Automated Tuning and Evaluations of Ecological Niche Models


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Documentation for package ‘ENMeval’ version 2.0.1

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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 --

boyce.cm Continuous Boyce Index (modified from ecospat package)
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.varimp enm.varimp generic for ENMdetails object
enm.varimp-method enm.varimp generic for ENMdetails object
enm.varimp<- enm.varimp generic for ENMdetails object
enm.varimp<--method enm.varimp 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 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.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