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71 lines
2.9 KiB
R
71 lines
2.9 KiB
R
# setwd("/home/darryl/Documents/CUSUM paper/weta")
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# library(RPresence)
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#
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#
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# # load a PRESENCE data file
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# filename<-system.file("extdata/weta.pao",package="RPresence")
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# weta.data<-read.pao(filename)
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#
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# ## convert indicator variables to categorical covariates
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# weta.data$unitcov$Habitat[weta.data$unitcov$Browsed==1] <- "browsed"
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# weta.data$unitcov$Habitat[weta.data$unitcov$Unbrowsed==1] <- "unbrowsed"
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# weta.data$survcov$Obs<-as.factor(
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# 1*weta.data$survcov$Obs1+
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# 2*weta.data$survcov$Obs2+
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# 3*weta.data$survcov$Obs3)
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#
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# ## fit some models
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# mod1<-occ.mod(model=list(psi~Habitat,p~SURVEY+Obs),data=weta.data,type="so")
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# mod2<-occ.mod(model=list(psi~Habitat,p~Obs),data=weta.data,type="so")
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# mod3<-occ.mod(model=list(psi~Habitat,p~SURVEY),data=weta.data,type="so")
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# mod4<-occ.mod(model=list(psi~Habitat,p~1),data=weta.data,type="so")
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# mod5<-occ.mod(model=list(psi~1,p~SURVEY+Obs),data=weta.data,type="so")
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# mod6<-occ.mod(model=list(psi~1,p~Obs),data=weta.data,type="so")
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# mod7<-occ.mod(model=list(psi~1,p~SURVEY),data=weta.data,type="so")
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# mod8<-occ.mod(model=list(psi~1,p~1),data=weta.data,type="so")
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#
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# r.8<-resid.test(mod8)
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# boot.8<-bootstrap.residuals(mod8,100,weta.data)
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#
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# jpeg("CUSUM_constant_%d.jpg",width=800,height=400,res=144)
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# par(mar=c(4,4,0,1)+0.3)
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# cusum.plot(weta.data$unitcov$Habitat,r.8$occ,boot.8$occ,ylab="Occupancy Residual",xlab="Habitat",xaxt="n",
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# ylim=c(-10,10))
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# axis(1,at=1:2,labels=c("Browsed","Unbrowsed"))
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#
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# cusum.plot(weta.data$survcov$Obs,r.8$det,boot.8$det,ylab="Detection Residual",xlab="Observer",xaxt="n",
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# ylim=c(-20,20))
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# axis(1,at=1:3,labels=LETTERS[1:3])
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#
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# cusum.plot(weta.data$survcov$SURVEY,r.8$det,boot.8$det,ylab="Detection Residual",xlab="Survey",xaxt="n",
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# ylim=c(-20,20))
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# axis(1,at=1:5,labels=1:5)
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#
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# cusum.plot(rep(weta.data$unitcov$Habitat,5),r.8$det,boot.8$det,ylab="Detection Residual",xlab="Habitat",xaxt="n",
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# ylim=c(-25,25))
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# axis(1,at=1:2,labels=c("Browsed","Unbrowsed"))
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# dev.off()
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#
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# r.1<-resid.test(mod1)
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# boot.1<-bootstrap.residuals(mod1,100,weta.data)
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#
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# jpeg("CUSUM_full_%d.jpg",width=800,height=400,res=144)
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# par(mar=c(4,4,0,1)+0.3)
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#
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# cusum.plot(weta.data$unitcov$Habitat,r.1$occ,boot.1$occ,ylab="Occupancy Residual",xlab="Habitat",xaxt="n",
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# ylim=c(-10,10))
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# axis(1,at=1:2,labels=c("Browsed","Unbrowsed"))
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#
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# cusum.plot(weta.data$survcov$Obs,r.1$det,boot.1$det,ylab="Detection Residual",xlab="Observer",xaxt="n",
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# ylim=c(-20,20))
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# axis(1,at=1:3,labels=LETTERS[1:3])
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#
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# cusum.plot(weta.data$survcov$SURVEY,r.1$det,boot.1$det,ylab="Detection Residual",xlab="Survey",xaxt="n",
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# ylim=c(-20,20))
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# axis(1,at=1:5,labels=1:5)
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#
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# cusum.plot(rep(weta.data$unitcov$Habitat,5),r.1$det,boot.1$det,ylab="Detection Residual",xlab="Habitat",xaxt="n",
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# ylim=c(-25,25))
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# axis(1,at=1:2,labels=c("Browsed","Unbrowsed"))
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# dev.off()
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