Package: ENMeval 2.0.4

ENMeval: Automated Tuning and Evaluations of Ecological Niche Models

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 niche 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>.

Authors:Jamie M. Kass [aut, cre], Robert Muscarella [aut], Peter J. Galante [aut], Corentin Bohl [aut], Gonzalo E. Buitrago-Pinilla [aut], Robert A. Boria [aut], Mariano Soley-Guardia [aut], Robert P. Anderson [aut]

ENMeval_2.0.4.tar.gz
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ENMeval_2.0.4.tgz(r-4.4-any)ENMeval_2.0.4.tgz(r-4.3-any)
ENMeval_2.0.4.tar.gz(r-4.5-noble)ENMeval_2.0.4.tar.gz(r-4.4-noble)
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ENMeval.pdf |ENMeval.html
ENMeval/json (API)
NEWS

# Install 'ENMeval' in R:
install.packages('ENMeval', repos = c('https://jamiemkass.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/jamiemkass/enmeval/issues

Datasets:

On CRAN:

8.55 score 49 stars 2 packages 274 scripts 2.2k downloads 92 mentions 76 exports 167 dependencies

Last updated 2 years agofrom:199bf01817. Checks:ERROR: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesFAILOct 31 2024
R-4.5-winWARNINGOct 31 2024
R-4.5-linuxWARNINGOct 31 2024
R-4.4-winWARNINGOct 31 2024
R-4.4-macWARNINGOct 31 2024
R-4.3-winWARNINGOct 31 2024
R-4.3-macWARNINGOct 31 2024

Exports:%>%aic.maxentbuildRMMcalc.niche.overlapclamp.varscorrected.varemp.bgemp.bg.grpemp.occsemp.occs.grpenm.argsenm.args<-enm.bioclimenm.errorsenm.errors<-enm.funenm.fun<-enm.maxent.jarenm.maxnetenm.msgsenm.msgs<-enm.nameenm.name<-enm.ncoefsenm.ncoefs<-enm.predictenm.predict<-enm.variable.importanceenm.variable.importance<-ENMdetailsENMevaluateENMevaluationENMevaluation_convertENMnullENMnullseval.algorithmeval.bgeval.bg.grpeval.clamp.directionseval.doClampeval.modelseval.occseval.occs.grpeval.occs.testingeval.other.settingseval.overlapeval.partition.methodeval.partition.settingseval.predictionseval.resultseval.results.partitionseval.rmmeval.taxon.nameeval.tune.settingseval.variable.importanceevalplot.envSim.histevalplot.envSim.mapevalplot.grpsevalplot.nullsevalplot.statsget.blockget.checkerboard1get.checkerboard2get.jackknifeget.randomkfoldnull.algorithmnull.doClampnull.emp.resultsnull.mod.settingsnull.no.iternull.other.settingsnull.partition.methodnull.partition.settingsnull.resultsnull.results.partitionssimilarity

Dependencies:apeaskpassassertthatbackportsbase64encBIENbitbit64blobbroombslibcachemcallrcellrangerclassclassIntclicliprcodetoolscolorspacecommonmarkconflictedcowplotcpp11crayoncrosstalkcrulcurldata.tableDBIdbplyrdigestdismodoParalleldoSNOWdplyrdtplyre1071evaluatefansifarverfasterizefastmapfontawesomeforcatsforeachfsgarglegenericsggplot2glmnetgluegoogledrivegooglesheets4gtablehavenhighrhmshtmltoolshtmlwidgetshttpcodehttpuvhttridsisobanditeratorsjquerylibjsonlitekableExtraKernSmoothknitrlabelinglaterlatticelazyevalleafletleaflet.providerslifecyclelubridatemagrittrmapsMASSMatrixmaxnetmemoisemgcvmimemodelrmunsellnlmeoaiopensslpillarpkgconfigplyrpngprettyunitsprocessxprogresspromisesproxypspurrrR6raggrangeModelMetadatarappdirsrasterRColorBrewerRcppRcppArmadilloRcppEigenreadrreadxlrebirdrematchrematch2reprexrgbifridigbiorlangrmarkdownRPostgreSQLrstudioapirvertnetrvests2sassscalesselectrsfshapeshinysnowsourcetoolsspspoccstringistringrsurvivalsvglitesyssystemfontsterratextshapingtibbletidyrtidyselecttidyversetimechangetinytextriebeardtzdbunitsurltoolsutf8uuidvctrsviridisLitevroomwhiskerwithrwkxfunxml2xtableyaml

Readme and manuals

Help Manual

Help pageTopics
Automated runs and evaluations of ecological niche modelsENMeval-package ENMeval
Calculate AICc from Maxent model predictionaic.maxent calc.aicc
Build metadata object from ENMeval resultsbuildRMM
Example occurrence dataset.bvariegatus
Calculate 10 percentile thresholdcalc.10p.trainThresh
Calculate Similarity of ENMs in Geographic Spacecalc.niche.overlap
Clamp predictor variablesclamp.vars
Corrected variance functioncorrected.var
emp.bg generic for ENMnull objectemp.bg emp.bg,ENMnull-method
emp.bg.grp generic for ENMnull objectemp.bg.grp emp.bg.grp,ENMnull-method
emp.occs generic for ENMnull objectemp.occs emp.occs,ENMnull-method
emp.occs.grp generic for ENMnull objectemp.occs.grp emp.occs.grp,ENMnull-method
enm.args generic for ENMdetails objectenm.args enm.args,ENMdetails-method enm.args<- enm.args<-,ENMdetails-method
ENMdetails bioclimenm.bioclim
enm.errors generic for ENMdetails objectenm.errors enm.errors,ENMdetails-method enm.errors<- enm.errors<-,ENMdetails-method
enm.fun generic for ENMdetails objectenm.fun enm.fun,ENMdetails-method enm.fun<- enm.fun<-,ENMdetails-method
ENMdetails maxent.jarenm.maxent.jar
ENMdetails maxnetenm.maxnet
enm.msgs generic for ENMdetails objectenm.msgs enm.msgs,ENMdetails-method enm.msgs<- enm.msgs<-,ENMdetails-method
eval.name generic for ENMdetails objectenm.name enm.name,ENMdetails-method enm.name<- enm.name<-,ENMdetails-method
enm.ncoefs generic for ENMdetails objectenm.ncoefs enm.ncoefs,ENMdetails-method enm.ncoefs<- enm.ncoefs<-,ENMdetails-method
enm.predict generic for ENMdetails objectenm.predict enm.predict,ENMdetails-method enm.predict<- enm.predict<-,ENMdetails-method
enm.variable.importance generic for ENMdetails objectenm.variable.importance enm.variable.importance,ENMdetails-method enm.variable.importance<- enm.variable.importance<-,ENMdetails-method
ENMdetails classENMdetails ENMdetails-class show,ENMdetails-method
Example ENMevaluation object.enmeval_results
Tune ecological niche model (ENM) settings and calculate evaluation statisticsENMevaluate
Convert old ENMevaluation objects to new onesENMevaluation_convert
ENMevaluation classENMevaluation ENMevaluation-class show,ENMevaluation-method
ENMnull classENMnull ENMnull-class show,ENMnull-method
Generate null ecological niche models (ENMs) and compare null with empirical performance metricsENMnulls
eval.algorithm generic for ENMevaluation objecteval.algorithm eval.algorithm,ENMevaluation-method
eval.bg generic for ENMevaluation objecteval.bg eval.bg,ENMevaluation-method
eval.bg.grp generic for ENMevaluation objecteval.bg.grp eval.bg.grp,ENMevaluation-method
eval.clamp.directions generic for ENMevaluation objecteval.clamp.directions eval.clamp.directions,ENMevaluation-method
eval.doClamp generic for ENMevaluation objecteval.doClamp eval.doClamp,ENMevaluation-method
eval.models generic for ENMevaluation objecteval.models eval.models,ENMevaluation-method eval.variable.importance,ENMevaluation-method
eval.occs generic for ENMevaluation objecteval.occs eval.occs,ENMevaluation-method
eval.occs.grp generic for ENMevaluation objecteval.occs.grp eval.occs.grp,ENMevaluation-method
eval.occs.testing generic for ENMevaluation objecteval.occs.testing eval.occs.testing,ENMevaluation-method
eval.other.settings generic for ENMevaluation objecteval.other.settings eval.other.settings,ENMevaluation-method
eval.overlap generic for ENMevaluation objecteval.overlap eval.overlap,ENMevaluation-method
eval.partition.method generic for ENMevaluation objecteval.partition.method eval.partition.method,ENMevaluation-method
eval.partition.settings generic for ENMevaluation objecteval.partition.settings eval.partition.settings,ENMevaluation-method
eval.predictions generic for ENMevaluation objecteval.predictions eval.predictions,ENMevaluation-method
eval.results generic for ENMevaluation objecteval.results eval.results,ENMevaluation-method
eval.results.partitions generic for ENMevaluation objecteval.results.partitions eval.results.partitions,ENMevaluation-method
eval.rmm generic for ENMevaluation objecteval.rmm eval.rmm,ENMevaluation-method
eval.taxon.name generic for ENMevaluation objecteval.taxon.name eval.taxon.name,ENMevaluation-method
eval.tune.settings generic for ENMevaluation objecteval.tune.settings eval.tune.settings,ENMevaluation-method
eval.variable.importance (variable importance) generic for ENMevaluation objecteval.variable.importance
Similarity histogram plots for partition groupsevalplot.envSim.hist
Similarity maps for partition groupsevalplot.envSim.map
Partition group plotsevalplot.grps
ENMnulls statistics plotevalplot.nulls
ENMevaluation statistics plotevalplot.stats
Look up ENMdetails abjectlookup.enm
Look up version of maxent.jarmaxentJARversion
null.algorithm generic for ENMnull objectnull.algorithm null.algorithm,ENMnull-method
null.doClamp generic for ENMnull objectnull.doClamp null.doClamp,ENMnull-method
null.emp.results generic for ENMnull objectnull.emp.results null.emp.results,ENMnull-method
null.mod.settings generic for ENMnull objectnull.mod.settings null.mod.settings,ENMnull-method
null.no.iter generic for ENMnull objectnull.no.iter null.no.iter,ENMnull-method
null.other.settings generic for ENMnull objectnull.other.settings null.other.settings,ENMnull-method
null.partition.method generic for ENMnull objectnull.partition.method null.partition.method,ENMnull-method
null.partition.settings generic for ENMnull objectnull.partition.settings null.partition.settings,ENMnull-method
null.results generic for ENMnull objectnull.results null.results,ENMnull-method
null.results.partitions generic for ENMnull objectnull.results.partitions null.results.partitions,ENMnull-method
Methods to partition data for evaluationget.block get.checkerboard1 get.checkerboard2 get.jackknife get.randomkfold partitions
Find NA cells in a RasterStackrasStackNAs
Calculate Multivariate Environmental Similaritysimilarity
Iterate tuning of ENMscv.enm tune.enm tune.parallel tune.regular tune.train tune.validate