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:
ENMeval_2.0.4.tar.gz
ENMeval_2.0.4.zip(r-4.5)ENMeval_2.0.4.zip(r-4.4)ENMeval_2.0.4.zip(r-4.3)
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)
ENMeval_2.0.4.tgz(r-4.4-emscripten)ENMeval_2.0.4.tgz(r-4.3-emscripten)
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')) |
Bug tracker:https://github.com/jamiemkass/enmeval/issues
- bvariegatus - Example occurrence dataset.
- enmeval_results - Example ENMevaluation object.
Last updated 2 years agofrom:199bf01817. Checks:ERROR: 1 WARNING: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | FAIL | Sep 01 2024 |
| R-4.5-win | WARNING | Sep 01 2024 |
| R-4.5-linux | WARNING | Sep 01 2024 |
| R-4.4-win | WARNING | Sep 01 2024 |
| R-4.4-mac | WARNING | Sep 01 2024 |
| R-4.3-win | WARNING | Sep 01 2024 |
| R-4.3-mac | WARNING | Sep 01 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 page | Topics |
|---|---|
| Automated runs and evaluations of ecological niche models | ENMeval-package ENMeval |
| Calculate AICc from Maxent model prediction | aic.maxent calc.aicc |
| Build metadata object from ENMeval results | buildRMM |
| Example occurrence dataset. | bvariegatus |
| Calculate 10 percentile threshold | calc.10p.trainThresh |
| Calculate Similarity of ENMs in Geographic Space | calc.niche.overlap |
| Clamp predictor variables | clamp.vars |
| Corrected variance function | corrected.var |
| emp.bg generic for ENMnull object | emp.bg emp.bg,ENMnull-method |
| emp.bg.grp generic for ENMnull object | emp.bg.grp emp.bg.grp,ENMnull-method |
| emp.occs generic for ENMnull object | emp.occs emp.occs,ENMnull-method |
| emp.occs.grp generic for ENMnull object | emp.occs.grp emp.occs.grp,ENMnull-method |
| enm.args generic for ENMdetails object | enm.args enm.args,ENMdetails-method enm.args<- enm.args<-,ENMdetails-method |
| ENMdetails bioclim | enm.bioclim |
| enm.errors generic for ENMdetails object | enm.errors enm.errors,ENMdetails-method enm.errors<- enm.errors<-,ENMdetails-method |
| enm.fun generic for ENMdetails object | enm.fun enm.fun,ENMdetails-method enm.fun<- enm.fun<-,ENMdetails-method |
| ENMdetails maxent.jar | enm.maxent.jar |
| ENMdetails maxnet | enm.maxnet |
| enm.msgs generic for ENMdetails object | enm.msgs enm.msgs,ENMdetails-method enm.msgs<- enm.msgs<-,ENMdetails-method |
| eval.name generic for ENMdetails object | enm.name enm.name,ENMdetails-method enm.name<- enm.name<-,ENMdetails-method |
| enm.ncoefs generic for ENMdetails object | enm.ncoefs enm.ncoefs,ENMdetails-method enm.ncoefs<- enm.ncoefs<-,ENMdetails-method |
| enm.predict generic for ENMdetails object | enm.predict enm.predict,ENMdetails-method enm.predict<- enm.predict<-,ENMdetails-method |
| enm.variable.importance generic for ENMdetails object | enm.variable.importance enm.variable.importance,ENMdetails-method enm.variable.importance<- enm.variable.importance<-,ENMdetails-method |
| ENMdetails class | ENMdetails ENMdetails-class show,ENMdetails-method |
| Example ENMevaluation object. | enmeval_results |
| Tune ecological niche model (ENM) settings and calculate evaluation statistics | ENMevaluate |
| Convert old ENMevaluation objects to new ones | ENMevaluation_convert |
| ENMevaluation class | ENMevaluation ENMevaluation-class show,ENMevaluation-method |
| ENMnull class | ENMnull ENMnull-class show,ENMnull-method |
| Generate null ecological niche models (ENMs) and compare null with empirical performance metrics | ENMnulls |
| eval.algorithm generic for ENMevaluation object | eval.algorithm eval.algorithm,ENMevaluation-method |
| eval.bg generic for ENMevaluation object | eval.bg eval.bg,ENMevaluation-method |
| eval.bg.grp generic for ENMevaluation object | eval.bg.grp eval.bg.grp,ENMevaluation-method |
| eval.clamp.directions generic for ENMevaluation object | eval.clamp.directions eval.clamp.directions,ENMevaluation-method |
| eval.doClamp generic for ENMevaluation object | eval.doClamp eval.doClamp,ENMevaluation-method |
| eval.models generic for ENMevaluation object | eval.models eval.models,ENMevaluation-method eval.variable.importance,ENMevaluation-method |
| eval.occs generic for ENMevaluation object | eval.occs eval.occs,ENMevaluation-method |
| eval.occs.grp generic for ENMevaluation object | eval.occs.grp eval.occs.grp,ENMevaluation-method |
| eval.occs.testing generic for ENMevaluation object | eval.occs.testing eval.occs.testing,ENMevaluation-method |
| eval.other.settings generic for ENMevaluation object | eval.other.settings eval.other.settings,ENMevaluation-method |
| eval.overlap generic for ENMevaluation object | eval.overlap eval.overlap,ENMevaluation-method |
| eval.partition.method generic for ENMevaluation object | eval.partition.method eval.partition.method,ENMevaluation-method |
| eval.partition.settings generic for ENMevaluation object | eval.partition.settings eval.partition.settings,ENMevaluation-method |
| eval.predictions generic for ENMevaluation object | eval.predictions eval.predictions,ENMevaluation-method |
| eval.results generic for ENMevaluation object | eval.results eval.results,ENMevaluation-method |
| eval.results.partitions generic for ENMevaluation object | eval.results.partitions eval.results.partitions,ENMevaluation-method |
| eval.rmm generic for ENMevaluation object | eval.rmm eval.rmm,ENMevaluation-method |
| eval.taxon.name generic for ENMevaluation object | eval.taxon.name eval.taxon.name,ENMevaluation-method |
| eval.tune.settings generic for ENMevaluation object | eval.tune.settings eval.tune.settings,ENMevaluation-method |
| eval.variable.importance (variable importance) generic for ENMevaluation object | eval.variable.importance |
| Similarity histogram plots for partition groups | evalplot.envSim.hist |
| Similarity maps for partition groups | evalplot.envSim.map |
| Partition group plots | evalplot.grps |
| ENMnulls statistics plot | evalplot.nulls |
| ENMevaluation statistics plot | evalplot.stats |
| Look up ENMdetails abject | lookup.enm |
| Look up version of maxent.jar | maxentJARversion |
| null.algorithm generic for ENMnull object | null.algorithm null.algorithm,ENMnull-method |
| null.doClamp generic for ENMnull object | null.doClamp null.doClamp,ENMnull-method |
| null.emp.results generic for ENMnull object | null.emp.results null.emp.results,ENMnull-method |
| null.mod.settings generic for ENMnull object | null.mod.settings null.mod.settings,ENMnull-method |
| null.no.iter generic for ENMnull object | null.no.iter null.no.iter,ENMnull-method |
| null.other.settings generic for ENMnull object | null.other.settings null.other.settings,ENMnull-method |
| null.partition.method generic for ENMnull object | null.partition.method null.partition.method,ENMnull-method |
| null.partition.settings generic for ENMnull object | null.partition.settings null.partition.settings,ENMnull-method |
| null.results generic for ENMnull object | null.results null.results,ENMnull-method |
| null.results.partitions generic for ENMnull object | null.results.partitions null.results.partitions,ENMnull-method |
| Methods to partition data for evaluation | get.block get.checkerboard1 get.checkerboard2 get.jackknife get.randomkfold partitions |
| Find NA cells in a RasterStack | rasStackNAs |
| Calculate Multivariate Environmental Similarity | similarity |
| Iterate tuning of ENMs | cv.enm tune.enm tune.parallel tune.regular tune.train tune.validate |
