guzhongru / enmsdm

Faster, better, smarter ecological niche modeling and species distribution modeling

enmSdm

This package is a complement to the popular `dismo` package for R by Robert Hijmans. Its contains a suite of efficiency functions for preparing data, training and evaluating species distribution models and ecological niche models, and comparing ecological niches.

You can install this package in R using these commands:

install.packages('devtools') # if you haven't done this already
library(devtools)
devtools::install_github('adamlilith/omnibus')
devtools::install_github('adamlilith/statisfactory')
devtools::install_github('adamlilith/legendary')
devtools::install_github('adamlilith/enmSdm')

NB: If for some reason these commands don't work, you can install the package(s) by downloading the latest zip/tar file from the zipTarFiles directory and installing the package(s) manually. If you do this, you will also have to install the omnibus, statisfactory, and legendary packages, which are on GitHub also under my account (adamlilith).

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)
• trainLars: Least-angle regression models (LARS)
• trainMaxEnt and trainMaxNet: Maxent models
• trainNs: Natural splines (NSs)
• trainRf: Random forests (RFs)

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)
• 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

• localSpatialCorrForValues: Calculate site-specific characteristic distance of local spatial autocorrelation for values associated with points or rasters
• 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
• interpolateRasters: Interpolate a stack of rasters
• longLatRasters: Generate rasters with values of longitude/latitude for cell values
• sampleRast and sampleRastStrat: Sample raster with/out replacement and possibly in a stratified manner

Range area based on minimum convex polygons

• mcpFromPolygons: Minimum convex polygon from a set of polygons and points
• areaFromPointsOrPoly: Area of a spatial polygon or set of points

Geographic utility functions

• convertTropicosCoords: Convert coordinates from the TROPICOS database
• coordPrecision: Calculate maximum possible coordinate precision
• dmsToDecimal: Convert degrees-minutes-seconds to decimal
• getCRS: Return a proj4string (coordinate reference system string) using a nickname
• pointDist: Geographic distance between set(s) of points
• xToCoords: Extract geographic coordinates from a data frame, matrix, or SpatialPoints* object