rm(list=ls())
#install unmarked if not installed
#install.packages("unmarked")
#load library
library(unmarked)
## Loading required package: reshape
## Loading required package: lattice
## Loading required package: parallel
## Loading required package: Rcpp
bfly<-read.csv("../Butterfly.csv")
bfly<-subset(bfly,select=c(Field,Border,Transect,Treatment,Date,Visit,CLLESSU))
library(reshape)
bfly$Transect=as.factor(bfly$Transect)
junk<-melt(bfly,id.var=c("Transect","Visit"),measure.var="CLLESSU")
j2=cast(junk,Transect ~ Visit)
covs<-subset(bfly,select=c(Transect,Treatment))
covs<-as.data.frame(with(covs,table(Transect,Treatment)))
covs<-subset(covs,Freq>0)
site.cov<-merge(j2,covs,by="Transect")[,8]
site.cov<-data.frame(treatment=site.cov)
y<-j2[,2:7]
y<-cbind(j2$"1",j2$"2",j2$"3",j2$"4",j2$"5",j2$"6")
S <- nrow(y) # number of sites
J <- 2 # number of secondary sampling occasions
T <- 3 # number of primary period
#dummy variables to createseasonal effects (need 2 for 3 occasions)
season<-as.factor(rep(c(1,2,3),S))
yearly.cov<-data.frame(season)
#additive time effects within season. to model effects change between seasons create an interaction term
secondary<-as.factor(rep(c(1,2,1,2,1,2),S))
second.cov<-data.frame(secondary)
butterfly<-unmarkedMultFrame(y=y,siteCovs=site.cov, numPrimary=T,yearlySiteCovs=yearly.cov,obsCovs=second.cov)
fm1<-colext(psiformula = ~1, gammaformula = ~1, epsilonformula = ~1,
pformula = ~1, data=butterfly)
#back transformations
backTransform(fm1,'det')
## Backtransformed linear combination(s) of Detection estimate(s)
##
## Estimate SE LinComb (Intercept)
## 0.497 0.033 -0.0116 1
##
## Transformation: logistic
backTransform(fm1,"psi")
## Backtransformed linear combination(s) of Initial estimate(s)
##
## Estimate SE LinComb (Intercept)
## 0.771 0.0607 1.22 1
##
## Transformation: logistic
backTransform(fm1,"col")
## Backtransformed linear combination(s) of Colonization estimate(s)
##
## Estimate SE LinComb (Intercept)
## 0.437 0.11 -0.254 1
##
## Transformation: logistic
backTransform(fm1,"ext")
## Backtransformed linear combination(s) of Extinction estimate(s)
##
## Estimate SE LinComb (Intercept)
## 0.0909 0.0529 -2.3 1
##
## Transformation: logistic
fm2<-colext(psiformula = ~treatment, gammaformula = ~1, epsilonformula = ~1,
pformula = ~1, data=butterfly)
fm3<-colext(psiformula= ~1, gammaformula = ~treatment, epsilonformula = ~1,
pformula = ~1, data=butterfly)
fm4<-colext(psiformula= ~1, gammaformula = ~1, epsilonformula = ~treatment,
pformula = ~1, data=butterfly)
fm1
##
## Call:
## colext(psiformula = ~1, gammaformula = ~1, epsilonformula = ~1,
## pformula = ~1, data = butterfly)
##
## Initial:
## Estimate SE z P(>|z|)
## 1.22 0.344 3.54 0.000406
##
## Colonization:
## Estimate SE z P(>|z|)
## -0.254 0.447 -0.568 0.57
##
## Extinction:
## Estimate SE z P(>|z|)
## -2.3 0.64 -3.6 0.00032
##
## Detection:
## Estimate SE z P(>|z|)
## -0.0116 0.132 -0.0879 0.93
##
## AIC: 1024.421
fm2
##
## Call:
## colext(psiformula = ~treatment, gammaformula = ~1, epsilonformula = ~1,
## pformula = ~1, data = butterfly)
##
## Initial:
## Estimate SE z P(>|z|)
## (Intercept) 0.243 0.619 0.392 0.695
## treatmentburncontrol 0.581 0.828 0.702 0.482
## treatmentdisk 7.775 18.476 0.421 0.674
## treatmentdiskcontrol 1.263 0.856 1.476 0.140
## treatmentfieldcontrol 0.298 0.817 0.365 0.715
##
## Colonization:
## Estimate SE z P(>|z|)
## -0.0662 0.403 -0.164 0.869
##
## Extinction:
## Estimate SE z P(>|z|)
## -2.07 0.57 -3.63 0.000279
##
## Detection:
## Estimate SE z P(>|z|)
## 0.0528 0.13 0.406 0.685
##
## AIC: 1022.907
fm3
##
## Call:
## colext(psiformula = ~1, gammaformula = ~treatment, epsilonformula = ~1,
## pformula = ~1, data = butterfly)
##
## Initial:
## Estimate SE z P(>|z|)
## 1.19 0.33 3.59 0.000329
##
## Colonization:
## Estimate SE z P(>|z|)
## (Intercept) -2.94 3.48 -0.844 0.399
## treatmentburncontrol 3.07 3.53 0.868 0.385
## treatmentdisk 2.95 3.94 0.749 0.454
## treatmentdiskcontrol 2.04 3.48 0.585 0.558
## treatmentfieldcontrol 3.86 3.62 1.068 0.285
##
## Extinction:
## Estimate SE z P(>|z|)
## -2.42 0.687 -3.52 0.000437
##
## Detection:
## Estimate SE z P(>|z|)
## -0.022 0.131 -0.168 0.867
##
## AIC: 1025.79
fm4
##
## Call:
## colext(psiformula = ~1, gammaformula = ~1, epsilonformula = ~treatment,
## pformula = ~1, data = butterfly)
##
## Initial:
## Estimate SE z P(>|z|)
## 1.19 0.341 3.49 0.000487
##
## Colonization:
## Estimate SE z P(>|z|)
## -0.18 0.432 -0.417 0.677
##
## Extinction:
## Estimate SE z P(>|z|)
## (Intercept) -1.112 0.958 -1.161 0.246
## treatmentburncontrol -1.803 1.717 -1.050 0.294
## treatmentdisk -0.589 1.280 -0.460 0.645
## treatmentdiskcontrol -2.822 3.511 -0.804 0.422
## treatmentfieldcontrol -0.539 1.176 -0.459 0.646
##
## Detection:
## Estimate SE z P(>|z|)
## 0.00403 0.132 0.0304 0.976
##
## AIC: 1029.132