spatstat v1.14-5

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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
fitted.ppm Fitted Conditional Intensity for Point Process Model
diameter Diameter of a Window
logLik.ppm Log Likelihood for Poisson Point Process Model
pcfcross Multitype pair correlation function
plot.fasp Plot a Function Array
rmhstart Determine Initial State for Metropolis-Hastings Simulation.
psp.object Class of Line Segment Patterns
rlabel Random Re-Labelling of Point Pattern
rsyst Simulate systematic random point pattern
summary.listof Summary of a List of Things
marktable Tabulate Marks in Neighbourhood of Every Point in a Point Pattern
lengths.psp Lengths of Line Segments
scanpp Read Point Pattern From Data File
cut.im Convert Pixel Image from Numeric to Factor
fasp.object Function Arrays for Spatial Patterns
distmap.owin Distance Map of Window
fv.object Data Frames of Function Values
rMaternI Simulate Matern Model I
eem Exponential Energy Marks
spatstat-deprecated Deprecated spatstat functions
crossdist.ppp Pairwise distances between two different point patterns
ppm Fit Point Process Model to Data
ewcdf Weighted Empirical Cumulative Distribution Function
rMaternII Simulate Matern Model II
subset.listof Extract or Replace Subset of a List of Things
gridweights Compute Quadrature Weights Based on Grid Counts
nbfires Point Patterns of New Brunswick Forest Fires
plot.ppm plot a Fitted Point Process Model
endpoints.psp Endpoints of Line Segment Pattern
dilate.owin Dilate a Window
kstest.ppm Kolmogorov-Smirnov Test for Point Process Model
rshift Random Shift
dirichlet Dirichlet Tessellation of Point Pattern
is.marked.ppm Test Whether A Point Process Model is Marked
inside.owin Test Whether Points Are Inside A Window
subset.ppp Extract or Replace Subset of Point Pattern
update.ppm Update a Fitted Point Process Model
pixelquad Quadrature Scheme Based on Pixel Grid
default.dummy Generate a Default Pattern of Dummy Points
quadratcount Quadrat counting for a point pattern
superimpose Superimpose Several Point Patterns
harmonic Basis for Harmonic Functions
letterR Window in Shape of Letter R
owin Create a Window
coef.ppm Coefficients of Fitted Point Process Model
japanesepines Japanese Pines Point Pattern
union.quad Union of Data and Dummy Points
tess Create a Tessellation
plot.ppp plot a Spatial Point Pattern
residualspaper Data and Code From JRSS Discussion Paper on Residuals
is.ppp Test Whether An Object Is A Point Pattern
rescale.ppp Convert Point Pattern to Another Unit of Length
localK Neighbourhood density function
crossdist.psp Pairwise distances between two different line segment patterns
murchison Murchison gold deposits
dummy.ppm Extract Dummy Points Used to Fit a Point Process Model
ganglia Beta Ganglion Cells in Cat Retina, Old Version
rescale.psp Convert Line Segment Pattern to Another Unit of Length
eroded.areas Areas of Morphological Erosions
finpines Pine saplings in Finland.
print.im Print Brief Details of an Image
rescale.im Convert Pixel Image to Another Unit of Length
crossing.psp Crossing Points of Two Line Segment Patterns
expand.owin Expand Window By Factor
corners Corners of a rectangle
by.im Apply Function to Image Broken Down by Factor
plot.plotppm Plot a plotppm Object Created by plot.ppm
lansing Lansing Woods Point Pattern
intersect.owin Intersection or Union of Two Windows
diagnose.ppm Diagnostic Plots for Fitted Point Process Model
demopat Artificial Data Point Pattern
mean.im Mean, Median and Range of Pixel Values in an Image
incircle Find Largest Circle Inside Window
multiplicity.ppp Count Multiplicity of Duplicate Points
rmpoint Generate N Random Multitype Points
Kmulti Marked K-Function
print.psp Print Brief Details of a Line Segment Pattern Dataset
with.fv Evaluate an Expression in a Function Table
pcf.ppp Pair Correlation Function of Point Pattern
ord.family Ord Interaction Process Family
matclust.estK Fit the Matern Cluster Point Process by Minimum Contrast
discretise Safely Convert Point Pattern Window to Binary Mask
eval.im Evaluate Expression Involving Pixel Images
rpoispp Generate Poisson Point Pattern
rotate.psp Rotate a Line Segment Pattern
is.multitype.ppm Test Whether A Point Process Model is Multitype
reduced.sample Reduced Sample Estimator using Histogram Data
BadGey Hybrid Geyer Point Process Model
is.multitype Test whether Object is Multitype
plot.psp plot a Spatial Line Segment Pattern
plot.kppm Plot a fitted cluster point process
erode.owin Erode a Window
quadratresample Resample a Point Pattern by Resampling Quadrats
distmap Distance Map
pairwise.family Pairwise Interaction Process Family
rmhcontrol Set Control Parameters for Metropolis-Hastings Algorithm.
rmh Simulate point patterns using the Metropolis-Hastings algorithm.
rshift.psp Randomly Shift a Line Segment Pattern
pairsat.family Saturated Pairwise Interaction Point Process Family
hist.im Histogram of Pixel Values in an Image
crossdist Pairwise distances
plot.listof Plot a List of Things
nnwhich Nearest neighbour
eval.hyper Evaluate an Expression in Each Row of a Hyperframe
model.matrix.ppm Extract Design Matrix from Point Process Model
subset.im Extract Subset of Image
is.im Test Whether An Object Is A Pixel Image
shift.im Apply Vector Translation To Pixel Image
km.rs Kaplan-Meier and Reduced Sample Estimator using Histograms
humberside Humberside Data on Childhood Leukaemia and Lymphoma
setcov Set Covariance of a Window
persp.im Perspective Plot of Pixel Image
subset.splitppp Extract or Replace Sub-Patterns
rmhmodel.list Define Point Process Model for Metropolis-Hastings Simulation.
rmhmodel Define Point Process Model for Metropolis-Hastings Simulation.
markcorr Mark Correlation Function
psp Create a Line Segment Pattern
rescale.owin Convert Window to Another Unit of Length
quadscheme Generate a Quadrature Scheme from a Point Pattern
is.marked.ppp Test Whether A Point Pattern is Marked
setmarks Set or Reset the Marks in a Point Pattern
rSSI Simulate Simple Sequential Inhibition
rMatClust Simulate Matern Cluster Process
print.owin Print Brief Details of a Spatial Window
pairdist.default Pairwise distances
summary.im Summarizing a Pixel Image
[.tess Extract or Replace Subset of Tessellation
im.object Class of Images
progressreport Print Progress Reports
rNeymanScott Simulate Neyman-Scott Process
quadrats Divide Region into Quadrats
is.subset.owin Determine Whether One Window is Contained In Another
distmap.psp Distance Map of Line Segment Pattern
rshift.ppp Randomly Shift a Point Pattern
vertices Vertices of a Window
predict.ppm Prediction from a Fitted Point Process Model
rmh.ppm Simulate from a Fitted Point Process Model
summary.owin Summary of a Spatial Window
rotate.owin Rotate a Window
ppp Create a Point Pattern
rotate.ppp Rotate a Point Pattern
quad.object Class of Quadrature Schemes
summary.psp Summary of a Line Segment Pattern Dataset
midpoints.psp Midpoints of Line Segment Pattern
rmh.default Simulate Point Process Models using the Metropolis-Hastings Algorithm.
ppm.object Class of Fitted Point Process Models
redwoodfull California Redwoods Point Pattern (Entire Dataset)
quadrat.test Chi-Squared Dispersion Test for Spatial Point Pattern Based on Quadrat Counts
rescue.rectangle Convert Window Back To Rectangle
rthin Random Thinning
spruces Spruces Point Pattern
rcell Simulate Baddeley-Silverman Cell Process
shift.psp Apply Vector Translation To Line Segment Pattern
copper Berman-Huntington points and lines data
plot.quad plot a Spatial Quadrature Scheme
rescale Convert dataset to another unit of length
tiles Extract List of Tiles in a Tessellation
gridcentres Rectangular grid of points
quantile.im Sample Quantiles of Pixel Image
print.ppm Print a Fitted Point Process Model
rpoisline Generate Poisson Random Line Process
profilepl Profile Maximum Pseudolikelihood
cut.ppp Classify Points in a Point Pattern
kaplan.meier Kaplan-Meier Estimator using Histogram Data
nncross Nearest Neighbour in Another Point Pattern
data.ppm Extract Original Data from a Fitted Point Process Model
delaunay Delaunay Triangulation of Point Pattern
fitin.ppm Extract the Interaction from a Fitted Point Process Model
plot.owin Plot a Spatial Window
redwood California Redwoods Point Pattern (Ripley's Subset)
ripras Estimate window from points alone
spatstat.options Internal Options in Spatstat Package
rmhmodel.default Build Point Process Model for Metropolis-Hastings Simulation.
OrdThresh Ord's Interaction model
distmap.ppp Distance Map of Point Pattern
summary.splitppp Summary of a Split Point Pattern
rotate Rotate
hamster Aherne's hamster tumour data
identify.ppp Identify Points in a Point Pattern
affine.psp Apply Affine Transformation To Line Segment Pattern
gpc2owin Convert Polygonal Region into Different Format
subset.fv Extract Subset of Function Values
spatstat-internal Internal spatstat functions
trim.rectangle Cut margins from rectangle
pcf.fasp Pair Correlation Function obtained from array of K functions
as.psp Convert Data To Class psp
nncorr Nearest-Neighbour Correlation of Marked Point Pattern
dirichlet.weights Compute Quadrature Weights Based on Dirichlet Tessellation
is.marked Test Whether Marks Are Present
split.im Divide Image Into Sub-images
rstrat Simulate Stratified Random Point Pattern
update.kppm Update a Fitted Cluster Point Process Model
effectfun Compute Fitted Effect of a Spatial Covariate in a Point Process Model
is.ppm Test Whether An Object Is A Fitted Point Process Model
nndist.psp Nearest neighbour distances between line segments
duplicated.ppp Determine Duplicated Points in a Spatial Point Pattern
square Square Window
kppm Fit cluster point process model
subset.fasp Extract Subset of Function Array
hyperframe Hyper Data Frame
Gest Nearest Neighbour Distance Function G
plot.im Plot a Pixel Image
model.images Compute Images of Constructed Covariates
mincontrast Method of Minimum Contrast
complement.owin Take Complement of a Window
Ord Generic Ord Interaction model
predict.kppm Prediction from a Fitted Cluster Point Process Model
plot.tess Plot a tessellation
pcf Pair Correlation Function
as.rectangle Window Frame
density.psp Kernel Smoothing of Line Segment Pattern
lurking Lurking variable plot
Gdot Multitype Nearest Neighbour Distance Function (i-to-any)
intersect.tess Intersection of Two Tessellations
eval.fv Evaluate Expression Involving Functions
rmhmodel.ppm Interpret Fitted Model for Metropolis-Hastings Simulation.
pcf.fv Pair Correlation Function obtained from K Function
nndist Nearest neighbour distances
Strauss The Strauss Point Process Model
qqplot.ppm Q-Q Plot of Residuals from Fitted Point Process Model
eval.fasp Evaluate Expression Involving Function Arrays
is.multitype.ppp Test Whether A Point Pattern is Multitype
matchingdist Distance for a Point Pattern Matching
pairdist.ppp Pairwise distances
pairdist Pairwise distances
levelset Level Set of a Pixel Image
append.psp Combine Two Line Segment Patterns
Kcross.inhom Inhomogeneous Cross K Function
print.ppp Print Brief Details of a Point Pattern Dataset
raster.x Cartesian Coordinates for a Pixel Raster
split.ppp Divide Point Pattern into Sub-patterns
summary.quad Summarizing a Quadrature Scheme
disc Circular Window
shift Apply Vector Translation
as.tess Convert Data To Tessellation
rjitter Random Perturbation of a Point Pattern
pppmatching.object Class of Point Matchings
pairdist.psp Pairwise distances between line segments
StraussHard The Strauss / Hard Core Point Process Model
residuals.ppm Residuals for Fitted Point Process Model
rGaussPoisson Simulate Gauss-Poisson Process
smooth.ppp Spatial smoothing of observations at irregular points
density.splitppp Kernel Smoothed Intensity of Split Point Pattern
Kmeasure Reduced Second Moment Measure
rmpoispp Generate Multitype Poisson Point Pattern
Poisson Poisson Point Process Model
Kdot Multitype K Function (i-to-any)
Fest Estimate the empty space function F
subset.psp Extract Subset of Line Segment Pattern
plot.hyperframe Plot Entries in a Hyperframe
swedishpines Swedish Pines Point Pattern
DiggleGratton Diggle-Gratton model
owin.object Class owin
vcov.ppm Variance-Covariance Matrix for a Fitted Point Process Model
stieltjes Compute Integral of Function Against Cumulative Distribution
quad.ppm Extract Quadrature Scheme Used to Fit a Point Process Model
rlinegrid Generate grid of parallel lines with random displacement
Lest L-function
rThomas Simulate Thomas Process
compatible.im Test Whether Two Pixel Images Are Compatible
Jmulti Marked J Function
Jcross Multitype J Function (i-to-j)
urkiola Urkiola Woods Point Pattern
nearest.raster.point Find Pixel Nearest to a Given Point
Kdot.inhom Inhomogeneous Multitype K Dot Function
MultiStrauss The Multitype Strauss Point Process Model
angles.psp Orientation Angles of Line Segments
anemones Beadlet Anemones Data
clarkevans Clark and Evans Aggregation Index
Lcross Multitype L-function (cross-type)
Iest Estimate the I-function
rshift.splitppp Randomly Shift a List of Point Patterns
Kest K-function
Gcross Multitype Nearest Neighbour Distance Function (i-to-j)
Jdot Multitype J Function (i-to-any)
bei Tropical rain forest trees
reach Interaction Distance of a Point Process
plot.fv Plot Function Valuesn
as.im Convert to Pixel Image
simulate.kppm Simulate a fitted cluster point process model.
summary.ppm Summarizing a Fitted Point Process Model
adaptive.density Intensity Estimate of Point Pattern Using Tessellation
allstats Calculate four standard summary functions of a point pattern.
ponderosa Ponderosa Pine Tree Point Pattern
compatible.fv Test Whether Two Function Objects Are Compatible
bounding.box.xy Convex Hull of Points
Ldot Multitype L-function (i-to-any)
alltypes Calculate Summary Statistic for All Types in a Multitype Point Pattern
unmark Remove Marks from a Marked Point Pattern
ants Harkness-Isham ants' nests data
compatible.fasp Test Whether Two Function Arrays Are Compatible
lgcp.estK Fit a Log-Gaussian Cox Point Process by Minimum Contrast
bdist.pixels Distance to Boundary of Window
Jest Estimate the J-function
as.matrix.im Convert Pixel Image to Matrix
envelope Simulation envelopes of summary function
bounding.box Bounding Box of a Window or Point Pattern
blur Apply Gaussian Blur to a Pixel Image
concatxy Concatenate x,y Coordinate Vectors
applynbd Apply Function to Every Neighbourhood in a Point Pattern
as.owin Convert Data To Class owin
bramblecanes Hutchings' Bramble Canes data
unitname Name for Unit of Length
runifpoint Generate N Uniform Random Points
im Create a Pixel Image Object
as.data.frame.ppp Coerce Point Pattern to a Data Frame
shift.ppp Apply Vector Translation To Point Pattern
interp.im Interpolate a Pixel Image
clickppp Interactively Add Points
is.owin Test Whether An Object Is A Window
runifdisc Generate N Uniform Random Points in a Disc
pppmatching Create a Point Matching
density.ppp Kernel Smoothed Intensity of Point Pattern
inforder.family Infinite Order Interaction Family
nztrees New Zealand Trees Point Pattern
crossdist.default Pairwise distances between two different sets of points
longleaf Longleaf Pines Point Pattern
simdat Simulated Point Pattern
rStrauss Perfect Simulation of the Strauss Process
print.quad Print a Quadrature Scheme
ppp.object Class of Point Patterns
Kcross Multitype K Function (Cross-type)
markstat Summarise Marks in Every Neighbourhood in a Point Pattern
rpoint Generate N Random Points
solutionset Evaluate Logical Expression Involving Pixel Images and Return Region Where Expression is True
selfcrossing.psp Crossing Points in a Line Segment Pattern
subsetget.im Reset Values in Subset of Image
PairPiece The Piecewise Constant Pairwise Interaction Point Process Model
[.quad Subset of Quadrature Scheme
thomas.estK Fit the Thomas Point Process by Minimum Contrast
affine Apply Affine Transformation
bdist.points Distance to Boundary of Window
Softcore The Soft Core Point Process Model
spatstat The Spatstat Package
plot.splitppp Plot a List of Point Patterns
Kest.fft K-function using FFT
spokes Spokes pattern of dummy points
Gmulti Marked Nearest Neighbour Distance Function
AreaInter The Area Interaction Point Process Model
affine.owin Apply Affine Transformation To Window
summary.ppp Summary of a Point Pattern Dataset
clickpoly Interactively Define a Polygon
as.mask Pixel Image Approximation of a Window
Saturated Saturated Pairwise Interaction model
affine.ppp Apply Affine Transformation To Point Pattern
areadiff Difference of Disc Areas
convexhull.xy Convex Hull of Points
cells Biological Cells Point Pattern
centroid.owin Centroid of a window
unique.ppp Extract Unique Points from a Spatial Point Pattern
betacells Beta Ganglion Cells in Cat Retina
amacrine Hughes' Amacrine Cell Data
chorley Chorley-Ribble Cancer Data
area.owin Area of a Window
LennardJones The Lennard-Jones Potential
as.ppp Convert Data To Class ppp
by.ppp Apply a Function to a Point Pattern Broken Down by Factor
suffstat Sufficient Statistic of Point Process Model
pppdist Distance Between Two Point Patterns
SatPiece Piecewise Constant Saturated Pairwise Interaction Point Process Model
Pairwise Generic Pairwise Interaction model
MultiStraussHard The Multitype/Hard Core Strauss Point Process Model
shift.owin Apply Vector Translation To Window
Kinhom Inhomogeneous K-function
Linhom L-function
Geyer Geyer's Saturation Point Process Model
anova.ppm ANOVA for Fitted Point Process Models
contour.im Contour plot of pixel image
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Date 23 October 2008
License GPL (>= 2)
URL http://www.spatstat.org
Packaged Fri Oct 24 10:28:47 2008; adrian

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