.ests)<-c("Age","B.S.mean","B.S.LCL","B.S.UCL","NB.S.mean","NB.S.LCL","NB.S.UCL","B.Psi.mean","B.Psi.LCL","B.Psi.UCL","NB.Psi.mean","NB.Psi.LCL","NB.Psi.UCL") for(x in 1:76){ B.S.age.subset<-as.numeric(subset(S.parameters$estimate,S.parameters$Age==x & S.parameters$stratum=="B")) B.S.lcl.subset<-as.numeric(subset(S.parameters$lcl,S.parameters$Age==x & S.parameters$stratum=="B")) B.S.ucl.subset<-as.numeric(subset(S.parameters$ucl,S.parameters$Age==x & S.parameters$stratum=="B")) f_2005_age.ests[x,1]<-x f_2005_age.ests[x,2]<-mean(B.S.age.subset) f_2005_age.ests[x,3]<-mean(B.S.lcl.subset) f_2005_age.ests[x,4]<-mean(B.S.ucl.subset) NB.S.age.subset<-as.numeric(subset(S.parameters$estimate,S.parameters$Age==x & S.parameters$stratum=="N")) NB.S.lcl.subset<-as.numeric(subset(S.parameters$lcl,S.parameters$Age==x & S.parameters$stratum=="N")) NB.S.ucl.subset<-as.numeric(subset(S.parameters$ucl,S.parameters$Age==x & S.parameters$stratum=="N")) f_2005_age.ests[x,5]<-mean(NB.S.age.subset) f_2005_age.ests[x,6]<-mean(NB.S.lcl.subset) f_2005_age.ests[x,7]<-mean(NB.S.ucl.subset) B.Psi.age.subset<-as.numeric(subset(Psi.parameters$estimate,Psi.parameters$Age==x & Psi.parameters$stratum=="B")) B.Psi.lcl.subset<-as.numeric(subset(Psi.parameters$lcl,Psi.parameters$Age==x & Psi.parameters$stratum=="B")) B.Psi.ucl.subset<-as.numeric(subset(Psi.parameters$ucl,Psi.parameters$Age==x & Psi.parameters$stratum=="B")) f_2005_age.ests[x,8]<-mean(B.Psi.age.subset) f_2005_age.ests[x,9]<-mean(B.Psi.lcl.subset) f_2005_age.ests[x,10]<-mean(B.Psi.ucl.subset) NB.Psi.age.subset<-as.numeric(subset(Psi.parameters$estimate,Psi.parameters$Age==x & Psi.parameters$stratum=="N")) NB.Psi.lcl.subset<-as.numeric(subset(Psi.parameters$lcl,Psi.parameters$Age==x & Psi.parameters$stratum=="N")) NB.Psi.ucl.subset<-as.numeric(subset(Psi.parameters$ucl,Psi.parameters$Age==x & Psi.parameters$stratum=="N")) f_2005_age.ests[x,11]<-mean(NB.Psi.age.subset) f_2005_age.ests[x,12]<-mean(NB.Psi.lcl.subset) f_2005_age.ests[x,13]<-mean(NB.Psi.ucl.subset) } write.table(f_2005_age.ests,"...") ######################################################################################################################################################################################################################## ######################################################################################################################################################################################################################## ################ # 2006 Females # ################ library(RMark) setwd("...") climate_2006<-read.table("...", header = TRUE) attach(climate_2006) climate06=data.frame(time=climate_2006[,1],mean_temp_C_2006,prec_mm_2006,sun_hrs_2006) # Mite data mites_f_2006<-read.table("...", header = TRUE) attach(mites_f_2006) multistrat_F_2006<-import.chdata("...", header = TRUE, field.names = NULL, field.types = NULL) multistrat_F_2006$Mite_F_06<-Mite_F_06 multistrat_F_2006$Mite_F_06_sq<-Mite_F_06^2 multistrat_F_2006$WL<-F_06_Winglength multistrat_F_2006$WL_sq<-F_06_Winglength_sq multistrat_F_2006<-na.omit(multistrat_F_2006) # And actual parameters for the real models f_2006.process=process.data(multistrat_F_2006,model="Multistrata") f_2006.ddl=make.design.data(f_2006.process) f_2006.ddl$p<-merge_design.covariates(f_2006.ddl$p,climate06) f_2006.ddl$S<-merge_design.covariates(f_2006.ddl$S,climate06) f_2006.ddl$Psi<-merge_design.covariates(f_2006.ddl$Psi,climate06) # All the models for the different parameters p=list(formula=~prec_mm_2006+sun_hrs_2006+mean_temp_C_2006+Mite_F_06+Mite_F_06_sq+stratum) S=list(formula=~Age:stratum+I(Age^2):stratum+Mite_F_06+Mite_F_06_sq+stratum) Psi.c=list(formula=~prec_mm_2006+sun_hrs_2006+mean_temp_C_2006+stratum) Psi.m=list(formula=~Mite_F_06+Mite_F_06_sq+stratum) Psi.s=list(formula=~WL+WL_sq+stratum) Psi.x=list(formula=~Age:stratum+I(Age^2):stratum+stratum) Psi.c.m=list(formula=~prec_mm_2006+sun_hrs_2006+mean_temp_C_2006+Mite_F_06+Mite_F_06_sq+stratum) Psi.c.s=list(formula=~prec_mm_2006+sun_hrs_2006+mean_temp_C_2006+WL+WL_sq+stratum) Psi.c.x=list(formula=~prec_mm_2006+sun_hrs_2006+mean_temp_C_2006+Age:stratum+I(Age^2):stratum+stratum) Psi.m.s=list(formula=~Mite_F_06+Mite_F_06_sq+WL+WL_sq+stratum) Psi.m.x=list(formula=~Age:stratum+I(Age^2):stratum+Mite_F_06+Mite_F_06_sq+stratum) Psi.s.x=list(formula=~Age:stratum+I(Age^2):stratum+WL+WL_sq+stratum) Psi.c.m.s=list(formula=~prec_mm_2006+sun_hrs_2006+mean_temp_C_2006+Mite_F_06+Mite_F_06_sq+WL+WL_sq+stratum) Psi.c.m.x=list(formula=~prec_mm_2006+sun_hrs_2006+mean_temp_C_2006+Mite_F_06+Mite_F_06_sq+Age:stratum+I(Age^2):stratum+stratum) Psi.c.s.x=list(formula=~prec_mm_2006+sun_hrs_2006+mean_temp_C_2006+Age:stratum+I(Age^2):stratum+stratum+WL+WL_sq) Psi.m.s.x=list(formula=~Age:stratum+I(Age^2):stratum+Mite_F_06+Mite_F_06_sq+WL+WL_sq+stratum) Psi.c.m.s.x=list(formula=~prec_mm_2006+sun_hrs_2006+mean_temp_C_2006+Mite_F_06+Mite_F_06_sq+Age:stratum+I(Age^2):stratum+WL+WL_sq+stratum) #p(c+m+strat),Phi(x+m+strat),Psi(strat+c) f_2006_p.c.m.strat_phi.X.m.strat_psi.strat.c=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p,S=S,Psi=Psi.c),output=F,adjust=F,model.name="f_2006_p.c.m.strat_phi.X.m.strat_psi.strat.c") #p(c+m+strat),Phi(x+m+strat),Psi(strat+m) f_2006_p.c.m.strat_phi.X.m.strat_psi.strat.m=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p,S=S,Psi=Psi.m),output=F,adjust=F,model.name="f_2006_p.c.m.strat_phi.X.m.strat_psi.strat.m") #p(c+m+strat),Phi(x+m+strat),Psi(strat+s) f_2006_p.c.m.strat_phi.X.m.strat_psi.strat.s=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p,S=S,Psi=Psi.s),output=F,adjust=F,model.name="f_2006_p.c.m.strat_phi.X.m.strat_psi.strat.s") #p(c+m+strat),Phi(x+m+strat),Psi(strat+x) f_2006_p.c.m.strat_phi.X.m.strat_psi.strat.x=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p,S=S,Psi=Psi.x),output=F,adjust=F,model.name="f_2006_p.c.m.strat_phi.X.m.strat_psi.strat.x") #p(c+m+strat),Phi(x+m+strat),Psi(strat+c+m) f_2006_p.c.m.strat_phi.X.m.strat_psi.strat.c.m=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p,S=S,Psi=Psi.c.m),output=F,adjust=F,model.name="f_2006_p.c.m.strat_phi.X.m.strat_psi.strat.c.m") #p(c+m+strat),Phi(x+m+strat),Psi(strat+c+s) f_2006_p.c.m.strat_phi.X.m.strat_psi.strat.c.s=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p,S=S,Psi=Psi.c.s),output=F,adjust=F,model.name="f_2006_p.c.m.strat_phi.X.m.strat_psi.strat.c.s") #p(c+m+strat),Phi(x+m+strat),Psi(strat+c+x) f_2006_p.c.m.strat_phi.X.m.strat_psi.strat.c.x=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p,S=S,Psi=Psi.c.x),output=F,adjust=F,model.name="f_2006_p.c.m.strat_phi.X.m.strat_psi.strat.c.x") #p(c+m+strat),Phi(x+m+strat),Psi(strat+m+s) f_2006_p.c.m.strat_phi.X.m.strat_psi.strat.m.s=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p,S=S,Psi=Psi.m.s),output=F,adjust=F,model.name="f_2006_p.c.m.strat_phi.X.m.strat_psi.strat.m.s") #p(c+m+strat),Phi(x+m+strat),Psi(strat+m+x) f_2006_p.c.m.strat_phi.X.m.strat_psi.strat.m.x=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p,S=S,Psi=Psi.m.x),output=F,adjust=F,model.name="f_2006_p.c.m.strat_phi.X.m.strat_psi.strat.m.x") #p(c+m+strat),Phi(x+m+strat),Psi(strat+s+x) f_2006_p.c.m.strat_phi.X.m.strat_psi.strat.s.x=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p,S=S,Psi=Psi.s.x),output=F,adjust=F,model.name="f_2006_p.c.m.strat_phi.X.m.strat_psi.strat.s.x") #p(c+m+strat),Phi(x+m+strat),Psi(strat+c+m+s) f_2006_p.c.m.strat_phi.X.m.strat_psi.strat.c.m.s=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p,S=S,Psi=Psi.c.m.s),output=F,adjust=F,model.name="f_2006_p.c.m.strat_phi.X.m.strat_psi.strat.c.m.s") #p(c+m+strat),Phi(x+m+strat),Psi(strat+c+m+x) f_2006_p.c.m.strat_phi.X.m.strat_psi.strat.c.m.x=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p,S=S,Psi=Psi.c.m.x),output=F,adjust=F,model.name="f_2006_p.c.m.strat_phi.X.m.strat_psi.strat.c.m.x") #p(c+m+strat),Phi(x+m+strat),Psi(strat+c+s+x) f_2006_p.c.m.strat_phi.X.m.strat_psi.strat.c.s.x=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p,S=S,Psi=Psi.c.s.x),output=F,adjust=F,model.name="f_2006_p.c.m.strat_phi.X.m.strat_psi.strat.c.s.x") #p(c+m+strat),Phi(x+m+strat),Psi(strat+m+s+x) f_2006_p.c.m.strat_phi.X.m.strat_psi.strat.m.s.x=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p,S=S,Psi=Psi.m.s.x),output=F,adjust=F,model.name="f_2006_p.c.m.strat_phi.X.m.strat_psi.strat.m.s.x") #p(c+m+strat),Phi(x+m+strat),Psi(strat+c+m+s+x) f_2006_p.c.m.strat_phi.X.m.strat_psi.strat.c.m.s.x=mark(f_2006.process,f_2006.ddl,model.parameters=list(p=p,S=S,Psi=Psi.c.m.s.x),output=F,adjust=F,model.name="f_2006_p.c.m.strat_phi.X.m.strat_psi.strat.c.m.s.x") # Collect models f_2006_new_model_set<-collect.models(lx=c("f_2006_p.c.m.strat_phi.X.m.strat_psi.strat.c","f_2006_p.c.m.strat_phi.X.m.strat_psi.strat.m","f_2006_p.c.m.strat_phi.X.m.strat_psi.strat.s","f_2006_p.c.m.strat_phi.X.m.strat_psi.strat.x","f_2006_p.c.m.strat_phi.X.m.strat_psi.strat.c.m","f_2006_p.c.m.strat_phi.X.m.strat_psi.strat.c.s","f_2006_p.c.m.strat_phi.X.m.strat_psi.strat.c.x","f_2006_p.c.m.strat_phi.X.m.strat_psi.strat.m.s","f_2006_p.c.m.strat_phi.X.m.strat_psi.strat.m.x","f_2006_p.c.m.strat_phi.X.m.strat_psi.strat.s.x","f_2006_p.c.m.strat_phi.X.m.strat_psi.strat.c.m.s","f_2006_p.c.m.strat_phi.X.m.strat_psi.strat.c.m.x","f_2006_p.c.m.strat_phi.X.m.strat_psi.strat.c.s.x","f_2006_p.c.m.strat_phi.X.m.strat_psi.strat.m.s.x","f_2006_p.c.m.strat_phi.X.m.strat_psi.strat.c.m.s.x")) write.table(f_2006_new_model_set[16],"...") # List of models: f_2006_models<-list(f_2006_p.c.m.strat_phi.X.m.strat_psi.strat.c,f_2006_p.c.m.strat_phi.X.m.strat_psi.strat.m,f_2006_p.c.m.strat_phi.X.m.strat_psi.strat.s,f_2006_p.c.m.strat_phi.X.m.strat_psi.strat.x,f_2006_p.c.m.strat_phi.X.m.strat_psi.strat.c.m,f_2006_p.c.m.strat_phi.X.m.strat_psi.strat.c.s,f_2006_p.c.m.strat_phi.X.m.strat_psi.strat.c.x,f_2006_p.c.m.strat_phi.X.m.strat_psi.strat.m.s,f_2006_p.c.m.strat_phi.X.m.strat_psi.strat.m.x,f_2006_p.c.m.strat_phi.X.m.strat_psi.strat.s.x,f_2006_p.c.m.strat_phi.X.m.strat_psi.strat.c.m.s,f_2006_p.c.m.strat_phi.X.m.strat_psi.strat.c.m.x,f_2006_p.c.m.strat_phi.X.m.strat_psi.strat.c.s.x,f_2006_p.c.m.strat_phi.X.m.strat_psi.strat.m.s.x,f_2006_p.c.m.strat_phi.X.m.strat_psi.strat.c.m.s.x) # Model selection table library(MuMIn) f06_model.table<-model.sel(f_2006_models) write.table(f06_model.table,"...") # Model averaging of those models with delta-AIC <2 model.avg(f_2006_models, subset = delta<2) # Calculation of the importance of different variables importance(f_2006_models) # Extracting parameters from the models S.parameters<-get.real(f_2006_p.c.m.strat_phi.X.m.strat_psi.strat.c.s,parameter="S",se=TRUE) p.parameters<-get.real(f_2006_p.c.m.strat_phi.X.m.strat_psi.strat.c.s,parameter="p",se=TRUE) Psi.parameters<-get.real(f_2006_p.c.m.strat_phi.X.m.strat_psi.strat.c.s,parameter="Psi",se=TRUE) # Now use those parameters to average across ages and give mean esimates LCLs and UCLs f_2006_age.ests<-matrix(ncol=10,nrow=56) colnames(f_2006_age.ests)<-c("Age","S.Estimate","S.LCL","S.UCL","p.Estimate","p.LCL","p.UCL","Psi.Estimate","Psi.LCL","Psi.UCL") for(x in 1:76){ S.age.subset<-as.numeric(subset(S.parameters$estimate,S.parameters$Age==x)) f_2006_age.ests[x,1]<-x f_2006_age.ests[x,2]<-mean(S.age.subset) f_2006_age.ests[x,3]<-mean(S.age.subset)-1.96*(sd(S.age.subset)/sqrt(length(S.age.subset))) f_2006_age.ests[x,4]<-mean(S.age.subset)+1.96*(sd(S.age.subset)/sqrt(length(S.age.subset))) p.age.subset<-as.numeric(subset(p.parameters$estimate,p.parameters$Age==x)) f_2006_age.ests[x,5]<-mean(p.age.subset) f_2006_age.ests[x,6]<-mean(p.age.subset)-1.96*(sd(p.age.subset)/sqrt(length(p.age.subset))) f_2006_age.ests[x,7]<-mean(p.age.subset)+1.96*(sd(p.age.subset)/sqrt(length(p.age.subset))) Psi.age.subset<-as.numeric(subset(Psi.parameters$estimate,Psi.parameters$Age==x)) f_2006_age.ests[x,8]<-mean(Psi.age.subset) f_2006_age.ests[x,9]<-mean(Psi.age.subset)-1.96*(sd(Psi.age.subset)/sqrt(length(Psi.age.subset))) f_2006_age.ests[x,10]<-mean(Psi.age.subset)+1.96*(sd(Psi.age.subset)/sqrt(length(Psi.age.subset))) } # Plot with error bars plot(f_2006_age.ests[,1],f_2006_age.ests[,2]) polygon(c(rev(f_2006_age.ests[,1]),f_2006_age.ests[,1]),c(rev(f_2006_age.ests[,3]),f_2006_age.ests[,4]),col = "grey75", border = FALSE) lines(f_2006_age.ests[,1], f_2006_age.ests[,2], lwd = 2) lines(f_2006_age.ests[,1], f_2006_age.ests[,3], col="red",lty=2) lines(f_2006_age.ests[,1], f_2006_age.ests[,4], col="red",lty=2) write.table(f_2006_age.ests,"...") save.image("...") # Now use those parameters to average across ages and give mean esimates LCLs and UCLs f_2006_age.ests<-matrix(ncol=13,nrow=56) colnames(f_2006_age.ests)<-c("Age","B.S.mean","B.S.LCL","B.S.UCL","NB.S.mean","NB.S.LCL","NB.S.UCL","B.Psi.mean","B.Psi.LCL","B.Psi.UCL","NB.Psi.mean","NB.Psi.LCL","NB.Psi.UCL") for(x in 1:56){ B.S.age.subset<-as.numeric(subset(S.parameters$estimate,S.parameters$Age==x & S.parameters$stratum=="B")) B.S.lcl.subset<-as.numeric(subset(S.parameters$lcl,S.parameters$Age==x & S.parameters$stratum=="B")) B.S.ucl.subset<-as.numeric(subset(S.parameters$ucl,S.parameters$Age==x & S.parameters$stratum=="B")) f_2006_age.ests[x,1]<-x f_2006_age.ests[x,2]<-mean(B.S.age.subset) f_2006_age.ests[x,3]<-mean(B.S.lcl.subset) f_2006_age.ests[x,4]<-mean(B.S.ucl.subset) NB.S.age.subset<-as.numeric(subset(S.parameters$estimate,S.parameters$Age==x & S.parameters$stratum=="N")) NB.S.lcl.subset<-as.numeric(subset(S.parameters$lcl,S.parameters$Age==x & S.parameters$stratum=="N")) NB.S.ucl.subset<-as.numeric(subset(S.parameters$ucl,S.parameters$Age==x & S.parameters$stratum=="N")) f_2006_age.ests[x,5]<-mean(NB.S.age.subset) f_2006_age.ests[x,6]<-mean(NB.S.lcl.subset) f_2006_age.ests[x,7]<-mean(NB.S.ucl.subset) B.Psi.age.subset<-as.numeric(subset(Psi.parameters$estimate,Psi.parameters$Age==x & Psi.parameters$stratum=="B")) B.Psi.lcl.subset<-as.numeric(subset(Psi.parameters$lcl,Psi.parameters$Age==x & Psi.parameters$stratum=="B")) B.Psi.ucl.subset<-as.numeric(subset(Psi.parameters$ucl,Psi.parameters$Age==x & Psi.parameters$stratum=="B")) f_2006_age.ests[x,8]<-mean(B.Psi.age.subset) f_2006_age.ests[x,9]<-mean(B.Psi.lcl.subset) f_2006_age.ests[x,10]<-mean(B.Psi.ucl.subset) NB.Psi.age.subset<-as.numeric(subset(Psi.parameters$estimate,Psi.parameters$Age==x & Psi.parameters$stratum=="N")) NB.Psi.lcl.subset<-as.numeric(subset(Psi.parameters$lcl,Psi.parameters$Age==x & Psi.parameters$stratum=="N")) NB.Psi.ucl.subset<-as.numeric(subset(Psi.parameters$ucl,Psi.parameters$Age==x & Psi.parameters$stratum=="N")) f_2006_age.ests[x,11]<-mean(NB.Psi.age.subset) f_2006_age.ests[x,12]<-mean(NB.Psi.lcl.subset) f_2006_age.ests[x,13]<-mean(NB.Psi.ucl.subset) } write.table(f_2006_age.ests,"...")