# spatstat v1.16-0

Monthly downloads

## Spatial Point Pattern analysis, model-fitting, simulation, tests

A package for analysing spatial data, mainly Spatial Point
Patterns, including multitype/marked points and spatial
covariates, in any two-dimensional spatial region. Contains
functions for plotting spatial data, exploratory data analysis,
model-fitting, simulation, spatial sampling, model diagnostics,
and formal inference. Data types include point patterns, line
segment patterns, spatial windows, and pixel images. Point
process models can be fitted to point pattern data. Cluster
type models are fitted by the method of minimum contrast. Very
general Gibbs point process models can be fitted to point
pattern data using a function ppm similar to lm or glm. Models
may include dependence on covariates, interpoint interaction
and dependence on marks. Fitted models can be simulated
automatically. Also provides facilities for formal inference
(such as chi-squared tests) and model diagnostics (including
simulation envelopes, residuals, residual plots and Q-Q plots).

## Functions in spatstat

Name | Description | |

Replace.im | Reset Values in Subset of Image | |

Iest | Estimate the I-function | |

Gest | Nearest Neighbour Distance Function G | |

Kmulti | Marked K-Function | |

Extract.im | Extract Subset of Image | |

OrdThresh | Ord's Interaction model | |

Kmeasure | Reduced Second Moment Measure | |

anemones | Beadlet Anemones Data | |

LennardJones | The Lennard-Jones Potential | |

as.im | Convert to Pixel Image | |

Extract.fasp | Extract Subset of Function Array | |

Linhom | L-function | |

affine.psp | Apply Affine Transformation To Line Segment Pattern | |

anova.ppm | ANOVA for Fitted Point Process Models | |

Gdot | Multitype Nearest Neighbour Distance Function (i-to-any) | |

bdist.pixels | Distance to Boundary of Window | |

bounding.box.xy | Convex Hull of Points | |

Jcross | Multitype J Function (i-to-j) | |

as.tess | Convert Data To Tessellation | |

Kdot | Multitype K Function (i-to-any) | |

chop.tess | Subdivide a Window or Tessellation using a Set of Lines | |

Extract.fv | Extract Subset of Function Values | |

crossdist | Pairwise distances | |

complement.owin | Take Complement of a Window | |

demopat | Artificial Data Point Pattern | |

disc | Circular Window | |

compatible.fasp | Test Whether Two Function Arrays Are Compatible | |

coef.ppm | Coefficients of Fitted Point Process Model | |

Extract.quad | Subset of Quadrature Scheme | |

as.data.frame.ppp | Coerce Point Pattern to a Data Frame | |

bdist.points | Distance to Boundary of Window | |

Jest | Estimate the J-function | |

dummy.ppm | Extract Dummy Points Used to Fit a Point Process Model | |

Kcross | Multitype K Function (Cross-type) | |

eem | Exponential Energy Marks | |

DiggleGratton | Diggle-Gratton model | |

SatPiece | Piecewise Constant Saturated Pairwise Interaction Point Process Model | |

append.psp | Combine Two Line Segment Patterns | |

Kdot.inhom | Inhomogeneous Multitype K Dot Function | |

blur | Apply Gaussian Blur to a Pixel Image | |

endpoints.psp | Endpoints of Line Segment Pattern | |

MultiStraussHard | The Multitype/Hard Core Strauss Point Process Model | |

Softcore | The Soft Core Point Process Model | |

Jdot | Multitype J Function (i-to-any) | |

Extract.listof | Extract or Replace Subset of a List of Things | |

as.rectangle | Window Frame | |

bramblecanes | Hutchings' Bramble Canes data | |

as.psp | Convert Data To Class psp | |

Ldot | Multitype L-function (i-to-any) | |

closing.owin | Morphological Closing of a Window | |

erode.owin | Erode a Window | |

StraussHard | The Strauss / Hard Core Point Process Model | |

as.mask | Pixel Image Approximation of a Window | |

MultiStrauss | The Multitype Strauss Point Process Model | |

Geyer | Geyer's Saturation Point Process Model | |

allstats | Calculate four standard summary functions of a point pattern. | |

Ord | Generic Ord Interaction model | |

Lest | L-function | |

eval.fv | Evaluate Expression Involving Functions | |

applynbd | Apply Function to Every Neighbourhood in a Point Pattern | |

colourmap | Colour Lookup Tables | |

Gcross | Multitype Nearest Neighbour Distance Function (i-to-j) | |

data.ppm | Extract Original Data from a Fitted Point Process Model | |

clarkevans | Clark and Evans Aggregation Index | |

is.marked.ppm | Test Whether A Point Process Model is Marked | |

discretise | Safely Convert Point Pattern Window to Binary Mask | |

Lcross.inhom | Inhomogeneous Cross Type L Function | |

concatxy | Concatenate x,y Coordinate Vectors | |

kaplan.meier | Kaplan-Meier Estimator using Histogram Data | |

default.dummy | Generate a Default Pattern of Dummy Points | |

Emark | Diagnostics for random marking | |

distmap.owin | Distance Map of Window | |

bounding.box | Bounding Box of a Window or Point Pattern | |

clickppp | Interactively Add Points | |

Extract.ppp | Extract or Replace Subset of Point Pattern | |

infline | Infinite Straight Lines | |

BadGey | Hybrid Geyer Point Process Model | |

crossdist.psp | Pairwise distances between two different line segment patterns | |

distmap.psp | Distance Map of Line Segment Pattern | |

copper | Berman-Huntington points and lines data | |

spatstat-internal | Internal spatstat functions | |

alltypes | Calculate Summary Statistic for All Types in a Multitype Point Pattern | |

Fest | Estimate the empty space function F | |

adaptive.density | Intensity Estimate of Point Pattern Using Tessellation | |

is.marked | Test Whether Marks Are Present | |

hist.im | Histogram of Pixel Values in an Image | |

interp.im | Interpolate a Pixel Image | |

as.matrix.im | Convert Pixel Image to Matrix | |

levelset | Level Set of a Pixel Image | |

model.matrix.ppm | Extract Design Matrix from Point Process Model | |

matchingdist | Distance for a Point Pattern Matching | |

localK | Neighbourhood density function | |

compatible.im | Test Whether Two Pixel Images Are Compatible | |

Lcross | Multitype L-function (cross-type) | |

murchison | Murchison gold deposits | |

im | Create a Pixel Image Object | |

gridcentres | Rectangular grid of points | |

iplot | Point and Click Interface for Displaying a Point Pattern | |

Kest | K-function | |

density.ppp | Kernel Smoothed Intensity of Point Pattern | |

cut.im | Convert Pixel Image from Numeric to Factor | |

Ldot.inhom | Inhomogeneous Multitype L Dot Function | |

plot.colourmap | Plot a Colour Map | |

ewcdf | Weighted Empirical Cumulative Distribution Function | |

longleaf | Longleaf Pines Point Pattern | |

amacrine | Hughes' Amacrine Cell Data | |

pcf.ppp | Pair Correlation Function of Point Pattern | |

ppp | Create a Point Pattern | |

cells | Biological Cells Point Pattern | |

Extract.psp | Extract Subset of Line Segment Pattern | |

effectfun | Compute Fitted Effect of a Spatial Covariate in a Point Process Model | |

ants | Harkness-Isham ants' nests data | |

midpoints.psp | Midpoints of Line Segment Pattern | |

lengths.psp | Lengths of Line Segments | |

heather | Diggle's Heather Data | |

mean.im | Mean, Median and Range of Pixel Values in an Image | |

envelope | Simulation envelopes of summary function | |

Kest.fft | K-function using FFT | |

japanesepines | Japanese Pines Point Pattern | |

matclust.estK | Fit the Matern Cluster Point Process by Minimum Contrast | |

crossdist.ppp | Pairwise distances between two different point patterns | |

PairPiece | The Piecewise Constant Pairwise Interaction Point Process Model | |

area.owin | Area of a Window | |

by.im | Apply Function to Image Broken Down by Factor | |

eval.im | Evaluate Expression Involving Pixel Images | |

Strauss | The Strauss Point Process Model | |

diameter | Diameter of a Window | |

as.data.frame.psp | Coerce Line Segment Pattern to a Data Frame | |

dirichlet | Dirichlet Tessellation of Point Pattern | |

is.subset.owin | Determine Whether One Window is Contained In Another | |

dirichlet.weights | Compute Quadrature Weights Based on Dirichlet Tessellation | |

kstest.ppm | Kolmogorov-Smirnov Test for Point Process Model | |

corners | Corners of a rectangle | |

bei | Tropical rain forest trees | |

diagnose.ppm | Diagnostic Plots for Fitted Point Process Model | |

AreaInter | The Area Interaction Point Process Model | |

affine | Apply Affine Transformation | |

kppm | Fit cluster point process model | |

Extract.splitppp | Extract or Replace Sub-Patterns | |

nncross | Nearest Neighbours Between Two Patterns | |

connected | Connected components of an image or window | |

im.object | Class of Images | |

clip.infline | Intersect Infinite Straight Lines with a Window | |

nndist | Nearest neighbour distances | |

nndist.psp | Nearest neighbour distances between line segments | |

Pairwise | Generic Pairwise Interaction model | |

Poisson | Poisson Point Process Model | |

convexhull.xy | Convex Hull of Points | |

compatible.fv | Test Whether Two Function Objects Are Compatible | |

affine.owin | Apply Affine Transformation To Window | |

convexhull | Convex Hull | |

eval.fasp | Evaluate Expression Involving Function Arrays | |

is.multitype | Test whether Object is Multitype | |

humberside | Humberside Data on Childhood Leukaemia and Lymphoma | |

print.ppm | Print a Fitted Point Process Model | |

pairdist.default | Pairwise distances | |

Saturated | Saturated Pairwise Interaction model | |

fitted.ppm | Fitted Conditional Intensity for Point Process Model | |

incircle | Find Largest Circle Inside Window | |

inside.owin | Test Whether Points Are Inside A Window | |

lut | Lookup Tables | |

plot.listof | Plot a List of Things | |

owin | Create a Window | |

mincontrast | Method of Minimum Contrast | |

fryplot | Fry Plot of Point Pattern | |

pairdist.psp | Pairwise distances between line segments | |

gridweights | Compute Quadrature Weights Based on Grid Counts | |

markconnect | Mark Connection Function | |

psp.object | Class of Line Segment Patterns | |

spatstat-deprecated | Deprecated spatstat functions | |

rGaussPoisson | Simulate Gauss-Poisson Process | |

pppmatching.object | Class of Point Matchings | |

as.owin | Convert Data To Class owin | |

pppmatching | Create a Point Matching | |

persp.im | Perspective Plot of Pixel Image | |

is.im | Test Whether An Object Is A Pixel Image | |

rMosaicField | Mosaic Random Field | |

hyperframe | Hyper Data Frame | |

quad.object | Class of Quadrature Schemes | |

pixelquad | Quadrature Scheme Based on Pixel Grid | |

lgcp.estK | Fit a Log-Gaussian Cox Point Process by Minimum Contrast | |

nztrees | New Zealand Trees Point Pattern | |

plot.tess | Plot a tessellation | |

crossdist.default | Pairwise distances between two different sets of points | |

nnwhich | Nearest neighbour | |

rshift | Random Shift | |

pcf | Pair Correlation Function | |

finpines | Pine saplings in Finland. | |

inforder.family | Infinite Order Interaction Family | |

ppm | Fit Point Process Model to Data | |

ord.family | Ord Interaction Process Family | |

plot.plotppm | Plot a plotppm Object Created by plot.ppm | |

plot.hyperframe | Plot Entries in a Hyperframe | |

plot.quad | plot a Spatial Quadrature Scheme | |

quantile.im | Sample Quantiles of Pixel Image | |

model.images | Compute Images of Constructed Covariates | |

multiplicity.ppp | Count Multiplicity of Duplicate Points | |

pcf.fv | Pair Correlation Function obtained from K Function | |

distmap | Distance Map | |

opening.owin | Morphological Opening of a Window | |

delaunay | Delaunay Triangulation of Point Pattern | |

centroid.owin | Centroid of a window | |

Extract.tess | Extract or Replace Subset of Tessellation | |

nncorr | Nearest-Neighbour Correlation Indices of Marked Point Pattern | |

predict.ppm | Prediction from a Fitted Point Process Model | |

project2segment | Move Point To Nearest Line | |

pairdist | Pairwise distances | |

duplicated.ppp | Determine Duplicated Points in a Spatial Point Pattern | |

rescale.owin | Convert Window to Another Unit of Length | |

raster.x | Cartesian Coordinates for a Pixel Raster | |

rescale.ppp | Convert Point Pattern to Another Unit of Length | |

quadratcount | Quadrat counting for a point pattern | |

distmap.ppp | Distance Map of Point Pattern | |

fasp.object | Function Arrays for Spatial Patterns | |

intersect.owin | Intersection or Union of Two Windows | |

density.psp | Kernel Smoothing of Line Segment Pattern | |

shift.im | Apply Vector Translation To Pixel Image | |

tiles | Extract List of Tiles in a Tessellation | |

letterR | Window in Shape of Letter R | |

eval.hyper | Evaluate an Expression in Each Row of a Hyperframe | |

fitin.ppm | Extract the Interaction from a Fitted Point Process Model | |

intersect.tess | Intersection of Two Tessellations | |

logLik.ppm | Log Likelihood for Poisson Point Process Model | |

pcfcross | Multitype pair correlation function | |

gpc2owin | Convert Polygonal Region into Different Format | |

psp | Create a Line Segment Pattern | |

marktable | Tabulate Marks in Neighbourhood of Every Point in a Point Pattern | |

is.multitype.ppm | Test Whether A Point Process Model is Multitype | |

is.marked.ppp | Test Whether A Point Pattern is Marked | |

quadratresample | Resample a Point Pattern by Resampling Quadrats | |

ponderosa | Ponderosa Pine Tree Point Pattern | |

hamster | Aherne's hamster tumour data | |

residualspaper | Data and Code From JRSS Discussion Paper on Residuals | |

identify.ppp | Identify Points in a Point Pattern | |

Hest | Spherical Contact Distribution Function | |

simplify.owin | Approximate a Polygon by a Simpler Polygon | |

harmonic | Basis for Harmonic Functions | |

pointsOnLines | Place Points Evenly Along Specified Lines | |

fv.object | Data Frames of Function Values | |

residuals.ppm | Residuals for Fitted Point Process Model | |

markvario | Mark Variogram | |

ganglia | Beta Ganglion Cells in Cat Retina, Old Version | |

pairsat.family | Saturated Pairwise Interaction Point Process Family | |

plot.im | Plot a Pixel Image | |

plot.splitppp | Plot a List of Point Patterns | |

Kcross.inhom | Inhomogeneous Cross K Function | |

summary.owin | Summary of a Spatial Window | |

Jmulti | Marked J Function | |

plot.ppp | plot a Spatial Point Pattern | |

vcov.ppm | Variance-Covariance Matrix for a Fitted Point Process Model | |

print.im | Print Brief Details of an Image | |

rlinegrid | Generate grid of parallel lines with random displacement | |

quadrat.test.splitppp | Chi-Squared Test of CSR for Split Point Pattern | |

print.quad | Print a Quadrature Scheme | |

summary.ppp | Summary of a Point Pattern Dataset | |

rmhstart | Determine Initial State for Metropolis-Hastings Simulation. | |

ppp.object | Class of Point Patterns | |

reach | Interaction Distance of a Point Process | |

rescale | Convert dataset to another unit of length | |

print.ppp | Print Brief Details of a Point Pattern Dataset | |

miplot | Morishita Index Plot | |

nearestsegment | Find Line Segment Nearest to Each Point | |

rshift.psp | Randomly Shift a Line Segment Pattern | |

plot.psp | plot a Spatial Line Segment Pattern | |

rcell | Simulate Baddeley-Silverman Cell Process | |

rMatClust | Simulate Matern Cluster Process | |

split.im | Divide Image Into Sub-images | |

print.owin | Print Brief Details of a Spatial Window | |

rmpoint | Generate N Random Multitype Points | |

km.rs | Kaplan-Meier and Reduced Sample Estimator using Histograms | |

is.owin | Test Whether An Object Is A Window | |

pixellate | Convert Point Pattern to Pixel Image | |

quadrats | Divide Region into Quadrats | |

rpoislinetess | Poisson Line Tessellation | |

redwoodfull | California Redwoods Point Pattern (Entire Dataset) | |

plot.fv | Plot Function Values | |

plot.ppm | plot a Fitted Point Process Model | |

unitname | Name for Unit of Length | |

unmark | Remove Marks | |

rthin | Random Thinning | |

Kinhom | Inhomogeneous K-function | |

is.ppp | Test Whether An Object Is A Point Pattern | |

rMaternII | Simulate Matern Model II | |

rstrat | Simulate Stratified Random Point Pattern | |

summary.ppm | Summarizing a Fitted Point Process Model | |

superimpose | Superimpose Several Point Patterns | |

profilepl | Profile Maximum Pseudolikelihood | |

markcorr | Mark Correlation Function | |

summary.splitppp | Summary of a Split Point Pattern | |

lansing | Lansing Woods Point Pattern | |

angles.psp | Orientation Angles of Line Segments | |

rmhmodel.ppm | Interpret Fitted Model for Metropolis-Hastings Simulation. | |

rpoisline | Generate Poisson Random Line Process | |

is.multitype.ppp | Test Whether A Point Pattern is Multitype | |

qqplot.ppm | Q-Q Plot of Residuals from Fitted Point Process Model | |

owin.object | Class owin | |

istat | Point and Click Interface for Exploratory Analysis of Point Pattern | |

lurking | Lurking variable plot | |

rmpoispp | Generate Multitype Poisson Point Pattern | |

nbfires | Point Patterns of New Brunswick Forest Fires | |

rmh.ppm | Simulate from a Fitted Point Process Model | |

smooth.ppp | Spatial smoothing of observations at irregular points | |

swedishpines | Swedish Pines Point Pattern | |

rshift.ppp | Randomly Shift a Point Pattern | |

rmhmodel | Define Point Process Model for Metropolis-Hastings Simulation. | |

spatstat.options | Internal Options in Spatstat Package | |

print.psp | Print Brief Details of a Line Segment Pattern Dataset | |

markcorrint | Mark Correlation Integral | |

pppdist | Distance Between Two Point Patterns | |

rotate | Rotate | |

rNeymanScott | Simulate Neyman-Scott Process | |

quad.ppm | Extract Quadrature Scheme Used to Fit a Point Process Model | |

rotate.owin | Rotate a Window | |

quadrat.test | Chi-Squared Dispersion Test for Spatial Point Pattern Based on Quadrat Counts | |

shift.owin | Apply Vector Translation To Window | |

pairdist.ppp | Pairwise distances | |

plot.fasp | Plot a Function Array | |

square | Square Window | |

rThomas | Simulate Thomas Process | |

rMosaicSet | Mosaic Random Set | |

ripras | Estimate window from points alone | |

tess | Create a Tessellation | |

rescale.psp | Convert Line Segment Pattern to Another Unit of Length | |

Gmulti | Marked Nearest Neighbour Distance Function | |

summary.psp | Summary of a Line Segment Pattern Dataset | |

runifpoint | Generate N Uniform Random Points | |

simulate.kppm | Simulate a fitted cluster point process model. | |

rStrauss | Perfect Simulation of the Strauss Process | |

update.ppm | Update a Fitted Point Process Model | |

runifpointOnLines | Generate N Uniform Random Points On Line Segments | |

rmhcontrol | Set Control Parameters for Metropolis-Hastings Algorithm. | |

shift | Apply Vector Translation | |

urkiola | Urkiola Woods Point Pattern | |

superimposePSP | Superimpose Several Line Segment Patterns | |

shift.ppp | Apply Vector Translation To Point Pattern | |

thomas.estK | Fit the Thomas Point Process by Minimum Contrast | |

rsyst | Simulate systematic random point pattern | |

pcf.fasp | Pair Correlation Function obtained from array of K functions | |

plot.kppm | Plot a fitted cluster point process | |

rescale.im | Convert Pixel Image to Another Unit of Length | |

contour.im | Contour plot of pixel image | |

density.splitppp | Kernel Smoothed Intensity of Split Point Pattern | |

shift.psp | Apply Vector Translation To Line Segment Pattern | |

rjitter | Random Perturbation of a Point Pattern | |

rmh | Simulate point patterns using the Metropolis-Hastings algorithm. | |

stieltjes | Compute Integral of Function Against Cumulative Distribution | |

rpoispp | Generate Poisson Point Pattern | |

trim.rectangle | Cut margins from rectangle | |

rmh.default | Simulate Point Process Models using the Metropolis-Hastings Algorithm. | |

ppm.object | Class of Fitted Point Process Models | |

split.ppp | Divide Point Pattern into Sub-patterns | |

is.convex | Test Whether a Window is Convex | |

rmhmodel.default | Build Point Process Model for Metropolis-Hastings Simulation. | |

spruces | Spruces Point Pattern | |

rotate.ppp | Rotate a Point Pattern | |

solutionset | Evaluate Logical Expression Involving Pixel Images and Return Region Where Expression is True | |

rlabel | Random Re-Labelling of Point Pattern | |

rpoint | Generate N Random Points | |

update.kppm | Update a Fitted Cluster Point Process Model | |

rshift.splitppp | Randomly Shift a List of Point Patterns | |

runifdisc | Generate N Uniform Random Points in a Disc | |

rescue.rectangle | Convert Window Back To Rectangle | |

simdat | Simulated Point Pattern | |

union.quad | Union of Data and Dummy Points | |

shapley | Galaxies in the Shapley Supercluster | |

predict.kppm | Prediction from a Fitted Cluster Point Process Model | |

spokes | Spokes pattern of dummy points | |

selfcrossing.psp | Crossing Points in a Line Segment Pattern | |

scanpp | Read Point Pattern From Data File | |

vertices | Vertices of a Window | |

summary.listof | Summary of a List of Things | |

redwood | California Redwoods Point Pattern (Ripley's Subset) | |

setcov | Set Covariance of a Window | |

reduced.sample | Reduced Sample Estimator using Histogram Data | |

rmhmodel.list | Define Point Process Model for Metropolis-Hastings Simulation. | |

quadscheme | Generate a Quadrature Scheme from a Point Pattern | |

with.fv | Evaluate an Expression in a Function Table | |

summary.quad | Summarizing a Quadrature Scheme | |

unique.ppp | Extract Unique Points from a Spatial Point Pattern | |

affine.ppp | Apply Affine Transformation To Point Pattern | |

by.ppp | Apply a Function to a Point Pattern Broken Down by Factor | |

chorley | Chorley-Ribble Cancer Data | |

betacells | Beta Ganglion Cells in Cat Retina | |

clickpoly | Interactively Define a Polygon | |

cut.ppp | Classify Points in a Point Pattern | |

crossing.psp | Crossing Points of Two Line Segment Patterns | |

is.ppm | Test Whether An Object Is A Fitted Point Process Model | |

markstat | Summarise Marks in Every Neighbourhood in a Point Pattern | |

plot.owin | Plot a Spatial Window | |

progressreport | Print Progress Reports | |

rMaternI | Simulate Matern Model I | |

rotate.psp | Rotate a Line Segment Pattern | |

rpoisppOnLines | Generate Poisson Point Pattern on Line Segments | |

setmarks | Set or Reset the Marks in a Point Pattern | |

summary.im | Summarizing a Pixel Image | |

spatstat | The Spatstat Package | |

areadiff | Difference of Disc Areas | |

as.ppp | Convert Data To Class ppp | |

dilate.owin | Dilate a Window | |

eroded.areas | Areas of Morphological Erosions | |

expand.owin | Expand Window By Factor | |

nearest.raster.point | Find Pixel Nearest to a Given Point | |

pairwise.family | Pairwise Interaction Process Family | |

rSSI | Simulate Simple Sequential Inhibition | |

suffstat | Sufficient Statistic of Point Process Model | |

No Results! |

## Last month downloads

## Details

Date | 01 July 2009 |

License | GPL (>= 2) |

URL | http://www.spatstat.org |

Packaged | 2009-07-03 01:41:32 UTC; adrian |

Repository | CRAN |

Date/Publication | 2009-07-02 13:36:55 |

depends | base (>= 2.7.0) , deldir (>= 0.0-7) , gpclib , graphics , mgcv , R (>= 2.7.0) , stats , utils |

suggests | maptools , rpanel , sm , tkrplot |

Contributors | Rolf Turner, Adrian Baddeley |

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