All functions

show(<ENMdetails>)

ENMdetails class

ENMeval-package

Automated runs and evaluations of ecological niche models

ENMevaluate()

Tune ecological niche model (ENM) settings and calculate evaluation statistics

show(<ENMevaluation>)

ENMevaluation class

show(<ENMnull>)

ENMnull class

ENMnulls()

Generate null ecological niche models (ENMs) and compare null with empirical performance metrics

aic.maxent()

Calculate AICc from Maxent model prediction

buildRMM()

Build metadata object from ENMeval results

bvariegatus

Example occurrence dataset.

calc.10p.trainThresh()

Calculate 10 percentile threshold

calc.niche.overlap()

Calculate Similarity of ENMs in Geographic Space

clamp.vars()

Clamp predictor variables

corrected.var()

Corrected variance function

emp.bg()

emp.bg generic for ENMnull object

emp.bg.grp()

emp.bg.grp generic for ENMnull object

emp.occs()

emp.occs generic for ENMnull object

emp.occs.grp()

emp.occs.grp generic for ENMnull object

enm.args() `enm.args<-`()

enm.args generic for ENMdetails object

enm.bioclim

ENMdetails bioclim

enm.errors() `enm.errors<-`()

enm.errors generic for ENMdetails object

enm.fun() `enm.fun<-`()

enm.fun generic for ENMdetails object

enm.maxent.jar

ENMdetails maxent.jar

enm.maxnet

ENMdetails maxnet

enm.msgs() `enm.msgs<-`()

enm.msgs generic for ENMdetails object

enm.name() `enm.name<-`()

eval.name generic for ENMdetails object

enm.ncoefs() `enm.ncoefs<-`()

enm.ncoefs generic for ENMdetails object

enm.predict() `enm.predict<-`()

enm.predict generic for ENMdetails object

enm.varimp() `enm.varimp<-`()

enm.varimp generic for ENMdetails object

enmeval_results

Example ENMevaluation object.

eval.algorithm()

eval.algorithm generic for ENMevaluation object

eval.bg()

eval.bg generic for ENMevaluation object

eval.bg.grp()

eval.bg.grp generic for ENMevaluation object

eval.clamp.directions()

eval.clamp.directions generic for ENMevaluation object

eval.doClamp()

eval.doClamp generic for ENMevaluation object

eval.models()

eval.models generic for ENMevaluation object

eval.occs()

eval.occs generic for ENMevaluation object

eval.occs.grp()

eval.occs.grp generic for ENMevaluation object

eval.occs.testing()

eval.occs.testing generic for ENMevaluation object

eval.other.settings()

eval.other.settings generic for ENMevaluation object

eval.overlap()

eval.overlap generic for ENMevaluation object

eval.partition.method()

eval.partition.method generic for ENMevaluation object

eval.partition.settings()

eval.partition.settings generic for ENMevaluation object

eval.predictions()

eval.predictions generic for ENMevaluation object

eval.results()

eval.results generic for ENMevaluation object

eval.results.partitions()

eval.results.partitions generic for ENMevaluation object

eval.rmm()

eval.rmm generic for ENMevaluation object

eval.taxon.name()

eval.taxon.name generic for ENMevaluation object

eval.tune.settings()

eval.tune.settings generic for ENMevaluation object

eval.variable.importance()

eval.variable.importance generic for ENMevaluation object

evalplot.envSim.hist()

Similarity histogram plots for partition groups

evalplot.envSim.map()

Similarity maps for partition groups

evalplot.grps()

Partition group plots

evalplot.nulls()

ENMnulls statistics plot

evalplot.stats()

ENMevaluation statistics plot

lookup.enm()

Look up ENMdetails abject

maxentJARversion()

Look up version of maxent.jar

null.algorithm()

null.algorithm generic for ENMnull object

null.emp.results()

null.emp.results generic for ENMnull object

null.mod.settings()

null.mod.settings generic for ENMnull object

null.no.iter()

null.no.iter generic for ENMnull object

null.other.settings()

null.other.settings generic for ENMnull object

null.partition.method()

null.partition.method generic for ENMnull object

null.partition.settings()

null.partition.settings generic for ENMnull object

null.results()

null.results generic for ENMnull object

null.results.partitions()

null.results.partitions generic for ENMnull object

get.block() get.checkerboard1() get.checkerboard2() get.jackknife() get.randomkfold()

Methods to partition data for evaluation

rasStackNAs()

Find NA cells in a RasterStack

similarity()

Calculate Multivariate Environmental Similarity

tune.train() tune.validate() tune.parallel() tune.regular() cv.enm()

Iterate tuning of ENMs