## ----setup, include = FALSE--------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>", fig.width=6, fig.height=4 ) ## ----------------------------------------------------------------------------- library(iccCounts) ## ----------------------------------------------------------------------------- AF_P<-icc_counts(AF,y="y",id="id",met="met",type="con") ## ----------------------------------------------------------------------------- ICC(AF_P) ## ----------------------------------------------------------------------------- VarComp(AF_P) ## ----------------------------------------------------------------------------- set.seed(100) AF_P.gof<-GOF_check(AF_P) ## ---- fig.width=6, fig.height=4----------------------------------------------- plot(AF_P.gof,type="envelope") ## ----------------------------------------------------------------------------- plot(AF_P.gof,type="dispersion") DispersionTest(AF_P.gof) ## ----------------------------------------------------------------------------- plot(AF_P.gof,type="zeros") ZeroTest(AF_P.gof) ## ----------------------------------------------------------------------------- AF_NB1<-icc_counts(AF,y="y",id="id",met="met",type="con", fam="nbinom1") AF_NB2<-icc_counts(AF,y="y",id="id",met="met",type="con", fam="nbinom2") AIC(AF_NB1$model) AIC(AF_NB2$model) ## ----------------------------------------------------------------------------- set.seed(100) AF_NB2.gof<-GOF_check(AF_NB2) ## ----------------------------------------------------------------------------- plot(AF_NB2.gof,type="envelope") ## ----------------------------------------------------------------------------- plot(AF_NB2.gof,type="dispersion") DispersionTest(AF_NB2.gof) ## ----------------------------------------------------------------------------- ICC(AF_NB2) ## ----------------------------------------------------------------------------- VarComp(AF_NB2) ## ----------------------------------------------------------------------------- G_P<-icc_counts(Grimso,y="Tot",id="TransectID") ICC(G_P) VarComp(G_P) ## ---- fig.height=12, fig.width=8---------------------------------------------- set.seed(100) G_P.gof<-GOF_check(G_P) plot(G_P.gof) ## ----------------------------------------------------------------------------- DispersionTest(G_P.gof) ZeroTest(G_P.gof) ## ----------------------------------------------------------------------------- EPP_P<-icc_counts(EPP,y="Social",id="id") ICC(EPP_P) VarComp(EPP_P) ## ----------------------------------------------------------------------------- set.seed(100) EPP_P.gof<-GOF_check(EPP_P) plot(EPP_P.gof,type="envelope") ## ----------------------------------------------------------------------------- plot(EPP_P.gof,type="dispersion") DispersionTest(EPP_P.gof) ## ----------------------------------------------------------------------------- plot(EPP_P.gof,type="zeros") ZeroTest(EPP_P.gof) ## ----------------------------------------------------------------------------- EPP_NB1<-icc_counts(EPP,y="Social",id="id",fam="nbinom1") EPP_NB2<-icc_counts(EPP,y="Social",id="id",fam="nbinom2") AIC(EPP_NB1$model) AIC(EPP_NB2$model) ## ----------------------------------------------------------------------------- set.seed(100) EPP_NB1.gof<-GOF_check(EPP_NB1) plot(EPP_NB1.gof,type="envelope") ## ----------------------------------------------------------------------------- plot(EPP_NB1.gof,type="dispersion") DispersionTest(EPP_NB1.gof) ## ----------------------------------------------------------------------------- plot(EPP_NB1.gof,type="zeros") ZeroTest(EPP_NB1.gof) ## ----------------------------------------------------------------------------- EPP_ZIP<-icc_counts(EPP,y="Social",id="id",fam="zip") ICC(EPP_ZIP) VarComp(EPP_ZIP) ## ----------------------------------------------------------------------------- set.seed(100) EPP_ZIP.gof<-GOF_check(EPP_ZIP) plot(EPP_ZIP.gof,type="envelope") ## ----------------------------------------------------------------------------- plot(EPP_ZIP.gof,type="dispersion") DispersionTest(EPP_ZIP.gof) plot(EPP_ZIP.gof,type="zeros") ZeroTest(EPP_ZIP.gof)