Automated Tuning and Evaluations of Ecological Niche Models
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Documentation for package ‘ENMeval’ version 2.0.4
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| 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 |