spatstat v1.14-1


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


Date 22 July 2008
License GPL (>= 2)
Packaged Tue Jul 29 13:29:05 2008; adrian

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