Dear list member,
I am running a maxent model in dismo package and I got AUC = 1, but I am
not sure if this is right. Is there a way to find out if my evaluation
is correct?
Here is my code:
# fit model
me <- maxent(predictores, dendro)
# plot showing importance of each variable
plot(me)
# predict to entire dataset
r <- predict(me, predictores, progress='text')
# r <- predict(me, predictors, progress='text', args=c("outputformat=raw"))
plot(r)
points(dendro)
# The below is equivalent (except that we use
# k-fold partitioning of the data for testing purposes
# extract values
pv <- data.frame(xyValues(predictores, dendro))
fp <- kfold(pv, k=5)
pvtrain <- pv[fp != 1, ]
pvtest <- pv[fp == 1, ]
head(pvtest)
# background data
bg <- randomPoints(predictores, 210)
av <- data.frame(xyValues(predictores, bg))
fb <- kfold(av, k=5)
avtrain <- av[fb != 1, ]
avtest <- av[fb == 1, ]
# combine train presence and background data
train <- rbind(pvtrain, avtrain)
# vector indicating presence or absence
p <- c(rep(1, nrow(pvtrain)), rep(0, nrow(avtrain)))
# fit maxent model
me2 <- maxent(x=train, p=p)
# predict to testing points
testp <- predict(me, pvtest)
head(testp)
testa <- predict(me, avtest)
#evaluate
e = evaluate(p=testp, a=testa)
e
plot(e, 'ROC')
RESULTADOS:
> e
class : ModelEvaluation
n presences : 14
n absences : 42
AUC : 1
cor : 0.9428767
TPR+TNR threshold: 0.04
Thank you very much in advance.
Best,
Manuel
--
*Manuel Spínola, Ph.D.*
Instituto Internacional en Conservación y Manejo de Vida Silvestre
Universidad Nacional
Apartado 1350-3000
Heredia
COSTA RICA
mspin...@una.ac.cr
mspinol...@gmail.com
Teléfono: (506) 2277-3598
Fax: (506) 2237-7036
Personal website: Lobito de río
<https://sites.google.com/site/lobitoderio/>
Institutional website: ICOMVIS <http://www.icomvis.una.ac.cr/>
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