spatstat v1.14-9

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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
Geyer Geyer's Saturation Point Process Model
Pairwise Generic Pairwise Interaction model
as.rectangle Window Frame
rNeymanScott Simulate Neyman-Scott Process
rmh.default Simulate Point Process Models using the Metropolis-Hastings Algorithm.
print.owin Print Brief Details of a Spatial Window
runifpoint Generate N Uniform Random Points
quad.object Class of Quadrature Schemes
cut.im Convert Pixel Image from Numeric to Factor
BadGey Hybrid Geyer Point Process Model
as.owin Convert Data To Class owin
Jcross Multitype J Function (i-to-j)
AreaInter The Area Interaction Point Process Model
Kdot.inhom Inhomogeneous Multitype K Dot Function
Gmulti Marked Nearest Neighbour Distance Function
bdist.pixels Distance to Boundary of Window
Kcross Multitype K Function (Cross-type)
Lest L-function
areadiff Difference of Disc Areas
default.dummy Generate a Default Pattern of Dummy Points
angles.psp Orientation Angles of Line Segments
as.mask Pixel Image Approximation of a Window
append.psp Combine Two Line Segment Patterns
Kmeasure Reduced Second Moment Measure
MultiStraussHard The Multitype/Hard Core Strauss Point Process Model
is.marked Test Whether Marks Are Present
crossdist Pairwise distances
hamster Aherne's hamster tumour data
intersect.tess Intersection of Two Tessellations
affine.ppp Apply Affine Transformation To Point Pattern
quadrats Divide Region into Quadrats
rsyst Simulate systematic random point pattern
area.owin Area of a Window
cells Biological Cells Point Pattern
Iest Estimate the I-function
distmap Distance Map
crossdist.ppp Pairwise distances between two different point patterns
rescue.rectangle Convert Window Back To Rectangle
Kest.fft K-function using FFT
is.owin Test Whether An Object Is A Window
affine.owin Apply Affine Transformation To Window
alltypes Calculate Summary Statistic for All Types in a Multitype Point Pattern
Lcross Multitype L-function (cross-type)
applynbd Apply Function to Every Neighbourhood in a Point Pattern
plot.kppm Plot a fitted cluster point process
levelset Level Set of a Pixel Image
eroded.areas Areas of Morphological Erosions
miplot Morishita Index Plot
simdat Simulated Point Pattern
as.ppp Convert Data To Class ppp
amacrine Hughes' Amacrine Cell Data
compatible.fv Test Whether Two Function Objects Are Compatible
dirichlet Dirichlet Tessellation of Point Pattern
longleaf Longleaf Pines Point Pattern
compatible.im Test Whether Two Pixel Images Are Compatible
is.subset.owin Determine Whether One Window is Contained In Another
Kmulti Marked K-Function
density.splitppp Kernel Smoothed Intensity of Split Point Pattern
Kest K-function
ants Harkness-Isham ants' nests data
Saturated Saturated Pairwise Interaction model
as.im Convert to Pixel Image
Gcross Multitype Nearest Neighbour Distance Function (i-to-j)
dummy.ppm Extract Dummy Points Used to Fit a Point Process Model
Jdot Multitype J Function (i-to-any)
bounding.box.xy Convex Hull of Points
nearestsegment Find Line Segment Nearest to Each Point
rmhcontrol Set Control Parameters for Metropolis-Hastings Algorithm.
fasp.object Function Arrays for Spatial Patterns
pppmatching.object Class of Point Matchings
clickppp Interactively Add Points
spatstat-deprecated Deprecated spatstat functions
ppm Fit Point Process Model to Data
murchison Murchison gold deposits
plot.fasp Plot a Function Array
harmonic Basis for Harmonic Functions
is.im Test Whether An Object Is A Pixel Image
corners Corners of a rectangle
crossdist.psp Pairwise distances between two different line segment patterns
LennardJones The Lennard-Jones Potential
PairPiece The Piecewise Constant Pairwise Interaction Point Process Model
nncross Nearest Neighbour in Another Point Pattern
rescale.im Convert Pixel Image to Another Unit of Length
clarkevans Clark and Evans Aggregation Index
im Create a Pixel Image Object
StraussHard The Strauss / Hard Core Point Process Model
contour.im Contour plot of pixel image
by.im Apply Function to Image Broken Down by Factor
identify.ppp Identify Points in a Point Pattern
ewcdf Weighted Empirical Cumulative Distribution Function
density.ppp Kernel Smoothed Intensity of Point Pattern
eem Exponential Energy Marks
concatxy Concatenate x,y Coordinate Vectors
shift.im Apply Vector Translation To Pixel Image
as.matrix.im Convert Pixel Image to Matrix
quantile.im Sample Quantiles of Pixel Image
complement.owin Take Complement of a Window
Linhom L-function
pairdist.ppp Pairwise distances
blur Apply Gaussian Blur to a Pixel Image
intersect.owin Intersection or Union of Two Windows
print.im Print Brief Details of an Image
envelope Simulation envelopes of summary function
setmarks Set or Reset the Marks in a Point Pattern
eval.fv Evaluate Expression Involving Functions
diameter Diameter of a Window
fryplot Fry Plot of Point Pattern
spatstat-internal Internal spatstat functions
qqplot.ppm Q-Q Plot of Residuals from Fitted Point Process Model
rjitter Random Perturbation of a Point Pattern
Fest Estimate the empty space function F
coef.ppm Coefficients of Fitted Point Process Model
profilepl Profile Maximum Pseudolikelihood
rmh.ppm Simulate from a Fitted Point Process Model
Poisson Poisson Point Process Model
matchingdist Distance for a Point Pattern Matching
distmap.ppp Distance Map of Point Pattern
eval.im Evaluate Expression Involving Pixel Images
Kcross.inhom Inhomogeneous Cross K Function
residuals.ppm Residuals for Fitted Point Process Model
km.rs Kaplan-Meier and Reduced Sample Estimator using Histograms
is.marked.ppm Test Whether A Point Process Model is Marked
is.ppp Test Whether An Object Is A Point Pattern
rMaternI Simulate Matern Model I
erode.owin Erode a Window
multiplicity.ppp Count Multiplicity of Duplicate Points
pixellate Convert Point Pattern to Pixel Image
Strauss The Strauss Point Process Model
rmhmodel.ppm Interpret Fitted Model for Metropolis-Hastings Simulation.
pairsat.family Saturated Pairwise Interaction Point Process Family
quadratresample Resample a Point Pattern by Resampling Quadrats
centroid.owin Centroid of a window
rotate Rotate
distmap.psp Distance Map of Line Segment Pattern
data.ppm Extract Original Data from a Fitted Point Process Model
rpoisline Generate Poisson Random Line Process
fv.object Data Frames of Function Values
rpoispp Generate Poisson Point Pattern
trim.rectangle Cut margins from rectangle
kaplan.meier Kaplan-Meier Estimator using Histogram Data
print.quad Print a Quadrature Scheme
plot.fv Plot Function Valuesn
subset.fasp Extract Subset of Function Array
print.psp Print Brief Details of a Line Segment Pattern Dataset
rescale.owin Convert Window to Another Unit of Length
subset.psp Extract Subset of Line Segment Pattern
inside.owin Test Whether Points Are Inside A Window
redwoodfull California Redwoods Point Pattern (Entire Dataset)
distmap.owin Distance Map of Window
chorley Chorley-Ribble Cancer Data
owin.object Class owin
Gest Nearest Neighbour Distance Function G
tess Create a Tessellation
kppm Fit cluster point process model
rStrauss Perfect Simulation of the Strauss Process
plot.ppp plot a Spatial Point Pattern
rotate.owin Rotate a Window
pairdist.default Pairwise distances
OrdThresh Ord's Interaction model
gridcentres Rectangular grid of points
endpoints.psp Endpoints of Line Segment Pattern
quadratcount Quadrat counting for a point pattern
predict.ppm Prediction from a Fitted Point Process Model
spruces Spruces Point Pattern
rlabel Random Re-Labelling of Point Pattern
model.matrix.ppm Extract Design Matrix from Point Process Model
as.data.frame.psp Coerce Line Segment Pattern to a Data Frame
vcov.ppm Variance-Covariance Matrix for a Fitted Point Process Model
persp.im Perspective Plot of Pixel Image
pppdist Distance Between Two Point Patterns
unmark Remove Marks
copper Berman-Huntington points and lines data
summary.im Summarizing a Pixel Image
allstats Calculate four standard summary functions of a point pattern.
psp.object Class of Line Segment Patterns
pairwise.family Pairwise Interaction Process Family
clickpoly Interactively Define a Polygon
rpoint Generate N Random Points
discretise Safely Convert Point Pattern Window to Binary Mask
nncorr Nearest-Neighbour Correlation of Marked Point Pattern
bramblecanes Hutchings' Bramble Canes data
spatstat.options Internal Options in Spatstat Package
compatible.fasp Test Whether Two Function Arrays Are Compatible
Ord Generic Ord Interaction model
with.fv Evaluate an Expression in a Function Table
bei Tropical rain forest trees
DiggleGratton Diggle-Gratton model
rmhmodel.default Build Point Process Model for Metropolis-Hastings Simulation.
expand.owin Expand Window By Factor
as.tess Convert Data To Tessellation
rescale Convert dataset to another unit of length
cut.ppp Classify Points in a Point Pattern
summary.splitppp Summary of a Split Point Pattern
ppm.object Class of Fitted Point Process Models
bounding.box Bounding Box of a Window or Point Pattern
localK Neighbourhood density function
rstrat Simulate Stratified Random Point Pattern
rmhstart Determine Initial State for Metropolis-Hastings Simulation.
pcf.fasp Pair Correlation Function obtained from array of K functions
raster.x Cartesian Coordinates for a Pixel Raster
anemones Beadlet Anemones Data
mincontrast Method of Minimum Contrast
crossdist.default Pairwise distances between two different sets of points
as.data.frame.ppp Coerce Point Pattern to a Data Frame
subset.fv Extract Subset of Function Values
im.object Class of Images
markstat Summarise Marks in Every Neighbourhood in a Point Pattern
thomas.estK Fit the Thomas Point Process by Minimum Contrast
rmh Simulate point patterns using the Metropolis-Hastings algorithm.
affine Apply Affine Transformation
rotate.ppp Rotate a Point Pattern
nnwhich Nearest neighbour
pairdist.psp Pairwise distances between line segments
MultiStrauss The Multitype Strauss Point Process Model
spatstat The Spatstat Package
residualspaper Data and Code From JRSS Discussion Paper on Residuals
effectfun Compute Fitted Effect of a Spatial Covariate in a Point Process Model
quad.ppm Extract Quadrature Scheme Used to Fit a Point Process Model
rshift.splitppp Randomly Shift a List of Point Patterns
as.psp Convert Data To Class psp
nztrees New Zealand Trees Point Pattern
betacells Beta Ganglion Cells in Cat Retina
mean.im Mean, Median and Range of Pixel Values in an Image
Jest Estimate the J-function
adaptive.density Intensity Estimate of Point Pattern Using Tessellation
by.ppp Apply a Function to a Point Pattern Broken Down by Factor
quadscheme Generate a Quadrature Scheme from a Point Pattern
hyperframe Hyper Data Frame
shift.owin Apply Vector Translation To Window
Softcore The Soft Core Point Process Model
interp.im Interpolate a Pixel Image
split.ppp Divide Point Pattern into Sub-patterns
plot.quad plot a Spatial Quadrature Scheme
dilate.owin Dilate a Window
crossing.psp Crossing Points of Two Line Segment Patterns
opening.owin Morphological Opening of a Window
lengths.psp Lengths of Line Segments
pcf.fv Pair Correlation Function obtained from K Function
gpc2owin Convert Polygonal Region into Different Format
stieltjes Compute Integral of Function Against Cumulative Distribution
progressreport Print Progress Reports
rshift.psp Randomly Shift a Line Segment Pattern
dirichlet.weights Compute Quadrature Weights Based on Dirichlet Tessellation
plot.splitppp Plot a List of Point Patterns
rshift.ppp Randomly Shift a Point Pattern
psp Create a Line Segment Pattern
affine.psp Apply Affine Transformation To Line Segment Pattern
model.images Compute Images of Constructed Covariates
is.ppm Test Whether An Object Is A Fitted Point Process Model
disc Circular Window
pppmatching Create a Point Matching
unitname Name for Unit of Length
letterR Window in Shape of Letter R
japanesepines Japanese Pines Point Pattern
runifdisc Generate N Uniform Random Points in a Disc
SatPiece Piecewise Constant Saturated Pairwise Interaction Point Process Model
unique.ppp Extract Unique Points from a Spatial Point Pattern
Kinhom Inhomogeneous K-function
superimpose Superimpose Several Point Patterns
summary.listof Summary of a List of Things
fitin.ppm Extract the Interaction from a Fitted Point Process Model
pairdist Pairwise distances
swedishpines Swedish Pines Point Pattern
spokes Spokes pattern of dummy points
Kdot Multitype K Function (i-to-any)
demopat Artificial Data Point Pattern
lgcp.estK Fit a Log-Gaussian Cox Point Process by Minimum Contrast
diagnose.ppm Diagnostic Plots for Fitted Point Process Model
inforder.family Infinite Order Interaction Family
print.ppm Print a Fitted Point Process Model
solutionset Evaluate Logical Expression Involving Pixel Images and Return Region Where Expression is True
humberside Humberside Data on Childhood Leukaemia and Lymphoma
is.multitype Test whether Object is Multitype
pcf.ppp Pair Correlation Function of Point Pattern
predict.kppm Prediction from a Fitted Cluster Point Process Model
nndist.psp Nearest neighbour distances between line segments
rshift Random Shift
midpoints.psp Midpoints of Line Segment Pattern
superimposePSP Superimpose Several Line Segment Patterns
matclust.estK Fit the Matern Cluster Point Process by Minimum Contrast
plot.listof Plot a List of Things
convexhull.xy Convex Hull of Points
anova.ppm ANOVA for Fitted Point Process Models
vertices Vertices of a Window
lansing Lansing Woods Point Pattern
split.im Divide Image Into Sub-images
plot.hyperframe Plot Entries in a Hyperframe
urkiola Urkiola Woods Point Pattern
subset.im Extract Subset of Image
rMatClust Simulate Matern Cluster Process
rSSI Simulate Simple Sequential Inhibition
plot.tess Plot a tessellation
lurking Lurking variable plot
bdist.points Distance to Boundary of Window
eval.fasp Evaluate Expression Involving Function Arrays
logLik.ppm Log Likelihood for Poisson Point Process Model
[.tess Extract or Replace Subset of Tessellation
rmpoispp Generate Multitype Poisson Point Pattern
rotate.psp Rotate a Line Segment Pattern
gridweights Compute Quadrature Weights Based on Grid Counts
duplicated.ppp Determine Duplicated Points in a Spatial Point Pattern
fitted.ppm Fitted Conditional Intensity for Point Process Model
shift.ppp Apply Vector Translation To Point Pattern
nearest.raster.point Find Pixel Nearest to a Given Point
nndist Nearest neighbour distances
hist.im Histogram of Pixel Values in an Image
incircle Find Largest Circle Inside Window
Gdot Multitype Nearest Neighbour Distance Function (i-to-any)
reach Interaction Distance of a Point Process
ganglia Beta Ganglion Cells in Cat Retina, Old Version
rThomas Simulate Thomas Process
markcorr Mark Correlation Function
ripras Estimate window from points alone
Jmulti Marked J Function
subset.ppp Extract or Replace Subset of Point Pattern
reduced.sample Reduced Sample Estimator using Histogram Data
shift.psp Apply Vector Translation To Line Segment Pattern
smooth.ppp Spatial smoothing of observations at irregular points
rlinegrid Generate grid of parallel lines with random displacement
square Square Window
summary.owin Summary of a Spatial Window
rmhmodel Define Point Process Model for Metropolis-Hastings Simulation.
simulate.kppm Simulate a fitted cluster point process model.
is.multitype.ppm Test Whether A Point Process Model is Multitype
subset.listof Extract or Replace Subset of a List of Things
rescale.psp Convert Line Segment Pattern to Another Unit of Length
closing.owin Morphological Closing of a Window
plot.psp plot a Spatial Line Segment Pattern
marktable Tabulate Marks in Neighbourhood of Every Point in a Point Pattern
plot.ppm plot a Fitted Point Process Model
selfcrossing.psp Crossing Points in a Line Segment Pattern
summary.psp Summary of a Line Segment Pattern Dataset
[.quad Subset of Quadrature Scheme
rMaternII Simulate Matern Model II
plot.im Plot a Pixel Image
delaunay Delaunay Triangulation of Point Pattern
rcell Simulate Baddeley-Silverman Cell Process
kstest.ppm Kolmogorov-Smirnov Test for Point Process Model
pcf Pair Correlation Function
pixelquad Quadrature Scheme Based on Pixel Grid
summary.ppm Summarizing a Fitted Point Process Model
finpines Pine saplings in Finland.
union.quad Union of Data and Dummy Points
rmpoint Generate N Random Multitype Points
nbfires Point Patterns of New Brunswick Forest Fires
shift Apply Vector Translation
subset.splitppp Extract or Replace Sub-Patterns
project2segment Move Point To Nearest Line
rGaussPoisson Simulate Gauss-Poisson Process
subsetget.im Reset Values in Subset of Image
ppp.object Class of Point Patterns
rmhmodel.list Define Point Process Model for Metropolis-Hastings Simulation.
is.multitype.ppp Test Whether A Point Pattern is Multitype
summary.quad Summarizing a Quadrature Scheme
redwood California Redwoods Point Pattern (Ripley's Subset)
scanpp Read Point Pattern From Data File
plot.plotppm Plot a plotppm Object Created by plot.ppm
density.psp Kernel Smoothing of Line Segment Pattern
print.ppp Print Brief Details of a Point Pattern Dataset
update.kppm Update a Fitted Cluster Point Process Model
owin Create a Window
summary.ppp Summary of a Point Pattern Dataset
tiles Extract List of Tiles in a Tessellation
ponderosa Ponderosa Pine Tree Point Pattern
setcov Set Covariance of a Window
rthin Random Thinning
rescale.ppp Convert Point Pattern to Another Unit of Length
suffstat Sufficient Statistic of Point Process Model
Ldot Multitype L-function (i-to-any)
ppp Create a Point Pattern
plot.owin Plot a Spatial Window
pcfcross Multitype pair correlation function
quadrat.test Chi-Squared Dispersion Test for Spatial Point Pattern Based on Quadrat Counts
ord.family Ord Interaction Process Family
is.marked.ppp Test Whether A Point Pattern is Marked
eval.hyper Evaluate an Expression in Each Row of a Hyperframe
update.ppm Update a Fitted Point Process Model
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Date 16 December 2008
License GPL (>= 2)
URL http://www.spatstat.org
Packaged Thu Dec 18 02:25:14 2008; adrian

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