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test.vif.occu <- function() {
set.seed(123)
data(frogs)
pferUMF <- unmarkedFrameOccu(pfer.bin)
siteCovs(pferUMF) <- data.frame(sitevar1 = rnorm(numSites(pferUMF)))
#Add some correlated covariates
obsvar2 = rnorm(numSites(pferUMF) * obsNum(pferUMF))
obsvar3 = rnorm(numSites(pferUMF) * obsNum(pferUMF),mean=obsvar2,sd=0.5)
obsCovs(pferUMF) <- data.frame(
obsvar1 = rnorm(numSites(pferUMF) * obsNum(pferUMF)),
obsvar2=obsvar2,obsvar3=obsvar3)
fm <- occu(~ obsvar1+obsvar2+obsvar3 ~ 1, pferUMF)
#No type provided
checkException(vif_vals <- vif(fm))
#Wrong type provided
checkException(vif_vals <- vif(fm, type='fake'))
#Not enough covs
checkException(vif_vals <- vif(fm, type='state'))
#Get values for det
vif_vals <- vif(fm, type='det')
checkEqualsNumeric(vif_vals, c(1.002240,4.49552,4.490039),tol=1e-4)
checkEquals(names(vif_vals),c('obsvar1','obsvar2','obsvar3'))
#Compare to typical way of calculating
set.seed(123)
vt <- lm(obsvar2~obsvar1+obsvar3,data=obsCovs(pferUMF))
vt_2 <- 1/(1-summary(vt)$r.squared)
checkEqualsNumeric(vif_vals[2],vt_2,tol=0.1)
}
test.vif.multinomPois <- function(){
set.seed(123)
data(ovendata)
ovenFrame <- unmarkedFrameMPois(ovendata.list$data,
siteCovs=as.data.frame(scale(ovendata.list$covariates[,-1])),
type = "removal")
fm1 <- multinomPois(~ 1 ~ ufc + trba, ovenFrame)
vif_vals <- vif(fm1, type='state')
checkEqualsNumeric(vif_vals, c(1.285886,1.285886), tol=1e-4)
}
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