Package: ENMTools 1.1.3

ENMTools: Analysis of Niche Evolution using Niche and Distribution Models

Constructing niche models and analyzing patterns of niche evolution. Acts as an interface for many popular modeling algorithms, and allows users to conduct Monte Carlo tests to address basic questions in evolutionary ecology and biogeography. Warren, D.L., R.E. Glor, and M. Turelli (2008) <doi:10.1111/j.1558-5646.2008.00482.x> Glor, R.E., and D.L. Warren (2011) <doi:10.1111/j.1558-5646.2010.01177.x> Warren, D.L., R.E. Glor, and M. Turelli (2010) <doi:10.1111/j.1600-0587.2009.06142.x> Cardillo, M., and D.L. Warren (2016) <doi:10.1111/geb.12455> D.L. Warren, L.J. Beaumont, R. Dinnage, and J.B. Baumgartner (2019) <doi:10.1111/ecog.03900>.

Authors:Dan Warren [aut, cre], Russell Dinnage [aut]

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ENMTools.pdf |ENMTools.html✨
ENMTools/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/danlwarren/enmtools/issues

On CRAN:

72 exports 100 stars 6.87 score 200 dependencies 181 mentions 109 scripts 732 downloads

Last updated 1 months agofrom:7b188291e6. Checks:OK: 7. Indexed: yes.

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Doc / VignettesOKSep 11 2024
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R-4.5-linuxOKSep 11 2024
R-4.4-winOKSep 11 2024
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Exports:add.envassert.extrasbackground.bufferbackground.points.bufferbackground.raster.bufferbackground.shape.bufferbackground.testcalc.B1calc.B2check.bgcheck.cladecheck.envcheck.extrascheck.speciesclamp.envcombine.speciesdrop.speciesenmtools.aocenmtools.bcenmtools.calibrateenmtools.cladeenmtools.dmenmtools.ecospat.bgenmtools.ecospat.idenmtools.gamenmtools.glmenmtools.hypervolumeenmtools.maxentenmtools.rfenmtools.rf.rangerenmtools.speciesenmtools.vipenv.breadthenv.evaluateenv.overlapeuro.worldclimfind.extrasfind.extras.missinggeog.range.overlaphypervolume.overlapiberolacerta.cladeidentity.testinstall.extrasinteractive.plotinteractive.plot.enmtools.modelinteractive.plot.enmtools.speciesload.enmtools.cladeload.enmtools.speciesmarginal.plotsmoses.listmultistack.pcanode.overlappoint.overlaprangebreak.blobrangebreak.linearrangebreak.ribbonraster.breadthraster.corraster.cor.matrixraster.cor.plotraster.overlapraster.pcaraster.residraster.standardizesave.enmtools.cladesave.enmtools.speciessim.pointsspecies.from.filethreespace.plottrimdupes.by.rastervisualize.enmvisualize.overlap

Dependencies:abindapeaskpassassertthatbackportsbase64encBIENbitbit64blobbootbroombslibcachemcallrcarcarDatacellrangerclassclassIntclicliprcodetoolscolorspacecommonmarkconflictedcorrplotcowplotcpp11crayoncrosstalkcrulcurldata.tableDBIdbplyrdeldirDerivdigestdismodoBydoParalleldoSNOWdplyrdtplyre1071ENMevalevaluatefansifarverfasterizefastmapfontawesomeforcatsforeachfsgarglegenericsggplot2ggpubrggrepelggsciggsignifglmnetgluegoogledrivegooglesheets4gridExtragtablehavenhighrhmshtmltoolshtmlwidgetshttpcodehttpuvhttridsisobanditeratorsjquerylibjsonlitekableExtraKernSmoothknitrlabelinglaterlatticelazyevalleafletleaflet.providerslhslifecyclelme4lubridatemagrittrmapsMASSMatrixMatrixModelsmaxnetmemoisemgcvmicrobenchmarkmimeminqamodelrmunsellnlmenloptrnnetnumDerivoaiopensslpbkrtestpillarpkgconfigplyrpngpolyclippolynomprettyunitsprocessxprogresspromisesproxypspurrrquantregR6raggrangeModelMetadatarappdirsrasterRColorBrewerRcppRcppArmadilloRcppEigenreadrreadxlrebirdrematchrematch2reprexrgbifridigbiorlangrmarkdownRPostgreSQLrstatixrstudioapirvertnetrvests2sassscalesselectrsfshapeshinysnowsourcetoolsspSparseMspatstat.dataspatstat.geomspatstat.randomspatstat.univarspatstat.utilsspoccstringistringrsurvivalsvglitesyssystemfontsterratextshapingtibbletidyrtidyselecttidyversetimechangetinytextriebeardtzdbunitsurltoolsutf8uuidvctrsviridisLitevroomwhiskerwithrwkxfunxml2xtableyaml

Readme and manuals

Help Manual

Help pageTopics
Takes an enmtools.species object and a set of environment layers, and adds the environmental predictor values to the occurrence data. Typically not called by the user directly. Code modified from Elith and Hijmans SDM with R tutorialadd.env
Assert that the extra packages needed for an ENMTools function are installed and availableassert.extras
Takes a set of points, a buffer radius, a buffer type, and a mask and returns either a raster, a polygon, or background points representing the species background. Code modified from Elith and Hijmans SDM with R tutorialbackground.buffer
Takes a set of points, a buffer radius, a sample size, and a mask and returns randomly sampled points from within that buffer radius. Code modified from Elith and Hijmans SDM with R tutorialbackground.points.buffer
Takes a set of points, a buffer radius, and a mask and returns a raster based on that buffer radius. Code modified from Elith and Hijmans SDM with R tutorialbackground.raster.buffer
Takes a set of points and a buffer radius, and returns a polygon. Code modified from Elith and Hijmans SDM with R tutorialbackground.shape.buffer
background.test Conduct a background test (also called a similarity test), as described in Warren et al. 2008. This test can either be run as an asymmetric test (species.1 vs background of species.2) or as a symmetric test (background of species.1 vs background of species.2). For GLM, Bioclim, and Domain models the replicates will be constructed from the background points supplied for each species. For Maxent, the replicates will be constructed from the range rasters stored in the enmtools.species objects.background.test
calc.B1, Calculates standardized version of Levins (1968) B1 measure of niche breadth given a vector of suitabilitiescalc.B1
calc.B2, Calculates standardized version of Levins (1968) B2 measure of niche breadth given a vector of suitabilitiescalc.B2
Takes an emtools.species object and adds background points if they're missing. Looks for range raster first, then goes for environmental layers.check.bg
Checking for complians of an enmtools.clade objectcheck.clade
Automating some basic tasks for using a raster stack for modeling. Checks rasters for same extent and resolution, and sets values in each layer to NA if there is an NA in any other layer.check.env
Check that the extra packages needed for an ENMTools function are installed and availablecheck.extras
Checking compliance for an object of class enmtools.species.check.species
Takes an emtools.model object and a set of environment layers and clamps the environment layers so that no variable falls outside of the range available in the training data.clamp.env
Takes a list of enmtools.species objects and combines them into a single enmtools.species objectcombine.species
Takes a an ENMTools clade object and a vector of species names. Drops the species from the tree and removes data from the clade object.drop.species
Takes an overlap matrix and a tree and runs permutation tests to determine the statistical significance of the relationship between overlap and timeenmtools.aoc
Takes an emtools.species object with presence and background points, and builds a Bioclim modelenmtools.bc
Takes an emtools.model object, and reformats it to run through the CalibratR package, calculates Continuous Boyce Index, and runs a Hosmer-Lemeshow goodness-of-fit test. Can either do a full CalibratR run or just return ECE/MCE statistics and plots.enmtools.calibrate
Defining a class for enmtools.clade. Each clade gets:enmtools.clade load.enmtools.clade save.enmtools.clade
Takes an emtools.species object with presence and background points, and builds a Domain modelenmtools.dm
enmtools.ecospat.bg, Runs an ecospat background/similarity test using enmtool.species objects.enmtools.ecospat.bg
enmtools.ecospat.id, Runs an ecospat identity test using enmtool.species objects.enmtools.ecospat.id
Takes an emtools.species object with presence and background points, and builds a gamenmtools.gam
Takes an enmtools.species object with presence and background points, and builds a GLMenmtools.glm
THIS FUNCTION IS CURRENTLY DISABLED. Takes an emtools.species object and environmental layers, and constructs a hypervolume using the R package hypervolumeenmtools.hypervolume
Takes an emtools.species object with presence and background points, and builds a maxent modelenmtools.maxent
Takes an emtools.species object with presence and background points, and builds a random forest modelenmtools.rf
Takes an emtools.species object with presence and background points, and builds a random forest model using the 'probability mode' in package `ranger`enmtools.rf.ranger
Defining a class for enmtools.species.enmtools.species load.enmtools.species save.enmtools.species
Takes an enmtools.model object, and performs variable importance analyses on it using methods from the vip packageenmtools.vip
Calculates breadth of a model in environment space using latin hypercube samplingenv.breadth
Calculates evaluation metrics (AUC, etc.) using latin hypercube sampling in environment spaceenv.evaluate
Calculates overlap between models in environment space using latin hypercube samplingenv.overlap
Worldclim data for Europeeuro.worldclim
Find the extra packages needed for an ENMTools functionfind.extras
Find the extra packages needed for an ENMTools function that are currently missing (not available)find.extras.missing
Takes two emtools.species objects with range rasters, calculates overlap between them as in Fitzpatrick and Turelli 2006. This metric divides the area of overlap between two species ranges by the smaller of the two areas of the species' individual ranges. It therefore ranges from 0 (no overlap) to 1 (ranges are the same or the smaller species' range is contained entirely within the larger).geog.range.overlap
Takes an emtools.species object and environmental layers, and constructs a hypervolume using the R package hypervolumehypervolume.overlap
GBIF data for a clade of Iberolacerta lizards from spainiberolacerta.clade
identity.test Conduct a niche identity/equivalency test as described in Warren et al. 2008.identity.test
install.extrasinstall.extras
Generic function for making interactive plots of ENMTools models and speciesinteractive.plot
Plot an enmtools.model object on an interactive mapinteractive.plot.enmtools.model
Plot an enmtools.species object on an interactive mapinteractive.plot.enmtools.species
marginal.plots Plots the marginal response of a model to an environmental variable with all other variables held at their mean in envmarginal.plots
Takes a list of enmtools.species objects and uses model selection to ask whether they're better treated jointly or separatelymoses.list
multistack.pca, simultaneous PCA on more than one stack of environmental rastersmultistack.pca
Takes an overlap matrix and a tree and returns average overlap at nodes using Fitzpatrick & Turelli averaging method. Typicall called via enmtools.aoc rather than used directly.node.overlap
Takes two emtools.species objects with range rasters, calculates overlap between them as in Cardillo and Warren 2016point.overlap
rangebreak.blob Conduct a blob rangebreak test as described in Glor and Warren 2011.rangebreak.blob
rangebreak.linear Conduct a linear rangebreak test as described in Glor and Warren 2011.rangebreak.linear
rangebreak.ribbon Conduct a ribbon rangebreak test as described in Glor and Warren 2011.rangebreak.ribbon
raster.breadth, applies measures of niche breadth to an ENMraster.breadth
Calculates the correlation coefficient between two rasters.raster.cor
Takes a raster stack and returns a data frame containing Pearson correlation coefficients between the included rastersraster.cor.matrix
Takes a raster stack and returns a data frame containing Pearson correlation coefficients between the included rastersraster.cor.plot
raster.overlap, measures overlap between two ENMsraster.overlap
raster.pca, PCA on a set of environmental rastersraster.pca
raster.resid Measure standardized residuals from a linear regression between two rasters.raster.resid
raster.standardize, standardizes all values in a raster fileraster.standardize
get terra to produce same output as raster::rasterToPointsrasterToPoints2
Simulate a point process from an enmtools.model objectsim.points
Takes a csv file and uses it to construct one or more enmtools.species objects. It constructs one object per unique value in the "species.col" column.species.from.file
threespace.plot, A plot that compares the environmental distribution of presence points, background points, and the set of supplied environmental layers.threespace.plot
Takes a set of points and a raster mask and returns a data frame trimmed so that only one point is returned per grid cell in the mask raster.trimdupes.by.raster
exportunwrap_list
visualize.enm, Makes a heatmap of suitability of habitat in environment space according to a given modelvisualize.enm
visualize.overlap, Makes a contour map of suitability of habitat in environment space for two modelsvisualize.overlap
exportwrap_list