Package: spatstat.explore 3.3-1.001

Adrian Baddeley

spatstat.explore: Exploratory Data Analysis for the 'spatstat' Family

Functionality for exploratory data analysis and nonparametric analysis of spatial data, mainly spatial point patterns, in the 'spatstat' family of packages. (Excludes analysis of spatial data on a linear network, which is covered by the separate package 'spatstat.linnet'.) Methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlation functions, segregation indices, mark dependence diagnostics, and kernel estimates of covariate effects. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Monte Carlo, Diggle-Cressie-Loosmore-Ford, Dao-Genton, two-stage Monte Carlo) and tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov, ANOVA) are also supported.

Authors:Adrian Baddeley [aut, cre, cph], Rolf Turner [aut, cph], Ege Rubak [aut, cph], Kasper Klitgaard Berthelsen [ctb], Warick Brown [cph], Achmad Choiruddin [ctb], Jean-Francois Coeurjolly [ctb], Ottmar Cronie [ctb], Tilman Davies [ctb, cph], Julian Gilbey [ctb], Jonatan Gonzalez [ctb], Yongtao Guan [ctb], Ute Hahn [ctb], Kassel Hingee [ctb, cph], Abdollah Jalilian [ctb], Frederic Lavancier [ctb], Marie-Colette van Lieshout [ctb, cph], Greg McSwiggan [ctb], Robin K Milne [cph], Tuomas Rajala [ctb], Suman Rakshit [ctb, cph], Dominic Schuhmacher [ctb], Rasmus Plenge Waagepetersen [ctb], Hangsheng Wang [ctb]

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NEWS

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

Peer review:

Bug tracker:https://github.com/spatstat/spatstat.explore/issues

On CRAN:

cluster-detectionconfidence-intervalshypothesis-testingk-functionroc-curvesscan-statisticssignificance-testingsimulation-envelopesspatial-analysisspatial-data-analysisspatial-sharpeningspatial-smoothingspatial-statistics

507 exports 8.39 score 14 dependencies 137 dependents 172 mentions 48.0k downloads

Last updated 2 days agofrom:b1ae49d0b4

Exports:[.fasp[.fv[.localpcfmatrix[.rat[.ssf[<-.fv$<-.fvadaptive.densityadjust.ratfvallstatsalltypesang2radapply.ssfas.data.frame.bw.optimas.data.frame.envelopeas.data.frame.fvas.function.fvas.function.rhohatas.function.ssfas.fvas.fv.bw.optimas.fv.data.frameas.fv.faspas.fv.fvas.fv.matrixas.im.scan.testas.im.ssfas.owin.quadrattestas.ppp.ssfas.tess.quadrattestassemble.plot.objectsaucauc.pppbandwidth.is.infiniteBartCalcberman.testberman.test.pppbermantestCalcbermantestEnginebind.fvbind.ratfvbits.envelopebits.testblurboycebw.abram.pppbw.CvLbw.CvL.adaptivebw.CvLHeatbw.digglebw.fracbw.optimbw.pcfbw.pplbw.pplHeatbw.relriskbw.relrisk.pppbw.scottbw.scott.isobw.smoothpppbw.stoyancalc.DRcalc.NNIRcalc.SAVEcalc.SIRcalc.TSEcbind.fvcdf.testcdf.test.pppcenstimeCDFestcheck.testfuncircdensitycircticksclarkevansclarkevans.testclarkevansCalcclustersetcollapse.anylistcollapse.fvcompatible.faspcompatible.fvcompatible.ratcompileCDFcompileKcompilepcfComplex.faspComplex.fvconform.ratfvcontour.ssfcor.imcov.imCressieReadNameCressieReadStatisticCressieReadSymbolcutoff2DkernelCVforPCFdclf.progressdclf.sigtracedclf.testdensity.pppdensity.ppplistdensity.pspdensity.splitpppdensityAdaptiveKernel.pppdensityAdaptiveKernel.ppplistdensityAdaptiveKernel.splitpppdensitycrossEnginedensityfundensityfun.pppdensityHeatdensityHeat.pppdensitypointsEnginedensityVoronoidensityVoronoi.pppderiv.fvDeviationdg.envelopedg.progressdg.sigtracedg.testdigestCovariatesdigital.volumedim.faspdimhatdimnames.faspdimnames<-.faspdistcdfdistributecbinddomain.quadrattestedge.Ripleyedge.TransEmarkensure.listargenvelopeenvelope.envelopeenvelope.hasenvelopeenvelope.matrixenvelope.pp3envelope.pppenvelopeArrayenvelopeEngineenvelopeProgressDataenvelopeTesteval.faspeval.fvevalCovarevaluate2DkernelevaluateCovariateevaluateCovariateAtPixelsevaluateCovariateAtPointsexactppmExpSmoothLogextractAtomicQtestsf3Cenginef3engineF3estfaspFestFhazardfindbestlegendposfindcbindFinhomflatfnameFmulti.inhomFmultiInhomFormatFaspFormulaeformula.fvformula<-formula<-.fvfryplotfrypointsfvfvexprmapfvlabelmapfvlabelsfvlabels<-fvlegendfvnamesfvnames<-g3Cengineg3engineG3estGcrossGcross.inhomGdotGdot.inhomGestgetSumFunGfoxGinhomGmultiGmulti.inhomGmultiInhomgood.correction.Kharmonise.fvharmonize.fvhasenvelopeHesthopskelhopskel.testhotboxidwIestimage.ssfimplemented.for.Kincrement.fvintegral.fvintegral.ssfis.atomicQtestis.poisson.exactppmis.scovis.stationary.exactppmJcrossJcross.inhomJdotJdot.inhomJestJfoxJinhomJmultiJmulti.inhomk3engineK3estKborder.engineKcrossKcross.inhomKdotKdot.inhomKestKest.fftKinhomKmarkKmeasureKmultiKmulti.inhomKnone.engineKountKrect.engineKscaledKsectorKwtsumlaslettLcrossLcross.inhomLdotLdot.inhomLestLinhomlocalKlocalKcrosslocalKcross.inhomlocalKdotlocalKenginelocalKinhomlocalKmultiEnginelocalLlocalLcrosslocalLcross.inhomlocalLdotlocalLinhomlocalpcflocalpcfenginelocalpcfinhomlocalpcfmatrixlohbootlookup2DkernelInfoLscaledmad.progressmad.sigtracemad.testmakefvlabelmarkconnectmarkcorrmarkcorrintmarkcrosscorrmarkmarkscattermarkmeanmarks.ssfmarks<-.ssfmarktablemarkvarmarkvariomaskLaslettmatch2DkernelNameMath.faspMath.fvmax.ssfmctest.progressmctest.sigtracemctestSigtraceEnginemeanlistfvmin.ssfmiplotnames<-.fvnearest.neighbournncleannnclean.pp3nnclean.pppnncleanEnginenncorrnndensitynndensity.pppnnmeannnorientnnvarioOps.faspOps.fvpairMeanpairorientpairs.impairs.listofpairs.solistpanel.contourpanel.histogrampanel.imagepcfpcf.fasppcf.fvpcf.ppppcf3enginepcf3estpcfcrosspcfcross.inhompcfdotpcfdot.inhompcfinhompcfmultipcfmulti.inhomplot.bermantestplot.bw.fracplot.bw.optimplot.cdftestplot.envelopeplot.faspplot.fvplot.laslettplot.localpcfmatrixplot.plotpairsimplot.quadrattestplot.rho2hatplot.rhohatplot.scan.testplot.spatialcdfplot.ssfplot.studpermutestpolyLaslettpoolpool.anylistpool.envelopepool.fasppool.fvpool.quadrattestpool.ratPPversionpredict.exactppmpredict.rho2hatpredict.rhohatprefixfvprint.bw.fracprint.bw.optimprint.densityfunprint.envelopeprint.exactppmprint.faspprint.fvprint.fvfunprint.hasenvelopeprint.laslettprint.localpcfmatrixprint.plotpairsimprint.quadrattestprint.ratprint.rho2hatprint.rhohatprint.Smoothfunprint.ssfprint.summary.bw.optimprint.summary.ssfQQversionquadrat.testquadrat.test.pppquadrat.test.quadratcountquadrat.test.splitpppquadrat.testEngineradcumintrange.ssfratratfvrebadge.as.crossfunrebadge.as.dotfunrebadge.fvrebadgeLabelsreconcile.fvrectcontactRelevantDeviationreload.or.computerelriskrelrisk.ppprename.fvresolve.2D.kernelresolve.foxall.windowresolve.lambdaresolve.lambda.pppresolve.lambdacrossresolve.lambdacross.pppresolve.reciplambdaresolve.reciplambda.pppresolveEinforho2hatrhohatrhohat.ppprhohat.quadrhohatCalcrhohatEnginermax.Rigidrmax.Ripleyrmax.rulermax.Transrocroc.ppprocDatarocModelroserose.defaultrose.densityrose.fvrose.histogramroseContinuousrotmeanscan.testscanBinomLRTSscanLRTSscanmeasurescanmeasure.imscanmeasure.pppscanPoisLRTSsdrsdr.pppsdrPredictsecond.moment.calcsecond.moment.enginesegregation.testsegregation.test.pppsewpcfsewsmodsharpensharpen.pppshift.quadratte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Dependencies:abinddeldirgoftestlatticeMatrixnlmepolyclipspatstat.dataspatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilstensor

Readme and manuals

Help Manual

Help pageTopics
The spatstat.explore Packagespatstat.explore-package spatstat.explore
Subset of spatially sampled function[.ssf
Adaptive Estimate of Intensity of Point Patternadaptive.density
Calculate four standard summary functions of a point pattern.allstats
Calculate Summary Statistic for All Types in a Multitype Point Patternalltypes
Coerce Envelope to Data Frameas.data.frame.envelope
Convert Function Value Table to Functionas.function.fv
Convert Function Table to Functionas.function.rhohat
Convert Data To Class fvas.fv as.fv.bw.optim as.fv.data.frame as.fv.fasp as.fv.fv as.fv.matrix
Convert Data To Class owinas.owin.quadrattest
Convert Data To Tessellationas.tess.quadrattest
Area Under ROC Curveauc auc.ppp
Berman's Tests for Point Process Modelberman.test berman.test.ppp
Combine Function Value Tablesbind.fv cbind.fv
Global Envelopes for Balanced Independent Two-Stage Testbits.envelope
Balanced Independent Two-Stage Monte Carlo Testbits.test
Apply Gaussian Blur to a Pixel Imageblur Smooth.im
Boyce Indexboyce
Abramson's Adaptive Bandwidths For Spatial Point Patternbw.abram.ppp
Cronie and van Lieshout's Criterion for Bandwidth Selection for Kernel Densitybw.CvL
Select Adaptive Bandwidth for Kernel Estimation Using Cronie-Van Lieshout Criterionbw.CvL.adaptive
Bandwidth Selection for Diffusion Smoother by Cronie-van Lieshout Rulebw.CvLHeat
Cross Validated Bandwidth Selection for Kernel Densitybw.diggle
Bandwidth Selection Based on Window Geometrybw.frac
Class of Optimized Bandwidthsbw.optim.object
Cross Validated Bandwidth Selection for Pair Correlation Functionbw.pcf
Likelihood Cross Validation Bandwidth Selection for Kernel Densitybw.ppl
Bandwidth Selection for Diffusion Smoother by Likelihood Cross-Validationbw.pplHeat
Cross Validated Bandwidth Selection for Relative Risk Estimationbw.relrisk bw.relrisk.ppp
Scott's Rule for Bandwidth Selection for Kernel Densitybw.scott bw.scott.iso
Cross Validated Bandwidth Selection for Spatial Smoothingbw.smoothppp
Stoyan's Rule of Thumb for Bandwidth Selectionbw.stoyan
Spatial Distribution Test for Point Pattern or Point Process Modelcdf.test cdf.test.ppp
Density Estimation for Circular Datacircdensity
Clark and Evans Aggregation Indexclarkevans
Clark and Evans Testclarkevans.test
Allard-Fraley Estimator of Cluster Featureclusterset
Collapse Several Function Tables into Onecollapse.anylist collapse.fv
Test Whether Function Arrays Are Compatiblecompatible.fasp
Test Whether Function Objects Are Compatiblecompatible.fv
Generic Calculation of Cumulative Distribution Function of DistancescompileCDF
Generic Calculation of K Function and Pair Correlation FunctioncompileK compilepcf
Covariance and Correlation between Imagescor.im cov.im
Progress Plot of Test of Spatial Patterndclf.progress mad.progress mctest.progress
Significance Trace of Cressie-Loosmore-Ford or Maximum Absolute Deviation Testdclf.sigtrace mad.sigtrace mctest.sigtrace
Diggle-Cressie-Loosmore-Ford and Maximum Absolute Deviation Testsdclf.test mad.test
Kernel Smoothed Intensity of Point Patterndensity.ppp
Kernel Smoothing of Line Segment Patterndensity.psp
Kernel Smoothed Intensity of Split Point Patterndensity.ppplist density.splitppp
Adaptive Kernel Estimate of Intensity of Point PatterndensityAdaptiveKernel.ppp
Adaptive Kernel Estimate of Intensity for Split Point PatterndensityAdaptiveKernel.ppplist densityAdaptiveKernel.splitppp
Kernel Estimate of Intensity as a Spatial Functiondensityfun densityfun.ppp
Diffusion Estimate of Point Pattern IntensitydensityHeat
Diffusion Estimate of Point Pattern IntensitydensityHeat.ppp
Intensity Estimate of Point Pattern Using Voronoi-Dirichlet TessellationdensityVoronoi densityVoronoi.ppp
Calculate Derivative of Function Valuesderiv.fv
Global Envelopes for Dao-Genton Testdg.envelope
Progress Plot of Dao-Genton Test of Spatial Patterndg.progress
Significance Trace of Dao-Genton Testdg.sigtrace
Dao-Genton Adjusted Goodness-Of-Fit Testdg.test
Estimate Dimension of Central Subspacedimhat
Distribution Function of Interpoint Distancedistcdf
Extract the Domain of any Spatial Objectdomain.quadrattest
Ripley's Isotropic Edge Correctionedge.Ripley rmax.Ripley
Translation Edge Correctionedge.Trans rmax.Trans
Diagnostics for random markingEmark Vmark
Simulation Envelopes of Summary Functionenvelope envelope.ppp
Recompute Envelopesenvelope.envelope
Simulation Envelopes of Summary Function for 3D Point Patternenvelope.pp3
Array of Simulation Envelopes of Summary FunctionenvelopeArray
Evaluate Expression Involving Function Arrayseval.fasp
Evaluate Expression Involving Functionseval.fv
Extract Subset of Function Array[.fasp
Extract or Replace Subset of Function Values$<-.fv [.fv [<-.fv
Empty Space Function of a Three-Dimensional Point PatternF3est
Function Arrays for Spatial Patternsfasp.object
Estimate the Empty Space Function or its Hazard RateFest Fhazard
Inhomogeneous Empty Space FunctionFinhom
Inhomogeneous Marked F-FunctionFmulti.inhom FmultiInhom
Extract or Change the Plot Formula for a Function Value Tableformula.fv formula<- formula<-.fv
Fry Plot of Point Patternfryplot frypoints
Create a Function Value Tablefv
Function Value Tablefv.object
Abbreviations for Groups of Columns in Function Value Tablefvnames fvnames<-
Nearest Neighbour Distance Distribution Function of a Three-Dimensional Point PatternG3est
Multitype Nearest Neighbour Distance Function (i-to-j)Gcross
Inhomogeneous Multitype G Cross FunctionGcross.inhom
Multitype Nearest Neighbour Distance Function (i-to-any)Gdot
Inhomogeneous Multitype G Dot FunctionGdot.inhom
Nearest Neighbour Distance Function GGest nearest.neighbour
Foxall's Distance FunctionsGfox Jfox
Inhomogeneous Nearest Neighbour FunctionGinhom
Marked Nearest Neighbour Distance FunctionGmulti
Inhomogeneous Marked G-FunctionGmulti.inhom GmultiInhom
Make Function Tables Compatibleharmonise.fv harmonize.fv
Spherical Contact Distribution FunctionHest
Hopkins-Skellam Testhopskel hopskel.test
Heat Kernel for a Two-Dimensional Rectanglehotbox
Inverse-distance weighted smoothing of observations at irregular pointsidw
Estimate the I-functionIest
Increments of a Functionincrement.fv
Compute Integral of Function Objectintegral.fv
Multitype J Function (i-to-j)Jcross
Inhomogeneous Multitype J function (i-to-j)Jcross.inhom
Multitype J Function (i-to-any)Jdot
Inhomogeneous Multitype J function (i-to-any)Jdot.inhom
Estimate the J-functionJest
Inhomogeneous J-functionJinhom
Marked J FunctionJmulti
Inhomogeneous Marked J-FunctionJmulti.inhom
K-function of a Three-Dimensional Point PatternK3est
Multitype K Function (Cross-type)Kcross
Inhomogeneous Cross K FunctionKcross.inhom
Multitype K Function (i-to-any)Kdot
Inhomogeneous Multitype K Dot FunctionKdot.inhom
K-functionKest
K-function using FFTKest.fft
Inhomogeneous K-functionKinhom
Mark-Weighted K FunctionKmark markcorrint
Reduced Second Moment MeasureKmeasure
Marked K-FunctionKmulti
Inhomogeneous Marked K-FunctionKmulti.inhom
Locally Scaled K-functionKscaled Lscaled
Sector K-functionKsector
Laslett's Transformlaslett
Multitype L-function (cross-type)Lcross
Inhomogeneous Cross Type L FunctionLcross.inhom
Multitype L-function (i-to-any)Ldot
Inhomogeneous Multitype L Dot FunctionLdot.inhom
L-functionLest
Inhomogeneous L-functionLinhom
Neighbourhood density functionlocalK localL
Local Multitype K Function (Cross-Type)localKcross localLcross
Inhomogeneous Multitype K FunctionlocalKcross.inhom localLcross.inhom
Local Multitype K Function (Dot-Type)localKdot localLdot
Inhomogeneous Neighbourhood Density FunctionlocalKinhom localLinhom
Local pair correlation functionlocalpcf localpcfinhom
Bootstrap Confidence Bands for Summary Functionlohboot
Mark Connection Functionmarkconnect
Mark Correlation Functionmarkcorr
Mark Cross-Correlation Functionmarkcrosscorr
Mark-Mark Scatter Plotmarkmarkscatter
Tabulate Marks in Neighbourhood of Every Point in a Point Patternmarktable
Mark Variogrammarkvario
S3 Group Generic Methods for Function ArraysComplex.fasp Math.fasp Ops.fasp Summary.fasp
S3 Group Generic Methods for Function TablesComplex.fv Math.fv Ops.fv Summary.fv
Methods for Intensity Functions of Two Spatial Covariatesmethods.rho2hat plot.rho2hat predict.rho2hat print.rho2hat
Methods for Intensity Functions of Spatial Covariatemethods.rhohat plot.rhohat predict.rhohat print.rhohat simulate.rhohat
Methods for Spatially Sampled Functionsas.function.ssf as.im.ssf as.ppp.ssf integral.ssf marks.ssf marks<-.ssf max.ssf methods.ssf min.ssf print.ssf range.ssf summary.ssf unmark.ssf
Morisita Index Plotmiplot
Nearest Neighbour Clutter Removalnnclean nnclean.pp3 nnclean.ppp
Nearest-Neighbour Correlation Indices of Marked Point Patternnncorr nnmean nnvario
Estimate Intensity of Point Pattern Using Nearest Neighbour Distancesnndensity nndensity.ppp
Nearest Neighbour Orientation Distributionnnorient
Mean of a Function of Interpoint DistancepairMean
Point Pair Orientation Distributionpairorient
Scatterplot Matrix for Pixel Imagespairs.im
Panel Plots using Colour Image or Contour Linespanel.contour panel.histogram panel.image
Pair Correlation Functionpcf
Pair Correlation Function obtained from array of K functionspcf.fasp
Pair Correlation Function obtained from K Functionpcf.fv
Pair Correlation Function of Point Patternpcf.ppp
Pair Correlation Function of a Three-Dimensional Point Patternpcf3est
Multitype pair correlation function (cross-type)pcfcross
Inhomogeneous Multitype Pair Correlation Function (Cross-Type)pcfcross.inhom
Multitype pair correlation function (i-to-any)pcfdot
Inhomogeneous Multitype Pair Correlation Function (Type-i-To-Any-Type)pcfdot.inhom
Inhomogeneous Pair Correlation Functionpcfinhom
Marked pair correlation functionpcfmulti
Plot Result of Berman Testplot.bermantest
Plot a Spatial Distribution Testplot.cdftest
Plot a Simulation Envelopeplot.envelope
Plot a Function Arrayplot.fasp
Plot Function Valuesplot.fv
Plot Laslett Transformplot.laslett
Display the result of a quadrat counting test.plot.quadrattest
Plot Result of Scan Testas.im.scan.test plot.scan.test
Plot a Spatially Sampled Functioncontour.ssf image.ssf plot.ssf
Plot a Studentised Permutation Testplot.studpermutest
Pool Datapool
Pool Data from a List of Objectspool.anylist
Pool Data from Several Envelopespool.envelope
Pool Data from Several Function Arrayspool.fasp
Pool Several Functionspool.fv
Pool Several Quadrat Testspool.quadrattest
Pool Data from Several Ratio Objectspool.rat
Transform a Function into its P-P or Q-Q VersionPPversion QQversion
Dispersion Test for Spatial Point Pattern Based on Quadrat Countsquadrat.test quadrat.test.ppp quadrat.test.quadratcount
Dispersion Test of CSR for Split Point Pattern Based on Quadrat Countsquadrat.test.splitppp
Radial Cumulative Integralradcumint
Ratio objectrat
Contact Distribution Function using Rectangular Structuring Elementrectcontact
Compute Unless Previously Savedreload.or.compute
Estimate of Spatially-Varying Relative Riskrelrisk
Nonparametric Estimate of Spatially-Varying Relative Riskrelrisk.ppp
Smoothed Relative Density of Pairs of Covariate Valuesrho2hat
Nonparametric Estimate of Intensity as Function of a Covariaterhohat rhohat.ppp rhohat.quad
Receiver Operating Characteristicroc roc.ppp
Rose Diagramrose rose.default rose.density rose.fv rose.histogram
Rotational Average of a Pixel Imagerotmean
Spatial Scan Testscan.test
Likelihood Ratio Test Statistic for Scan TestscanLRTS
Sufficient Dimension Reductionsdr sdr.ppp
Compute Predictors from Sufficient Dimension ReductionsdrPredict
Test of Spatial Segregation of Typessegregation.test segregation.test.ppp
Data Sharpening of Point Patternsharpen sharpen.ppp
Spatial smoothing of dataSmooth
Apply Smoothing to Function ValuesSmooth.fv
Spatial smoothing of observations at irregular pointsmarkmean markvar Smooth.ppp
Smooth a Spatially Sampled FunctionSmooth.ssf
Smooth Interpolation of Marks as a Spatial FunctionSmoothfun Smoothfun.ppp
Estimate the Spatial Covariance Function of a Random Fieldspatcov
Spatial Cumulative Distribution Functionspatialcdf
Spatially Weighted Median of Values at PointsSpatialMedian.ppp
Spatially Weighted Median or QuantileSpatialMedian SpatialQuantile
Spatially Weighted Quantile of Values at PointsSpatialQuantile.ppp
Spatially Sampled Functionssf
Stienen Diagramstienen stienenSet
Studentised Permutation Teststudpermu.test
Distance Between Linear SpacessubspaceDistance
Confidence Interval for Threshold of Numerical PredictorthresholdCI
Select Threshold to Convert Numerical Predictor to Binary PredictorthresholdSelect
Pixel Values Along a Transecttransect.im
Third order summary statisticTstat
Estimate Variance of Summary Statistic by Subdivisionvarblock
Extract Window of Spatial ObjectWindow.quadrattest
Evaluate an Expression in a Function Tablewith.fv
Evaluate Expression in a Spatially Sampled Functionapply.ssf with.ssf