enmSdm: enmSdm: Species distribution modeling and ecological niche...

In adamlilith/enmSdm: Tools for Modeling Niches and Distributions of Species

enmSdm: Species distribution modeling and ecological niche modeling

Description

This package contains tools for modeling the distributions and niches of species or species-like entities. Its main features are a set of functions for training ENMs, evaluating niche overlap, and correcting for sampling bias.

Details

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Data preparation

elimCellDups Eliminate duplicate points in each cell of a raster
geoFold Generate geographically distinct k-folds
geoThin and geoThinApprox Geographically thin points

Model training

trainByCrossValid Wrapper for implementing some trainXYZ function across cross-validation folds (see also summaryByCrossValid).
trainBrt Boosted regression trees (BRTs)
trainCrf Conditional regression trees (CRFs)
trainGam Generalized additive models (GAMs)
trainGlm Generalized linear models (GLMs)
trainGlmDredge Generalized linear models (GLMs)
trainMaxEnt and trainMaxNet Maxent models
trainNs Natural splines (NSs)
trainRf Random forests (RFs)

Model prediction

predictEnmSdm Predict most model types using default settings
predictMaxNet Predict MaxNet (MaxEnt) model

Model evaluation

aucWeighted AUC (with/out site weights)
aucMultiWeighted Multivariate version of AUC (with/out site weight)
contBoyce Continuous Boyce Index (with/out site weights)
contBoyce2x "2X coverage" version of the Continuous Boyce Index (with/out site weights)
fpb Fpb (with/out site weights)
thresholdWeighted Thresholds to convert continuous predictions to binary predictions (with/out site weights)
thresholdStats Model performance statistics based on thresholded predictions (with/out site weights)
tjursR2Weighted Tjur's R2 (with/out site weights)
tssWeighted True Skill Statistic (TSS) (with/out site weights)
modelSize Number of response values in a model object

Niche overlap

compareNiches Niche overlap metrics
compareResponse Compare niche model responses to a single variable
mop Calculate mobility-oriented parity, a measure of multivariate distance as per Saupe et al. 2012.
nicheOverlap Calculate niche overlap as per Broennimann et al. Global Ecology and Biogeography 21:481-497.
randPointsRespectingSelf Randomize geographic points while approximately respecting observed spatial autocorrelation structure between points
randPointsRespectingSelfOther2 Randomize two sets of geographic points while approximately respecting observed spatial autocorrelation structure between and within sets
randPointsBatch Call randPointsRespectingSelf or randPointsRespectingSelfOther2 multiple times
randPointsBatchExtract Extract environment from a set of rasters for sets of randomized points generated using 'randPointsBatch'
randPointsBatchSampled Collate all sets of randomized points generated using 'randPointsBatch'
randPointsBatchNicheOverlap Calculate niche overlap between sets of randomized points that were generated using 'randPointsBatch'

Spatial autocorrelation

spatialCorrForPoints Calculate pairwise distance-based measure of global spatial autocorrelation between geographic points
spatialCorrForPointsSummary Characteristic cluster size of spatial points (distance of global autocorrelation)
spatialCorrForPointsPlot Plot observed and null distributions of pairwise distance-based measure of global spatial autocorrelation
spatialCorrForPointsWeight Assign weights to points based on pairwise distance-based measure of global spatial autocorrelation

Functions for rasters

bioticVelocity Velocity of movement across a series of rasters
extractLarge Like extract(), but for large-memory spatial objects
getCores Get number of processor cores
interpolateRasters Interpolate a stack of rasters
longLatRasters Generate rasters with values of longitude/latitude for cell values
rastWithSquareCells Create a raster with square cells
sampleRast and sampleRastStrat Sample raster with/out replacement and possibly in a stratified manner
squareRastCells Resample a raster so cells are "square"

Range area based on minimum convex polygons

mcpFromPolys Minimum convex polygon from a set of polygons and points

Geographic utility functions

convertTropicosCoords Convert coordinates from the TROPICOS database
coordPrecision Calculate maximum possible coordinate precision
createPlotPoly Create a 'SpatialPolygon' the same size as a plot region
decimalToDms Convert decimal coordinate to degrees-minutes-seconds
dmsToDecimal Convert degrees-minutes-seconds coordinate to decimal
getCRS Return a proj4string (coordinate reference system string) using a nickname
getEPSG Return a EPSG code0 (coordinate reference system code) using a nickname
pointDist Geographic distance between set(s) of points
svToSpatial Convert SpatVector object to a Spatial* object.
xToCoords Extract geographic coordinates from a data frame, matrix, or SpatialPoints* object

Data

lemurs: Lemur occurrences
mad0: Madagascar spatial object

Author(s)

Adam B. Smith

adamlilith/enmSdm documentation built on Jan. 6, 2023, 11 a.m.