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ENMTools (version 1.1.2)

Analysis of Niche Evolution using Niche and Distribution Models

Description

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) Glor, R.E., and D.L. Warren (2011) Warren, D.L., R.E. Glor, and M. Turelli (2010) Cardillo, M., and D.L. Warren (2016) D.L. Warren, L.J. Beaumont, R. Dinnage, and J.B. Baumgartner (2019) .

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Install

install.packages('ENMTools')

Monthly Downloads

720

Version

1.1.2

License

GPL-2

Maintainer

Last Published

January 16th, 2024

Functions in ENMTools (1.1.2)

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.

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

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.

Takes an overlap matrix and a tree and runs permutation tests to determine the statistical significance of the relationship between overlap and time

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

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

Checking compliance for an object of class enmtools.species.

enmtools.ecospat.bg

enmtools.ecospat.bg, Runs an ecospat background/similarity test using enmtool.species objects.

Takes an emtools.species object with presence and background points, and builds a random forest model

enmtools.ecospat.id

enmtools.ecospat.id, Runs an ecospat identity test using enmtool.species objects.

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`

Takes an enmtools.species object with presence and background points, and builds a GLM

Takes an emtools.species object with presence and background points, and builds a gam

Takes an emtools.species object with presence and background points, and builds a Domain model

Defining a class for enmtools.clade. Each clade gets:

enmtools.species

Defining a class for enmtools.species.

Calculates evaluation metrics (AUC, etc.) using latin hypercube sampling in environment space

Calculates breadth of a model in environment space using latin hypercube sampling

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)

hypervolume.overlap

Takes an emtools.species object and environmental layers, and constructs a hypervolume using the R package hypervolume

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).

Calculates overlap between models in environment space using latin hypercube sampling

Worldclim data for Europe

Takes a list of enmtools.species objects and uses model selection to ask whether they're better treated jointly or separately

Takes an enmtools.model object, and performs variable importance analyses on it using methods from the vip package

marginal.plots Plots the marginal response of a model to an environmental variable with all other variables held at their mean in env

multistack.pca, simultaneous PCA on more than one stack of environmental rasters

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.

iberolacerta.clade

GBIF data for a clade of Iberolacerta lizards from spain

identity.test Conduct a niche identity/equivalency test as described in Warren et al. 2008.

raster.cor.plot

Takes a raster stack and returns a data frame containing Pearson correlation coefficients between the included rasters

raster.cor.matrix

Takes a raster stack and returns a data frame containing Pearson correlation coefficients between the included rasters

raster.pca, PCA on a set of environmental rasters

interactive.plot.enmtools.species

Plot an enmtools.species object on an interactive map

interactive.plot.enmtools.model

Plot an enmtools.model object on an interactive map

raster.overlap, measures overlap between two ENMs

Calculates the correlation coefficient between two rasters.

rasterToPoints2

get terra to produce same output as raster::rasterToPoints

rangebreak.ribbon

rangebreak.ribbon Conduct a ribbon 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.

Simulate a point process from an enmtools.model object

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.

raster.breadth, applies measures of niche breadth to an 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

raster.standardize

raster.standardize, standardizes all values in a raster file

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.

raster.resid Measure standardized residuals from a linear regression between two rasters.

threespace.plot

threespace.plot, A plot that compares the environmental distribution of presence points, background points, and the set of supplied environmental layers.

interactive.plot

Generic function for making interactive plots of ENMTools models and species

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.

calc.B2, Calculates standardized version of Levins (1968) B2 measure of niche breadth given a vector of suitabilities

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

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

Check that the extra packages needed for an ENMTools function are installed and available

Assert that the extra packages needed for an ENMTools function are installed and available

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

Takes an emtools.species object and adds background points if they're missing. Looks for range raster first, then goes for environmental layers.

Takes an emtools.species object with presence and background points, and builds a Bioclim model

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.

Checking for complians of an enmtools.clade object

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.

calc.B1, Calculates standardized version of Levins (1968) B1 measure of niche breadth given a vector of suitabilities