Automated Tuning and Evaluations of Ecological Niche Models
ENMnull class
Generate null ecological niche models (ENMs) and compare null with emp...
eval.algorithm generic for ENMevaluation object
eval.bg.grp generic for ENMevaluation object
eval.bg generic for ENMevaluation object
eval.clamp.directions generic for ENMevaluation object
eval.doClamp generic for ENMevaluation object
eval.models generic for ENMevaluation object
eval.occs.grp generic for ENMevaluation object
eval.occs generic for ENMevaluation object
eval.occs.testing generic for ENMevaluation object
eval.other.settings generic for ENMevaluation object
eval.overlap generic for ENMevaluation object
eval.partition.method generic for ENMevaluation object
eval.partition.settings generic for ENMevaluation object
eval.predictions generic for ENMevaluation object
eval.results.partitions generic for ENMevaluation object
eval.results generic for ENMevaluation object
eval.rmm generic for ENMevaluation object
eval.taxon.name generic for ENMevaluation object
eval.tune.settings generic for ENMevaluation object
eval.variable.importance (variable importance) generic for ENMevaluati...
Similarity histogram plots for partition groups
Similarity maps for partition groups
Partition group plots
ENMnulls statistics plot
ENMevaluation statistics plot
Load ENMevaluation object
Look up ENMdetails abject
Look up version of maxent.jar
Predict raster for maxnet
null.algorithm generic for ENMnull object
null.doClamp generic for ENMnull object
null.emp.results generic for ENMnull object
null.mod.settings generic for ENMnull object
null.no.iter generic for ENMnull object
null.other.settings generic for ENMnull object
null.partition.method generic for ENMnull object
null.partition.settings generic for ENMnull object
null.results.partitions generic for ENMnull object
null.results generic for ENMnull object
Calculate AICc from Maxent model prediction
Build metadata object from ENMeval results
Calculate 10 percentile threshold
Calculate Similarity of ENMs in Geographic Space
Clamp predictor variables
Corrected variance function
emp.bg.grp generic for ENMnull object
emp.bg generic for ENMnull object
emp.occs.grp generic for ENMnull object
emp.occs generic for ENMnull object
enm.args generic for ENMdetails object
ENMdetails bioclim
enm.errors generic for ENMdetails object
enm.fun generic for ENMdetails object
ENMdetails maxent.jar
ENMdetails maxnet
enm.msgs generic for ENMdetails object
eval.name generic for ENMdetails object
enm.ncoefs generic for ENMdetails object
enm.predict generic for ENMdetails object
enm.variable.importance generic for ENMdetails object
ENMdetails class
Automated runs and evaluations of ecological niche models
Tune ecological niche model (ENM) settings and calculate evaluation st...
Convert old ENMevaluation objects to new ones
ENMevaluation class
Parse Maxent lambdas information
Methods to partition data for evaluation
Internal plotting function
Save ENMevaluation object
Iterate tuning of ENMs
Runs ecological niche models over all combinations of user-defined settings (i.e., tuning), performs cross validation to evaluate models, and returns data tables to aid in selection of optimal model settings that balance goodness-of-fit and model complexity. Also has functions to partition data spatially (or not) for cross validation, to plot multiple visualizations of results, to run null models to estimate significance and effect sizes of performance metrics, and to calculate range overlap between model predictions, among others. The package was originally built for Maxent models (Phillips et al. 2006, Phillips et al. 2017), but the current version allows possible extensions for any modeling algorithm. The extensive vignette, which guides users through most package functionality but unfortunately has a file size too big for CRAN, can be found here on the package's Github Pages website: <https://jamiemkass.github.io/ENMeval/articles/ENMeval-2.0-vignette.html>.