Package: spatstat.linnet 3.2-1.001

Adrian Baddeley

spatstat.linnet: Linear Networks Functionality of the 'spatstat' Family

Defines types of spatial data on a linear network and provides functionality for geometrical operations, data analysis and modelling of data on a linear network, in the 'spatstat' family of packages. Contains definitions and support for linear networks, including creation of networks, geometrical measurements, topological connectivity, geometrical operations such as inserting and deleting vertices, intersecting a network with another object, and interactive editing of networks. Data types defined on a network include point patterns, pixel images, functions, and tessellations. Exploratory methods include kernel estimation of intensity on a network, K-functions and pair correlation functions on a network, simulation envelopes, nearest neighbour distance and empty space distance, relative risk estimation with cross-validated bandwidth selection. 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. Parametric models can be fitted to point pattern data using the function lppm() similar to glm(). Only Poisson models are implemented so far. Models may involve dependence on covariates and dependence on marks. Models are fitted by maximum likelihood. Fitted point process models can be simulated, automatically. Formal hypothesis tests of a fitted model are supported (likelihood ratio test, analysis of deviance, Monte Carlo tests) along with basic tools for model selection (stepwise(), AIC()) and variable selection (sdr). Tools for validating the fitted model include simulation envelopes, residuals, residual plots and Q-Q plots, leverage and influence diagnostics, partial residuals, and added variable plots. Random point patterns on a network can be generated using a variety of models.

Authors:Adrian Baddeley [aut, cre, cph], Rolf Turner [aut, cph], Ege Rubak [aut, cph], Greg McSwiggan [aut, cph], Tilman Davies [ctb, cph], Mehdi Moradi [ctb, cph], Suman Rakshit [ctb, cph], Ottmar Cronie [ctb]

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NEWS

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

Peer review:

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

On CRAN:

density-estimationheat-equationkernel-density-estimationnetwork-analysispoint-processesspatial-data-analysisstatistical-analysisstatistical-inferencestatistical-models

315 exports 6 stars 7.19 score 18 dependencies 45 dependents 172 mentions 12.6k downloads

Last updated 2 days agofrom:ed7bd970f6

Exports:[.linim[.linnet[.lpp[<-.linimaddVerticesaffine.linimaffine.linnetaffine.lppanova.lppmApplyConnectedas.data.frame.linfunas.data.frame.linimas.data.frame.lintessas.function.linfunas.im.linimas.linfunas.linfun.linfunas.linfun.linimas.linfun.lintessas.linimas.linim.defaultas.linim.linfunas.linim.linimas.linnetas.linnet.linfunas.linnet.linimas.linnet.linnetas.linnet.lintessas.linnet.lppas.linnet.lppmas.linnet.pspas.lppas.owin.linfunas.owin.linnetas.owin.lintessas.owin.lppas.owin.lppmas.ppm.lppmas.ppp.lppas.psp.linnetas.psp.lppauc.lppauc.lppmbeginsberman.test.lppberman.test.lppmboundingradius.linnetbranchlabelfunbw.lpplbw.relrisk.lppbw.relrisklppbw.voronoicdf.test.lppcdf.test.lppmchop.linnetcircumradius.linnetclickjoinclicklppcoef.lppmComplex.linimComplex.linimlistconnected.linnetconnected.lppcountendscrossdist.lppcrossing.linnetcut.lppdata.lppmdefault.linnet.tolerancedelaunayNetworkdeletebranchdeletebranch.linnetdeletebranch.lppdensity.linnetdensity.lppdensity.splitppxdensityEqualSplitdensityfun.lppdensityHeat.lppdensitypointsLPPdensityQuick.lppdensityVoronoi.lppdeviance.lppmdiameter.linnetdirichletNetworkdistfun.lppdistmap.lppdivide.linnetDoCountCrossEndsDoCountEndsdomain.linfundomain.lintessdomain.lppdomain.lppmemend.lppmenvelope.lppenvelope.lppmeval.linimevaluateNetCovariateevaluateNetCovariateAlongNetworkevaluateNetCovariateAtPointsexactlppmextractAIC.lppmextractbranchextractbranch.linnetextractbranch.lppFDMKERNELfitted.lppmflatdensityatpointslppflatdensityfunlppformula.lppmgetglmdata.lppmgetglmfit.lppmgetglmsubset.lppmhasglmfit.lppmheatkernelapproxidentify.lppinsertVerticesintegral.linfunintegral.linimintensity.lppintersect.lintessis.connected.linnetis.marked.lppmis.multitype.lppis.multitype.lppmis.poisson.exactlppmis.poisson.lppmis.stationary.exactlppmis.stationary.lppmjoinVerticesldtEnginelineardirichletlineardisclineardiscEnginelineardisclengthlinearEuclidEnginelinearJinhomlinearKlinearKcrosslinearKcross.inhomlinearKdotlinearKdot.inhomlinearKenginelinearKEuclidlinearKEuclidInhomlinearKinhomlinearKmultilinearKmulti.inhomlinearKmultiEnginelinearmarkconnectlinearmarkequallinearpcflinearpcfcrosslinearpcfcross.inhomlinearpcfdotlinearpcfdot.inhomlinearpcfenginelinearpcfEuclidlinearpcfEuclidInhomlinearpcfinhomlinearpcfmultilinearpcfmulti.inhomlinearPCFmultiEnginelineartileindexlinequadlinfunlinimLinimListOpLinimOplinnetlintesslixellatelocal2lpplogLik.lppmlooHeatLPPlooVoronoiLPPlpplppmlppm.formulalppm.lppmakeLinnetTolerancemarks.linnetmarks.lintessmarks<-.linnetmarks<-.lintessmarks<-.lppMath.linimMath.linimlistmean.linimmedian.linimmodel.frame.lppmmodel.images.lppmmodel.matrix.lppmnncross.lppnndist.lppnnfromvertexnnfun.lppnnwhich.lppnobjects.lintessnobs.lppmnsegments.linnetnsegments.lppnvertices.linnetOps.linimOps.linimlistpairdist.lpppairs.linimpersp.linfunpersp.linimpixellate.linnetplot.linfunplot.linimplot.linnetplot.lintessplot.lppplot.lppmpoints.lpppointsAlongNetworkpredict.exactlppmpredict.lppmprint.exactlppmprint.linfunprint.linimprint.linnetprint.lintessprint.lppprint.lppmprint.summary.linimprint.summary.linnetprint.summary.lintessprint.summary.lpppseudoR2.lppmqkdeEnginequantile.linimquantilefun.linimrcelllpprelrisk.lpprepairNetworkresampleNetworkDataFramerescale.linnetrescale.lppresolve.heat.stepsresolve.lambda.lppresponse.exactlppmresponse.lppmrhohat.lpprhohat.lppmrjitter.lpprjitterlpprlpprmaxEuclideanroc.lpproc.lppmrotate.linnetrotate.lpprpoislpprSwitzerlpprThomaslppruniflppscalardilate.linimscalardilate.linnetscalardilate.lppsdr.lppshift.linimshift.linnetshift.lppsimulate.lppmSmooth.lppsortalongsegmentspatialCovariateEvidence.exactlppmspatialCovariateEvidence.lppmsubset.lppsummary.linfunsummary.linimSummary.linimSummary.linimlistsummary.linnetsummary.lintesssummary.lppsummary.lppmsuperimpose.lppterminalverticesterms.lppmtext.lppthinNetworktile.lengthstilenames.lintesstilenames<-.lintesstraceTessLinnettreebranchlabelstreepruneunitname.linnetunitname.lppunitname<-.linnetunitname<-.lppunmark.lintessunmark.lppunstack.lintessunstack.lppupdate.lppmupdateData.lppmvalid.lppmvalidate.lpp.coordsvcov.lppmvertexdegreevertices.linnetvnnFindvolume.linnetWindow.linnetWindow.lintessWindow.lppWindow.lppmWindow<-.linnetWindow<-.lpp

Dependencies:abinddeldirgoftestlatticeMatrixmgcvnlmepolycliprpartspatstat.dataspatstat.explorespatstat.geomspatstat.modelspatstat.randomspatstat.sparsespatstat.univarspatstat.utilstensor

Readme and manuals

Help Manual

Help pageTopics
The spatstat.linnet Packagespatstat.linnet-package spatstat.linnet
Add New Vertices to a Linear NetworkaddVertices
Apply Geometrical Transformations to a Linear Networkaffine.linnet rescale.linnet rotate.linnet scalardilate.linnet shift.linnet
Apply Geometrical Transformations to Point Pattern on a Linear Networkaffine.lpp rescale.lpp rotate.lpp scalardilate.lpp shift.lpp
ANOVA for Fitted Point Process Models on Linear Networkanova.lppm
Convert Network Tessellation to Data Frameas.data.frame.lintess
Convert Data to a Function on a Linear Networkas.linfun as.linfun.linim as.linfun.lintess
Convert to Pixel Image on Linear Networkas.linim as.linim.default as.linim.linfun as.linim.linim
Extract Linear Network from Data on a Linear Networkas.linnet.linfun as.linnet.linim as.linnet.lintess as.linnet.lpp
Convert Line Segment Pattern to Linear Networkas.linnet.psp
Convert Data to a Point Pattern on a Linear Networkas.lpp
Convert Data on a Network to class owinas.owin.lpp as.owin.lppm
Area Under ROC Curve for Data on a Networkauc.lpp auc.lppm
Check Start of Character Stringbegins
Berman's Tests for Point Process Model on a Networkberman.test.lpp berman.test.lppm
Tree Branch Membership Labelling Functionbranchlabelfun
Likelihood Cross Validation Bandwidth Selection for Kernel Density on a Linear Networkbw.lppl
Cross Validated Bandwidth Selection for Relative Risk Estimation on a Networkbw.relrisk.lpp
Cross Validated Bandwidth Selection for Voronoi Estimator of Intensity on a Networkbw.voronoi
Spatial Distribution Test for Points on a Linear Networkcdf.test.lpp cdf.test.lppm
Divide a Linear Network into Tiles Using Infinite Lineschop.linnet
Interactively join vertices on a plotclickjoin
Interactively Add Points on a Linear Networkclicklpp
Connected Components of a Linear Networkconnected.linnet
Connected Components of a Point Pattern on a Linear Networkconnected.lpp
Pairwise distances between two point patterns on a linear networkcrossdist.lpp
Crossing Points between Linear Network and Other Linescrossing.linnet
Classify Points in a Point Pattern on a Networkcut.lpp
Extract Original Data from a Fitted Point Process Model on a Networkdata.lppm
Linear Network of Delaunay Triangulation or Dirichlet TessellationdelaunayNetwork dirichletNetwork
Delete or Extract a Branch of a Treedeletebranch deletebranch.linnet deletebranch.lpp extractbranch extractbranch.linnet extractbranch.lpp
Kernel Smoothing of Linear Networkdensity.linnet
Kernel Estimate of Intensity on a Linear Networkdensity.lpp density.splitppx
Equal-Split Algorithm for Kernel Density on a NetworkdensityEqualSplit
Kernel Estimate of Intensity on a Linear Network as a Spatial Functiondensityfun.lpp
Kernel Density on a Network using Heat EquationdensityHeat.lpp
Kernel Estimation of Intensity on a Network using a 2D KerneldensityQuick.lpp
Intensity Estimate of Point Pattern on Linear Network Using Voronoi-Dirichlet TessellationdensityVoronoi.lpp
Diameter and Bounding Radius of a Linear Networkboundingradius.linnet diameter.linnet
Distance Map on Linear Networkdistfun.lpp
Distance Map of Point Pattern on Linear Networkdistmap.lpp
Divide Linear Network at Cut Pointsdivide.linnet
Extract the Linear Network on which Spatial Data are Defineddomain.linfun domain.lintess domain.lpp domain.lppm
Envelope for Point Patterns on Linear Networkenvelope.lpp envelope.lppm
Evaluate Expression Involving Pixel Images on Linear Networkeval.linim
Extract Subset of Pixel Image on Linear Network[.linim
Extract Subset of Linear Network[.linnet
Extract Subset of Point Pattern on Linear Network[.lpp
Fitted Intensity for Point Process on Linear Networkfitted.lppm
Approximation to Heat Kernel on Linear Network at Source Pointheatkernelapprox
Identify Points in a Point Pattern on a Linear Networkidentify.lpp
Insert New Vertices in a Linear NetworkinsertVertices
Integral on a Linear Networkintegral.linfun integral.linim
Empirical Intensity of Point Pattern on Linear Networkintensity.lpp
Intersection of Tessellations on a Linear Networkintersect.lintess
Determine Whether a Linear Network is Connectedis.connected.linnet
Test Whether A Point Process Model is Markedis.marked.lppm
Test Whether A Point Pattern on a Network is Multitypeis.multitype.lpp
Test Whether A Point Process Model is Multitypeis.multitype.lppm
Recognise Stationary and Poisson Point Process Models on a Networkis.poisson.lppm is.stationary.lppm
Join Vertices in a NetworkjoinVertices
Dirichlet Tessellation on a Linear Networklineardirichlet
Compute Disc of Given Radius in Linear Networkcountends lineardisc lineardisclength
Inhomogeneous Linear J-function for Point Processes on Linear NetworkslinearJinhom
Linear K FunctionlinearK
Multitype K Function (Cross-type) for Linear Point PatternlinearKcross
Inhomogeneous multitype K Function (Cross-type) for Linear Point PatternlinearKcross.inhom
Multitype K Function (Dot-type) for Linear Point PatternlinearKdot
Inhomogeneous multitype K Function (Dot-type) for Linear Point PatternlinearKdot.inhom
Linear K Function Using Euclidean DistancelinearKEuclid
Inhomogeneous Linear K Function Based on Euclidean DistanceslinearKEuclidInhom
Inhomogeneous Linear K FunctionlinearKinhom
Mark Connection Function for Multitype Point Pattern on Linear Networklinearmarkconnect
Mark Connection Function for Multitype Point Pattern on Linear Networklinearmarkequal
Linear Pair Correlation Functionlinearpcf
Multitype Pair Correlation Function (Cross-type) for Linear Point Patternlinearpcfcross
Inhomogeneous Multitype Pair Correlation Function (Cross-type) for Linear Point Patternlinearpcfcross.inhom
Multitype Pair Correlation Function (Dot-type) for Linear Point Patternlinearpcfdot
Inhomogeneous Multitype Pair Correlation Function (Dot-type) for Linear Point Patternlinearpcfdot.inhom
Linear Pair Correlation Function Using Euclidean DistancelinearpcfEuclid
Inhomogeneous Linear Pair Correlation Function Based on Euclidean DistanceslinearpcfEuclidInhom
Inhomogeneous Linear Pair Correlation Functionlinearpcfinhom
Determine Which Tile Contains Each Given Point on a Linear Networklineartileindex
Quadrature Scheme on a Linear Networklinequad
Function on a Linear Networklinfun
Create Pixel Image on Linear Networklinim
Create a Linear Networklinnet
Tessellation on a Linear Networklintess
Subdivide Segments of a Networklixellate
Create Point Pattern on Linear Networklpp
Fit Point Process Model to Point Pattern on Linear Networklppm lppm.formula lppm.lpp
Marks of a Networkmarks.linnet marks<-.linnet
Marks of a Tessellation on a Networkmarks.lintess marks<-.lintess unmark.lintess
S3 Group Generic Methods for Images on a Linear NetworkComplex.linim Math.linim Ops.linim Summary.linim
Mean, Median, Quantiles of Pixel Values on a Linear Networkmean.linim median.linim quantile.linim quantilefun.linim
Methods for Functions on Linear Networkas.data.frame.linfun as.function.linfun as.owin.linfun methods.linfun plot.linfun print.linfun summary.linfun
Methods for Images on a Linear Networkaffine.linim as.data.frame.linim as.im.linim methods.linim print.linim scalardilate.linim shift.linim summary.linim
Methods for Linear Networksas.linnet as.linnet.linnet as.owin.linnet as.psp.linnet methods.linnet nsegments.linnet nvertices.linnet pixellate.linnet print.linnet summary.linnet unitname.linnet unitname<-.linnet vertexdegree vertices.linnet volume.linnet Window.linnet
Methods for Point Patterns on a Linear Networkas.ppp.lpp as.psp.lpp marks<-.lpp methods.lpp nsegments.lpp print.lpp print.summary.lpp summary.lpp unitname.lpp unitname<-.lpp unmark.lpp
Methods for Fitted Point Process Models on a Linear Networkas.linnet.lppm coef.lppm deviance.lppm emend.lppm extractAIC.lppm formula.lppm logLik.lppm methods.lppm nobs.lppm print.lppm response.lppm summary.lppm terms.lppm update.lppm valid.lppm vcov.lppm
Extract the Variables in a Point Process Model on a Networkmodel.frame.lppm
Compute Images of Constructed Covariatesmodel.images.lppm
Extract Design Matrix from Point Process Model on a Networkmodel.matrix.lppm
Nearest Neighbours on a Linear Networknncross.lpp
Nearest neighbour distances on a linear networknndist.lpp
Nearest Data Point From Each Vertex in a Networknnfromvertex
Nearest Neighbour Map on Linear Networknnfun.lpp
Identify Nearest Neighbours on a Linear Networknnwhich.lpp
Pairwise shortest-path distances between points on a linear networkpairdist.lpp
Scatterplot Matrix for Pixel Images on a Linear Networkpairs.linim
Perspective View of Function on a Linear Networkpersp.linfun
Perspective View of Pixel Image on a Linear Networkpersp.linim
Plot Pixel Image on Linear Networkplot.linim
Plot a linear networkplot.linnet
Plot a Tessellation on a Linear Networkplot.lintess
Plot Point Pattern on Linear Networkplot.lpp
Plot a Fitted Point Process Model on a Linear Networkplot.lppm
Draw Points on Existing Plotpoints.lpp
Predict Point Process Model on Linear Networkpredict.lppm
Calculate Pseudo-R-Squared for Point Process Model on Linear NetworkpseudoR2.lppm
Simulate Cell Process on Linear Networkrcelllpp
Nonparametric Estimate of Spatially-Varying Relative Risk on a Networkrelrisk.lpp
Repair Internal Data in a Linear NetworkrepairNetwork
Reset Values in Subset of Image on Linear Network[<-.linim
Nonparametric Estimate of Intensity as Function of a Covariaterhohat.lpp rhohat.lppm
Random Perturbation of a Point Pattern on a Networkrjitter.lpp
Random Points on a Linear Networkrlpp
Receiver Operating Characteristic for Data on a Networkroc.lpp roc.lppm
Poisson Point Process on a Linear Networkrpoislpp
Switzer-type Point Process on Linear NetworkrSwitzerlpp
Simulate Thomas Process on Linear NetworkrThomaslpp
Uniform Random Points on a Linear Networkruniflpp
Sufficient Dimension Reduction for a Point Pattern on a Linear Networksdr.lpp
Simulate a Fitted Point Process Model on a Linear Networksimulate.lppm
Spatial Smoothing of Observations on a NetworkSmooth.lpp
Subset of Point Pattern Satisfying A Conditionsubset.lpp
Superimpose Several Point Patterns on Linear Networksuperimpose.lpp
Terminal Vertices of a Linear Networkterminalvertices
Add Text Labels to Point Pattern on a Networktext.lpp
Remove Vertices or Segments from a Linear NetworkthinNetwork
Compute Lengths of Tiles in a Tessellation on a Networktile.lengths
Names of Tiles in a Tessellation on a Networktilenames.lintess tilenames<-.lintess
Label Vertices of a Tree by Branch Membershiptreebranchlabels
Prune Tree to Given Leveltreeprune
Separate Multiple Columns of Marksunstack.lintess unstack.lpp
Extract Window of Spatial Object on a NetworkWindow.lpp Window.lppm