spatstat v1.14-6

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by Adrian Baddeley

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
Kcross Multitype K Function (Cross-type)
PairPiece The Piecewise Constant Pairwise Interaction Point Process Model
is.owin Test Whether An Object Is A Window
endpoints.psp Endpoints of Line Segment Pattern
letterR Window in Shape of Letter R
psp.object Class of Line Segment Patterns
ppm Fit Point Process Model to Data
quadrats Divide Region into Quadrats
rmhstart Determine Initial State for Metropolis-Hastings Simulation.
split.ppp Divide Point Pattern into Sub-patterns
update.ppm Update a Fitted Point Process Model
rthin Random Thinning
centroid.owin Centroid of a window
subset.im Extract Subset of Image
Kdot Multitype K Function (i-to-any)
Fest Estimate the empty space function F
as.mask Pixel Image Approximation of a Window
adaptive.density Intensity Estimate of Point Pattern Using Tessellation
ganglia Beta Ganglion Cells in Cat Retina, Old Version
Lcross Multitype L-function (cross-type)
fasp.object Function Arrays for Spatial Patterns
area.owin Area of a Window
plot.kppm Plot a fitted cluster point process
crossdist.default Pairwise distances between two different sets of points
Poisson Poisson Point Process Model
corners Corners of a rectangle
compatible.fasp Test Whether Two Function Arrays Are Compatible
harmonic Basis for Harmonic Functions
Ldot Multitype L-function (i-to-any)
Iest Estimate the I-function
eval.im Evaluate Expression Involving Pixel Images
Gmulti Marked Nearest Neighbour Distance Function
diagnose.ppm Diagnostic Plots for Fitted Point Process Model
BadGey Hybrid Geyer Point Process Model
owin.object Class owin
Jest Estimate the J-function
MultiStrauss The Multitype Strauss Point Process Model
Lest L-function
hamster Aherne's hamster tumour data
print.owin Print Brief Details of a Spatial Window
Pairwise Generic Pairwise Interaction model
eem Exponential Energy Marks
eroded.areas Areas of Morphological Erosions
bramblecanes Hutchings' Bramble Canes data
cut.im Convert Pixel Image from Numeric to Factor
pairdist.default Pairwise distances
expand.owin Expand Window By Factor
is.ppm Test Whether An Object Is A Fitted Point Process Model
pairdist.psp Pairwise distances between line segments
Kdot.inhom Inhomogeneous Multitype K Dot Function
ppm.object Class of Fitted Point Process Models
fitted.ppm Fitted Conditional Intensity for Point Process Model
chorley Chorley-Ribble Cancer Data
is.marked.ppm Test Whether A Point Process Model is Marked
distmap.owin Distance Map of Window
as.ppp Convert Data To Class ppp
coef.ppm Coefficients of Fitted Point Process Model
as.matrix.im Convert Pixel Image to Matrix
ppp Create a Point Pattern
Gest Nearest Neighbour Distance Function G
pcfcross Multitype pair correlation function
SatPiece Piecewise Constant Saturated Pairwise Interaction Point Process Model
as.psp Convert Data To Class psp
is.ppp Test Whether An Object Is A Point Pattern
eval.fasp Evaluate Expression Involving Function Arrays
distmap.psp Distance Map of Line Segment Pattern
affine Apply Affine Transformation
longleaf Longleaf Pines Point Pattern
clickpoly Interactively Define a Polygon
rstrat Simulate Stratified Random Point Pattern
finpines Pine saplings in Finland.
nztrees New Zealand Trees Point Pattern
compatible.im Test Whether Two Pixel Images Are Compatible
as.data.frame.ppp Coerce Point Pattern to a Data Frame
is.im Test Whether An Object Is A Pixel Image
Saturated Saturated Pairwise Interaction model
affine.psp Apply Affine Transformation To Line Segment Pattern
anemones Beadlet Anemones Data
as.rectangle Window Frame
identify.ppp Identify Points in a Point Pattern
by.im Apply Function to Image Broken Down by Factor
affine.owin Apply Affine Transformation To Window
Softcore The Soft Core Point Process Model
pppdist Distance Between Two Point Patterns
StraussHard The Strauss / Hard Core Point Process Model
areadiff Difference of Disc Areas
plot.ppm plot a Fitted Point Process Model
rpoisline Generate Poisson Random Line Process
cells Biological Cells Point Pattern
ord.family Ord Interaction Process Family
demopat Artificial Data Point Pattern
print.im Print Brief Details of an Image
Strauss The Strauss Point Process Model
rotate.owin Rotate a Window
pairsat.family Saturated Pairwise Interaction Point Process Family
unmark Remove Marks
matchingdist Distance for a Point Pattern Matching
vertices Vertices of a Window
is.multitype.ppm Test Whether A Point Process Model is Multitype
as.owin Convert Data To Class owin
pcf.fv Pair Correlation Function obtained from K Function
multiplicity.ppp Count Multiplicity of Duplicate Points
rescale.im Convert Pixel Image to Another Unit of Length
blur Apply Gaussian Blur to a Pixel Image
bei Tropical rain forest trees
rmhmodel.ppm Interpret Fitted Model for Metropolis-Hastings Simulation.
density.psp Kernel Smoothing of Line Segment Pattern
summary.ppm Summarizing a Fitted Point Process Model
bounding.box.xy Convex Hull of Points
duplicated.ppp Determine Duplicated Points in a Spatial Point Pattern
clarkevans Clark and Evans Aggregation Index
discretise Safely Convert Point Pattern Window to Binary Mask
bdist.points Distance to Boundary of Window
lengths.psp Lengths of Line Segments
Jmulti Marked J Function
Kcross.inhom Inhomogeneous Cross K Function
shift.ppp Apply Vector Translation To Point Pattern
spatstat The Spatstat Package
rmpoint Generate N Random Multitype Points
by.ppp Apply a Function to a Point Pattern Broken Down by Factor
levelset Level Set of a Pixel Image
subsetget.im Reset Values in Subset of Image
rThomas Simulate Thomas Process
allstats Calculate four standard summary functions of a point pattern.
gpc2owin Convert Polygonal Region into Different Format
anova.ppm ANOVA for Fitted Point Process Models
marktable Tabulate Marks in Neighbourhood of Every Point in a Point Pattern
spruces Spruces Point Pattern
default.dummy Generate a Default Pattern of Dummy Points
quad.object Class of Quadrature Schemes
murchison Murchison gold deposits
km.rs Kaplan-Meier and Reduced Sample Estimator using Histograms
owin Create a Window
print.quad Print a Quadrature Scheme
Kinhom Inhomogeneous K-function
spatstat-deprecated Deprecated spatstat functions
predict.kppm Prediction from a Fitted Cluster Point Process Model
mincontrast Method of Minimum Contrast
rescale.ppp Convert Point Pattern to Another Unit of Length
rmhmodel.list Define Point Process Model for Metropolis-Hastings Simulation.
ppp.object Class of Point Patterns
quad.ppm Extract Quadrature Scheme Used to Fit a Point Process Model
stieltjes Compute Integral of Function Against Cumulative Distribution
ewcdf Weighted Empirical Cumulative Distribution Function
copper Berman-Huntington points and lines data
Jcross Multitype J Function (i-to-j)
rmhmodel.default Build Point Process Model for Metropolis-Hastings Simulation.
rshift.ppp Randomly Shift a Point Pattern
trim.rectangle Cut margins from rectangle
betacells Beta Ganglion Cells in Cat Retina
model.images Compute Images of Constructed Covariates
update.kppm Update a Fitted Cluster Point Process Model
plot.fasp Plot a Function Array
subset.ppp Extract or Replace Subset of Point Pattern
model.matrix.ppm Extract Design Matrix from Point Process Model
print.ppm Print a Fitted Point Process Model
fv.object Data Frames of Function Values
selfcrossing.psp Crossing Points in a Line Segment Pattern
as.im Convert to Pixel Image
print.ppp Print Brief Details of a Point Pattern Dataset
shift.im Apply Vector Translation To Pixel Image
dummy.ppm Extract Dummy Points Used to Fit a Point Process Model
eval.fv Evaluate Expression Involving Functions
urkiola Urkiola Woods Point Pattern
matclust.estK Fit the Matern Cluster Point Process by Minimum Contrast
subset.listof Extract or Replace Subset of a List of Things
rGaussPoisson Simulate Gauss-Poisson Process
im Create a Pixel Image Object
quadscheme Generate a Quadrature Scheme from a Point Pattern
runifpoint Generate N Uniform Random Points
bounding.box Bounding Box of a Window or Point Pattern
incircle Find Largest Circle Inside Window
pcf.ppp Pair Correlation Function of Point Pattern
gridweights Compute Quadrature Weights Based on Grid Counts
is.multitype.ppp Test Whether A Point Pattern is Multitype
Ord Generic Ord Interaction model
rlinegrid Generate grid of parallel lines with random displacement
summary.ppp Summary of a Point Pattern Dataset
Linhom L-function
ponderosa Ponderosa Pine Tree Point Pattern
midpoints.psp Midpoints of Line Segment Pattern
AreaInter The Area Interaction Point Process Model
nndist.psp Nearest neighbour distances between line segments
subset.psp Extract Subset of Line Segment Pattern
clickppp Interactively Add Points
rmhmodel Define Point Process Model for Metropolis-Hastings Simulation.
logLik.ppm Log Likelihood for Poisson Point Process Model
kppm Fit cluster point process model
rNeymanScott Simulate Neyman-Scott Process
lurking Lurking variable plot
amacrine Hughes' Amacrine Cell Data
pppmatching.object Class of Point Matchings
project2segment Move Point To Nearest Line
rjitter Random Perturbation of a Point Pattern
reach Interaction Distance of a Point Process
[.quad Subset of Quadrature Scheme
rpoispp Generate Poisson Point Pattern
contour.im Contour plot of pixel image
pppmatching Create a Point Matching
plot.quad plot a Spatial Quadrature Scheme
Gdot Multitype Nearest Neighbour Distance Function (i-to-any)
ripras Estimate window from points alone
setcov Set Covariance of a Window
summary.listof Summary of a List of Things
rescale Convert dataset to another unit of length
plot.fv Plot Function Valuesn
solutionset Evaluate Logical Expression Involving Pixel Images and Return Region Where Expression is True
inforder.family Infinite Order Interaction Family
psp Create a Line Segment Pattern
humberside Humberside Data on Childhood Leukaemia and Lymphoma
suffstat Sufficient Statistic of Point Process Model
raster.x Cartesian Coordinates for a Pixel Raster
density.ppp Kernel Smoothed Intensity of Point Pattern
crossdist Pairwise distances
delaunay Delaunay Triangulation of Point Pattern
rescue.rectangle Convert Window Back To Rectangle
plot.listof Plot a List of Things
spokes Spokes pattern of dummy points
Jdot Multitype J Function (i-to-any)
crossdist.psp Pairwise distances between two different line segment patterns
plot.tess Plot a tessellation
Kest.fft K-function using FFT
progressreport Print Progress Reports
is.marked.ppp Test Whether A Point Pattern is Marked
dirichlet.weights Compute Quadrature Weights Based on Dirichlet Tessellation
rsyst Simulate systematic random point pattern
vcov.ppm Variance-Covariance Matrix for a Fitted Point Process Model
density.splitppp Kernel Smoothed Intensity of Split Point Pattern
rcell Simulate Baddeley-Silverman Cell Process
reduced.sample Reduced Sample Estimator using Histogram Data
nearest.raster.point Find Pixel Nearest to a Given Point
effectfun Compute Fitted Effect of a Spatial Covariate in a Point Process Model
eval.hyper Evaluate an Expression in Each Row of a Hyperframe
LennardJones The Lennard-Jones Potential
persp.im Perspective Plot of Pixel Image
tiles Extract List of Tiles in a Tessellation
subset.fv Extract Subset of Function Values
print.psp Print Brief Details of a Line Segment Pattern Dataset
summary.owin Summary of a Spatial Window
cut.ppp Classify Points in a Point Pattern
thomas.estK Fit the Thomas Point Process by Minimum Contrast
append.psp Combine Two Line Segment Patterns
quantile.im Sample Quantiles of Pixel Image
localK Neighbourhood density function
distmap.ppp Distance Map of Point Pattern
applynbd Apply Function to Every Neighbourhood in a Point Pattern
Kmulti Marked K-Function
rStrauss Perfect Simulation of the Strauss Process
qqplot.ppm Q-Q Plot of Residuals from Fitted Point Process Model
complement.owin Take Complement of a Window
rlabel Random Re-Labelling of Point Pattern
affine.ppp Apply Affine Transformation To Point Pattern
pairdist Pairwise distances
shift.psp Apply Vector Translation To Line Segment Pattern
data.ppm Extract Original Data from a Fitted Point Process Model
intersect.tess Intersection of Two Tessellations
shift.owin Apply Vector Translation To Window
crossdist.ppp Pairwise distances between two different point patterns
summary.splitppp Summary of a Split Point Pattern
mean.im Mean, Median and Range of Pixel Values in an Image
summary.im Summarizing a Pixel Image
residuals.ppm Residuals for Fitted Point Process Model
nbfires Point Patterns of New Brunswick Forest Fires
markstat Summarise Marks in Every Neighbourhood in a Point Pattern
kstest.ppm Kolmogorov-Smirnov Test for Point Process Model
union.quad Union of Data and Dummy Points
spatstat-internal Internal spatstat functions
swedishpines Swedish Pines Point Pattern
predict.ppm Prediction from a Fitted Point Process Model
rmh Simulate point patterns using the Metropolis-Hastings algorithm.
nearestsegment Find Line Segment Nearest to Each Point
pairwise.family Pairwise Interaction Process Family
pixelquad Quadrature Scheme Based on Pixel Grid
rmpoispp Generate Multitype Poisson Point Pattern
pcf.fasp Pair Correlation Function obtained from array of K functions
im.object Class of Images
nndist Nearest neighbour distances
plot.im Plot a Pixel Image
rMaternI Simulate Matern Model I
rmh.default Simulate Point Process Models using the Metropolis-Hastings Algorithm.
spatstat.options Internal Options in Spatstat Package
as.data.frame.psp Coerce Line Segment Pattern to a Data Frame
square Square Window
quadratresample Resample a Point Pattern by Resampling Quadrats
plot.owin Plot a Spatial Window
envelope Simulation envelopes of summary function
interp.im Interpolate a Pixel Image
markcorr Mark Correlation Function
runifdisc Generate N Uniform Random Points in a Disc
rpoint Generate N Random Points
pcf Pair Correlation Function
kaplan.meier Kaplan-Meier Estimator using Histogram Data
hist.im Histogram of Pixel Values in an Image
profilepl Profile Maximum Pseudolikelihood
rMaternII Simulate Matern Model II
is.subset.owin Determine Whether One Window is Contained In Another
plot.hyperframe Plot Entries in a Hyperframe
rmhcontrol Set Control Parameters for Metropolis-Hastings Algorithm.
quadrat.test Chi-Squared Dispersion Test for Spatial Point Pattern Based on Quadrat Counts
summary.psp Summary of a Line Segment Pattern Dataset
pairdist.ppp Pairwise distances
quadratcount Quadrat counting for a point pattern
erode.owin Erode a Window
gridcentres Rectangular grid of points
[.tess Extract or Replace Subset of Tessellation
with.fv Evaluate an Expression in a Function Table
rMatClust Simulate Matern Cluster Process
plot.splitppp Plot a List of Point Patterns
Gcross Multitype Nearest Neighbour Distance Function (i-to-j)
superimpose Superimpose Several Point Patterns
rotate Rotate
diameter Diameter of a Window
rshift Random Shift
scanpp Read Point Pattern From Data File
rescale.psp Convert Line Segment Pattern to Another Unit of Length
unique.ppp Extract Unique Points from a Spatial Point Pattern
inside.owin Test Whether Points Are Inside A Window
tess Create a Tessellation
dirichlet Dirichlet Tessellation of Point Pattern
unitname Name for Unit of Length
superimposePSP Superimpose Several Line Segment Patterns
plot.psp plot a Spatial Line Segment Pattern
nncross Nearest Neighbour in Another Point Pattern
rotate.ppp Rotate a Point Pattern
hyperframe Hyper Data Frame
simulate.kppm Simulate a fitted cluster point process model.
Geyer Geyer's Saturation Point Process Model
Kest K-function
rshift.psp Randomly Shift a Line Segment Pattern
MultiStraussHard The Multitype/Hard Core Strauss Point Process Model
plot.ppp plot a Spatial Point Pattern
crossing.psp Crossing Points of Two Line Segment Patterns
smooth.ppp Spatial smoothing of observations at irregular points
residualspaper Data and Code From JRSS Discussion Paper on Residuals
distmap Distance Map
angles.psp Orientation Angles of Line Segments
disc Circular Window
concatxy Concatenate x,y Coordinate Vectors
compatible.fv Test Whether Two Function Objects Are Compatible
lansing Lansing Woods Point Pattern
alltypes Calculate Summary Statistic for All Types in a Multitype Point Pattern
simdat Simulated Point Pattern
redwoodfull California Redwoods Point Pattern (Entire Dataset)
Kmeasure Reduced Second Moment Measure
split.im Divide Image Into Sub-images
fitin.ppm Extract the Interaction from a Fitted Point Process Model
subset.splitppp Extract or Replace Sub-Patterns
dilate.owin Dilate a Window
intersect.owin Intersection or Union of Two Windows
bdist.pixels Distance to Boundary of Window
setmarks Set or Reset the Marks in a Point Pattern
plot.plotppm Plot a plotppm Object Created by plot.ppm
rmh.ppm Simulate from a Fitted Point Process Model
rotate.psp Rotate a Line Segment Pattern
shift Apply Vector Translation
japanesepines Japanese Pines Point Pattern
convexhull.xy Convex Hull of Points
lgcp.estK Fit a Log-Gaussian Cox Point Process by Minimum Contrast
ants Harkness-Isham ants' nests data
as.tess Convert Data To Tessellation
nnwhich Nearest neighbour
redwood California Redwoods Point Pattern (Ripley's Subset)
OrdThresh Ord's Interaction model
rescale.owin Convert Window to Another Unit of Length
rshift.splitppp Randomly Shift a List of Point Patterns
is.multitype Test whether Object is Multitype
nncorr Nearest-Neighbour Correlation of Marked Point Pattern
subset.fasp Extract Subset of Function Array
summary.quad Summarizing a Quadrature Scheme
is.marked Test Whether Marks Are Present
rSSI Simulate Simple Sequential Inhibition
DiggleGratton Diggle-Gratton model
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Date 07 November 2008
License GPL (>= 2)
URL http://www.spatstat.org
Packaged Sat Nov 8 04:03:51 2008; adrian

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