# Automated Tuning and Evaluations of Ecological Niche Models

## Documentation for package ‘ENMeval’ version 2.0.4

- DESCRIPTION file.
- Package NEWS.

## Help Pages

A B C E G L M N P R S T

ENMeval-package | Automated runs and evaluations of ecological niche models

## -- A --

aic.maxent | Calculate AICc from Maxent model prediction

## -- B --

buildRMM | Build metadata object from ENMeval results
bvariegatus | Example occurrence dataset.

## -- C --

calc.10p.trainThresh | Calculate 10 percentile threshold
calc.aicc | Calculate AICc from Maxent model prediction
calc.niche.overlap | Calculate Similarity of ENMs in Geographic Space
clamp.vars | Clamp predictor variables
corrected.var | Corrected variance function
cv.enm | Iterate tuning of ENMs

## -- E --

emp.bg | emp.bg generic for ENMnull object
emp.bg-method | emp.bg generic for ENMnull object
emp.bg.grp | emp.bg.grp generic for ENMnull object
emp.bg.grp-method | emp.bg.grp generic for ENMnull object
emp.occs | emp.occs generic for ENMnull object
emp.occs-method | emp.occs generic for ENMnull object
emp.occs.grp | emp.occs.grp generic for ENMnull object
emp.occs.grp-method | emp.occs.grp generic for ENMnull object
enm.args | enm.args generic for ENMdetails object
enm.args-method | enm.args generic for ENMdetails object
enm.args<- | enm.args generic for ENMdetails object
enm.args<--method | enm.args generic for ENMdetails object
enm.bioclim | ENMdetails bioclim
enm.errors | enm.errors generic for ENMdetails object
enm.errors-method | enm.errors generic for ENMdetails object
enm.errors<- | enm.errors generic for ENMdetails object
enm.errors<--method | enm.errors generic for ENMdetails object
enm.fun | enm.fun generic for ENMdetails object
enm.fun-method | enm.fun generic for ENMdetails object
enm.fun<- | enm.fun generic for ENMdetails object
enm.fun<--method | enm.fun generic for ENMdetails object
enm.maxent.jar | ENMdetails maxent.jar
enm.maxnet | ENMdetails maxnet
enm.msgs | enm.msgs generic for ENMdetails object
enm.msgs-method | enm.msgs generic for ENMdetails object
enm.msgs<- | enm.msgs generic for ENMdetails object
enm.msgs<--method | enm.msgs generic for ENMdetails object
enm.name | eval.name generic for ENMdetails object
enm.name-method | eval.name generic for ENMdetails object
enm.name<- | eval.name generic for ENMdetails object
enm.name<--method | eval.name generic for ENMdetails object
enm.ncoefs | enm.ncoefs generic for ENMdetails object
enm.ncoefs-method | enm.ncoefs generic for ENMdetails object
enm.ncoefs<- | enm.ncoefs generic for ENMdetails object
enm.ncoefs<--method | enm.ncoefs generic for ENMdetails object
enm.predict | enm.predict generic for ENMdetails object
enm.predict-method | enm.predict generic for ENMdetails object
enm.predict<- | enm.predict generic for ENMdetails object
enm.predict<--method | enm.predict generic for ENMdetails object
enm.variable.importance | enm.variable.importance generic for ENMdetails object
enm.variable.importance-method | enm.variable.importance generic for ENMdetails object
enm.variable.importance<- | enm.variable.importance generic for ENMdetails object
enm.variable.importance<--method | enm.variable.importance generic for ENMdetails object
ENMdetails | ENMdetails class
ENMdetails-class | ENMdetails class
ENMeval | Automated runs and evaluations of ecological niche models
ENMevaluate | Tune ecological niche model (ENM) settings and calculate evaluation statistics
ENMevaluation | ENMevaluation class
ENMevaluation-class | ENMevaluation class
ENMevaluation_convert | Convert old ENMevaluation objects to new ones
enmeval_results | Example ENMevaluation object.
ENMnull | ENMnull class
ENMnull-class | ENMnull class
ENMnulls | Generate null ecological niche models (ENMs) and compare null with empirical performance metrics
eval.algorithm | eval.algorithm generic for ENMevaluation object
eval.algorithm-method | eval.algorithm generic for ENMevaluation object
eval.bg | eval.bg generic for ENMevaluation object
eval.bg-method | eval.bg generic for ENMevaluation object
eval.bg.grp | eval.bg.grp generic for ENMevaluation object
eval.bg.grp-method | eval.bg.grp generic for ENMevaluation object
eval.clamp.directions | eval.clamp.directions generic for ENMevaluation object
eval.clamp.directions-method | eval.clamp.directions generic for ENMevaluation object
eval.doClamp | eval.doClamp generic for ENMevaluation object
eval.doClamp-method | eval.doClamp generic for ENMevaluation object
eval.models | eval.models generic for ENMevaluation object
eval.models-method | eval.models generic for ENMevaluation object
eval.occs | eval.occs generic for ENMevaluation object
eval.occs-method | eval.occs generic for ENMevaluation object
eval.occs.grp | eval.occs.grp generic for ENMevaluation object
eval.occs.grp-method | eval.occs.grp generic for ENMevaluation object
eval.occs.testing | eval.occs.testing generic for ENMevaluation object
eval.occs.testing-method | eval.occs.testing generic for ENMevaluation object
eval.other.settings | eval.other.settings generic for ENMevaluation object
eval.other.settings-method | eval.other.settings generic for ENMevaluation object
eval.overlap | eval.overlap generic for ENMevaluation object
eval.overlap-method | eval.overlap generic for ENMevaluation object
eval.partition.method | eval.partition.method generic for ENMevaluation object
eval.partition.method-method | eval.partition.method generic for ENMevaluation object
eval.partition.settings | eval.partition.settings generic for ENMevaluation object
eval.partition.settings-method | eval.partition.settings generic for ENMevaluation object
eval.predictions | eval.predictions generic for ENMevaluation object
eval.predictions-method | eval.predictions generic for ENMevaluation object
eval.results | eval.results generic for ENMevaluation object
eval.results-method | eval.results generic for ENMevaluation object
eval.results.partitions | eval.results.partitions generic for ENMevaluation object
eval.results.partitions-method | eval.results.partitions generic for ENMevaluation object
eval.rmm | eval.rmm generic for ENMevaluation object
eval.rmm-method | eval.rmm generic for ENMevaluation object
eval.taxon.name | eval.taxon.name generic for ENMevaluation object
eval.taxon.name-method | eval.taxon.name generic for ENMevaluation object
eval.tune.settings | eval.tune.settings generic for ENMevaluation object
eval.tune.settings-method | eval.tune.settings generic for ENMevaluation object
eval.variable.importance | eval.variable.importance (variable importance) generic for ENMevaluation object
eval.variable.importance-method | eval.models 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

## -- G --

get.block | Methods to partition data for evaluation
get.checkerboard1 | Methods to partition data for evaluation
get.checkerboard2 | Methods to partition data for evaluation
get.jackknife | Methods to partition data for evaluation
get.randomkfold | Methods to partition data for evaluation

## -- L --

lookup.enm | Look up ENMdetails abject

## -- M --

maxentJARversion | Look up version of maxent.jar

## -- N --

null.algorithm | null.algorithm generic for ENMnull object
null.algorithm-method | null.algorithm generic for ENMnull object
null.doClamp | null.doClamp generic for ENMnull object
null.doClamp-method | null.doClamp generic for ENMnull object
null.emp.results | null.emp.results generic for ENMnull object
null.emp.results-method | null.emp.results generic for ENMnull object
null.mod.settings | null.mod.settings generic for ENMnull object
null.mod.settings-method | null.mod.settings generic for ENMnull object
null.no.iter | null.no.iter generic for ENMnull object
null.no.iter-method | null.no.iter generic for ENMnull object
null.other.settings | null.other.settings generic for ENMnull object
null.other.settings-method | null.other.settings generic for ENMnull object
null.partition.method | null.partition.method generic for ENMnull object
null.partition.method-method | null.partition.method generic for ENMnull object
null.partition.settings | null.partition.settings generic for ENMnull object
null.partition.settings-method | null.partition.settings generic for ENMnull object
null.results | null.results generic for ENMnull object
null.results-method | null.results generic for ENMnull object
null.results.partitions | null.results.partitions generic for ENMnull object
null.results.partitions-method | null.results.partitions generic for ENMnull object

## -- P --

partitions | Methods to partition data for evaluation

## -- R --

rasStackNAs | Find NA cells in a RasterStack

## -- S --

show-method | ENMdetails class
show-method | ENMevaluation class
show-method | ENMnull class
similarity | Calculate Multivariate Environmental Similarity

## -- T --

tune.enm | Iterate tuning of ENMs
tune.parallel | Iterate tuning of ENMs
tune.regular | Iterate tuning of ENMs
tune.train | Iterate tuning of ENMs
tune.validate | Iterate tuning of ENMs