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
).
elimCellDups
: Eliminate duplicate points in each cell of a rastergeoFold
: Generate geographically distinct k-foldsgeoThin
andgeoThinApprox
: Geographically thin points
trainByCrossValid
: Wrapper for implementing sometrainXYZ
function across cross-validation folds (see alsosummaryByCrossValid
).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
andtrainMaxNet
: Maxent modelstrainNs
: Natural splines (NSs)trainRf
: Random forests (RFs)
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
compareNiches
: Niche overlap metricscompareResponse
: Compare niche model responses to a single variablemop
: 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 21:481-497randPointsRespectingSelf
: Randomize geographic points while approximately respecting observed spatial autocorrelation structure between pointsrandPointsRespectingSelfOther2
: Randomize two sets of geographic points while approximately respecting observed spatial autocorrelation structure between and within setsrandPointsBatch
: CallrandPointsRespectingSelf
orrandPointsRespectingSelfOther2
multiple timesrandPointsBatchExtract
: Extract environment from a set of rasters for sets of randomized points generated usingrandPointsBatch
randPointsBatchSampled
: Collate all sets of randomized points generated usingrandPointsBatch
randPointsBatchNicheOverlap
: Calculate niche overlap between sets of randomized points that were generated usingrandPointsBatch
localSpatialCorrForValues
: Calculate site-specific characteristic distance of local spatial autocorrelation for values associated with points or rastersspatialCorrForPoints
: Calculate pairwise distance-based measure of global spatial autocorrelation between geographic pointsspatialCorrForPointsSummary
: Characteristic cluster size of spatial points (distance of global autocorrelation)spatialCorrForPointsPlot
: Plot observed and null distributions of pairwise distance-based measure of global spatial autocorrelationspatialCorrForPointsWeight
: Assign weights to points based on pairwise distance-based measure of global spatial autocorrelation
bioticVelocity
: Velocity of movement across a series of rastersinterpolateRasters
: Interpolate a stack of rasterslongLatRasters
: Generate rasters with values of longitude/latitude for cell valuessampleRast
andsampleRastStrat
: Sample raster with/out replacement and possibly in a stratified manner
mcpFromPolygons
: Minimum convex polygon from a set of polygons and pointsareaFromPointsOrPoly
: Area of a spatial polygon or set of points
convertTropicosCoords
: Convert coordinates from the TROPICOS databasecoordPrecision
: Calculate maximum possible coordinate precisiondmsToDecimal
: Convert degrees-minutes-seconds to decimalgetCRS
: Return a proj4string (coordinate reference system string) using a nicknamepointDist
: Geographic distance between set(s) of pointsxToCoords
: Extract geographic coordinates from a data frame, matrix, or SpatialPoints* object