Package: spatialEco 2.0-3

spatialEco: Spatial Analysis and Modelling Utilities

Utilities to support spatial data manipulation, query, sampling and modelling in ecological applications. Functions include models for species population density, spatial smoothing, multivariate separability, point process model for creating pseudo- absences and sub-sampling, Quadrant-based sampling and analysis, auto-logistic modeling, sampling models, cluster optimization, statistical exploratory tools and raster-based metrics.

Authors:Jeffrey S. Evans [aut, cre], Melanie A. Murphy [ctb], Karthik Ram [ctb]

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spatialEco.pdf |spatialEco.html✨
spatialEco/json (API)
NEWS

# Install 'spatialEco' in R:
install.packages('spatialEco', repos = c('https://jeffreyevans.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/jeffreyevans/spatialeco/issues

Datasets:
  • ants - Ant Biodiversity Data
  • chen - Cross-correlation data from Chen
  • cor.data - Various correlation structures
  • pu - Biodiversity Planning Units

On CRAN:

biodiversityconservationecologyr-spatialrasterspatialvector

128 exports 105 stars 5.02 score 14 dependencies 2 dependents 16 mentions 632 scripts 1.6k downloads

Last updated 6 months agofrom:05b16fd9de. Checks:OK: 5 NOTE: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKAug 31 2024
R-4.5-winOKAug 31 2024
R-4.5-linuxOKAug 31 2024
R-4.4-winOKAug 31 2024
R-4.4-macOKAug 31 2024
R-4.3-winNOTEAug 31 2024
R-4.3-macNOTEAug 31 2024

Exports:all_pairwiseannulus.matrixaspline.downscalebackgroundbbox_polybearing.distancebreeding.densitybuilt.indexcgls_urlschaeclassBreakscollinearcombineconcordanceconf.intervalconvexHullcorrelogramcross.tabcrossCorrelationcsicurvaturedahidate_seqdaymet.pointdaymet.tilesdispersiondissectiondivergenceeffect.sizeerase.pointextract.verticesfuzzySumgaussian.kernelgeo.buffergroup.pdfhexagonshlihli.pthsphybrid.kmeansidw.smoothingimpute.loessinsertinsert.valuesis.emptykendallkl.divergenceknnlailocal.min.maxloess.bootloess.cilogistic.regressionmax_extentmean_anglemomentsmorans.plotnninth.valueso.ringoli.awsoptimal.koptimized.sample.varianceoutliersoverlapparea.sampleparse.bitspartial.corpoly_trendpoly.regressionpolyPerimeterpp.subsampleproximity.indexpseudo.absencequadratsrandom.rasterraster.changeraster.deviationraster.downscaleraster.entropyraster.gaussian.smoothraster.invertraster.kendallraster.mdsraster.modified.ttestraster.momentsraster.transformationraster.volraster.ZscorerasterCorrelationrasterDistanceremove_duplicatesremove.holesrm.extrotate.polygonsa.transsample.annulussampleTransectsarseparabilitysf_dissolvesf.kdesg.smoothshannonsshiftsievesimilaritysmooth.time.seriessobalsp.kdespatial.selectspatialEcoNewsspectral.separabilityspherical.sdsquareBuffersrrstratified.randomsubsample.distanceswvitime_to_eventtopo.distancetpitrasptrend.linetrivrmwinsorizewt.centroid

Dependencies:classclassIntDBIe1071KernSmoothmagrittrMASSproxyRcpps2sfterraunitswk

Readme and manuals

Help Manual

Help pageTopics
All pairwise combinationsall_pairwise
Annulus matrixannulus.matrix
Ant Biodiversity Dataants
Raster Downscale using adaptive regression splinesaspline.downscale
Background samplebackground
Bounding box polygonbbox_poly
Bearing and Distancebearing.distance
Breeding density areas (aka, core habitat areas)breeding.density
built indexbuilt.index
Provide URL's for Copernicus Global Land Service datasetscgls_urls
Canine-Human Age Equivalentchae
Cross-correlation data from Chen (2015)chen
Class breaksclassBreaks
Collinearity testcollinear
raster combinecombine
Concordance test for binomial modelsconcordance
Confidence interval for mean or medianconf.interval
Alpha Convex HullconvexHull
Various correlation structurescor.data
Correlogramcorrelogram
Class comparison between two nominal rasterscross.tab
Spatial cross correlationcrossCorrelation
Cosine Similarity Indexcsi
Surface curvaturecurvature
Diurnal Anisotropic Heat Indexdahi
date sequencedate_seq
DAYMET point valuesdaymet.point
DAYMET Tile ID'sdaymet.tiles
Dispersion (H-prime)dispersion
Dissectiondissection
divergencedivergence
Cohen's-d effect sizeeffect.size
Elevation rasterelev
Erase pointserase.point
Extract vertices for polygons or linesextract.vertices
Fuzzy SumfuzzySum
Gaussian Kernelgaussian.kernel
Buffer geographic datageo.buffer
Probability density plot by groupgroup.pdf
Hexagonshexagons
Heat Load Indexhli
Point estimate of Heat Load Indexhli.pt
Hierarchical Slope Positionhsp
Hybrid K-meanshybrid.kmeans
Inverse Distance Weighted smoothingidw.smoothing
Impute loessimpute.loess
Insert a row or column into a data.frameinsert
Insert Valuesinsert.values
is.emptyis.empty
Kendall tau trend with continuity correction for time-serieskendall
Kullback-Leibler divergence (relative entropy)kl.divergence
Spatial K nearest neighborknn
Leaf Area Indexlai
Local minimum and maximumlocal.min.max
Loess Bootstraploess.boot
Loess with confidence intervalsloess.ci
Logistic and Auto-logistic regressionlogistic.regression
Maximum extent of multiple rastersmax_extent
Mean Anglemean_angle
momentsmoments
Autocorrelation Plotmorans.plot
Average Nearest Neighbor Index (NNI)nni
Nth valuesnth.values
Inhomogeneous O-ringo.ring
Query AWS-OLIoli.aws
optimalKoptimal.k
Optimized sample varianceoptimized.sample.variance
Outliersoutliers
Niche overlap (Warren's-I)overlap
Percent area sampleparea.sample
Parse bitsparse.bits
Partial and Semi-partial correlationpartial.cor
Plot effect sizeplot.effect.size
Plot Loess Bootstrapplot.loess.boot
Polynomial trendpoly_trend
Local Polynomial Regressionpoly.regression
Polygon perimeterpolyPerimeter
Point process random subsamplepp.subsample
Print spatial cross correlationprint.cross.cor
Print effect sizeprint.effect.size
Print Loess bootstrap modelprint.loess.boot
Print poly_trendprint.poly.trend
Proximity Indexproximity.index
Pseudo-absence random samplespseudo.absence
Biodiversity Planning Unitspu
Quadratsquadrats
Random rasterrandom.raster
Raster change between two nominal rastersraster.change
Raster local deviation from the global trendraster.deviation
Raster Downscaleraster.downscale
Raster Entropyraster.entropy
Gaussian smoothing of rasterraster.gaussian.smooth
Invert rasterraster.invert
Kendall tau trend with continuity correction for raster time-seriesraster.kendall
Raster multidimensional scaling (MDS)raster.mds
Dutilleul moving window bivariate raster correlationraster.modified.ttest
Raster momentsraster.moments
Statistical transformation for rastersraster.transformation
Raster Percent Volumeraster.vol
Modified z-score for a rasterraster.Zscore
Raster correlationrasterCorrelation
Raster DistancerasterDistance
Remove duplicate geometriesremove_duplicates
Remove or return polygon holesremove.holes
Remove extensionrm.ext
Rotate polygonrotate.polygon
Trigonometric transformation of a slope and aspect interactionsa.trans
Sample annulussample.annulus
Sample transectsampleTransect
Surface Area Ratiosar
separabilityseparability
Dissolve polygonssf_dissolve
Spatial kernel density estimatesf.kde sp.kde
Savitzky-Golay smoothing filtersg.smooth
Shannon's Diversity (Entropy) Indexshannons
shiftshift
Sieve raster datasieve
Ecological similaritysimilarity
Smooth Raster Time-seriessmooth.time.series
Sobel-Feldman operatorsobal
Spatial Selectspatial.select
spatialEco newsspatialEcoNews
spectral separabilityspectral.separability
Spherical Variance or Standard Deviation of Surfacespherical.sd
Square buffersquareBuffer
Surface Relief Ratiosrr
Stratified random samplestratified.random
Distance-based subsamplingsubsample.distance
Summary of spatial cross correlationsummary.cross.cor
Summarizing effect sizesummary.effect.size
Summarizing Loess bootstrap modelssummary.loess.boot
Senescence weighted Vegetation Index (swvi)swvi
Time to eventtime_to_event
Landsat 5 TM SceneTM5
Topographic distancetopo.distance
Topographic Position Index (tpi)tpi
Solar-radiation Aspect Indextrasp
trend.linetrend.line
Terrain Ruggedness Indextri
Vector Ruggedness Measure (VRM)vrm
Winsorize transformationwinsorize
Weighted centroidwt.centroid