add.env                 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
                        tutorial
assert.extras           Assert that the extra packages needed for an
                        ENMTools function are installed and available
background.buffer       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
                        tutorial
background.points.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
                        tutorial
background.raster.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 tutorial
background.shape.buffer
                        Takes a set of points and a buffer radius, and
                        returns a polygon. Code modified from Elith and
                        Hijmans SDM with R tutorial
background.test         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.
calc.B1                 calc.B1, Calculates standardized version of
                        Levins (1968) B1 measure of niche breadth given
                        a vector of suitabilities
calc.B2                 calc.B2, Calculates standardized version of
                        Levins (1968) B2 measure of niche breadth given
                        a vector of suitabilities
check.bg                Takes an emtools.species object and adds
                        background points if they're missing. Looks for
                        range raster first, then goes for environmental
                        layers.
check.clade             Checking for complians of an enmtools.clade
                        object
check.env               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.extras            Check that the extra packages needed for an
                        ENMTools function are installed and available
check.species           Checking compliance for an object of class
                        enmtools.species.
clamp.env               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.
combine.species         Takes a list of enmtools.species objects and
                        combines them into a single enmtools.species
                        object
drop.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.
enmtools.aoc            Takes an overlap matrix and a tree and runs
                        permutation tests to determine the statistical
                        significance of the relationship between
                        overlap and time
enmtools.bc             Takes an emtools.species object with presence
                        and background points, and builds a Bioclim
                        model
enmtools.calibrate      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.clade          Defining a class for enmtools.clade.  Each
                        clade gets:
enmtools.dm             Takes an emtools.species object with presence
                        and background points, and builds a Domain
                        model
enmtools.ecospat.bg     enmtools.ecospat.bg, Runs an ecospat
                        background/similarity test using
                        enmtool.species objects.
enmtools.ecospat.id     enmtools.ecospat.id, Runs an ecospat identity
                        test using enmtool.species objects.
enmtools.gam            Takes an emtools.species object with presence
                        and background points, and builds a gam
enmtools.glm            Takes an enmtools.species object with presence
                        and background points, and builds a GLM
enmtools.hypervolume    THIS FUNCTION IS CURRENTLY DISABLED.  Takes an
                        emtools.species object and environmental
                        layers, and constructs a hypervolume using the
                        R package hypervolume
enmtools.maxent         Takes an emtools.species object with presence
                        and background points, and builds a maxent
                        model
enmtools.rf             Takes an emtools.species object with presence
                        and background points, and builds a random
                        forest model
enmtools.rf.ranger      Takes an emtools.species object with presence
                        and background points, and builds a random
                        forest model using the 'probability mode' in
                        package 'ranger'
enmtools.species        Defining a class for enmtools.species.
enmtools.vip            Takes an enmtools.model object, and performs
                        variable importance analyses on it using
                        methods from the vip package
env.breadth             Calculates breadth of a model in environment
                        space using latin hypercube sampling
env.evaluate            Calculates evaluation metrics (AUC, etc.) using
                        latin hypercube sampling in environment space
env.overlap             Calculates overlap between models in
                        environment space using latin hypercube
                        sampling
euro.worldclim          Worldclim data for Europe
find.extras             Find the extra packages needed for an ENMTools
                        function
find.extras.missing     Find the extra packages needed for an ENMTools
                        function that are currently missing (not
                        available)
geog.range.overlap      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).
hypervolume.overlap     Takes an emtools.species object and
                        environmental layers, and constructs a
                        hypervolume using the R package hypervolume
iberolacerta.clade      GBIF data for a clade of Iberolacerta lizards
                        from spain
identity.test           identity.test Conduct a niche
                        identity/equivalency test as described in
                        Warren et al. 2008.
install.extras          install.extras
interactive.plot        Generic function for making interactive plots
                        of ENMTools models and species
interactive.plot.enmtools.model
                        Plot an enmtools.model object on an interactive
                        map
interactive.plot.enmtools.species
                        Plot an enmtools.species object on an
                        interactive map
marginal.plots          marginal.plots Plots the marginal response of a
                        model to an environmental variable with all
                        other variables held at their mean in env
moses.list              Takes a list of enmtools.species objects and
                        uses model selection to ask whether they're
                        better treated jointly or separately
multistack.pca          multistack.pca, simultaneous PCA on more than
                        one stack of environmental rasters
node.overlap            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.
point.overlap           Takes two emtools.species objects with range
                        rasters, calculates overlap between them as in
                        Cardillo and Warren 2016
rangebreak.blob         rangebreak.blob Conduct a blob rangebreak test
                        as described in Glor and Warren 2011.
rangebreak.linear       rangebreak.linear Conduct a linear rangebreak
                        test as described in Glor and Warren 2011.
rangebreak.ribbon       rangebreak.ribbon Conduct a ribbon rangebreak
                        test as described in Glor and Warren 2011.
raster.breadth          raster.breadth, applies measures of niche
                        breadth to an ENM
raster.cor              Calculates the correlation coefficient between
                        two rasters.
raster.cor.matrix       Takes a raster stack and returns a data frame
                        containing Pearson correlation coefficients
                        between the included rasters
raster.cor.plot         Takes a raster stack and returns a data frame
                        containing Pearson correlation coefficients
                        between the included rasters
raster.overlap          raster.overlap, measures overlap between two
                        ENMs
raster.pca              raster.pca, PCA on a set of environmental
                        rasters
raster.resid            raster.resid Measure standardized residuals
                        from a linear regression between two rasters.
raster.standardize      raster.standardize, standardizes all values in
                        a raster file
rasterToPoints2         get terra to produce same output as
                        raster::rasterToPoints
sim.points              Simulate a point process from an enmtools.model
                        object
species.from.file       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.
threespace.plot         threespace.plot, A plot that compares the
                        environmental distribution of presence points,
                        background points, and the set of supplied
                        environmental layers.
trimdupes.by.raster     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.
unwrap_list             export
visualize.enm           visualize.enm, Makes a heatmap of suitability
                        of habitat in environment space according to a
                        given model
visualize.overlap       visualize.overlap, Makes a contour map of
                        suitability of habitat in environment space for
                        two models
wrap_list               export
