spatstat v1.14-0

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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
clickpoly Interactively Define a Polygon
OrdThresh Ord's Interaction model
by.ppp Apply a Function to a Point Pattern Broken Down by Factor
copper Berman-Huntington points and lines data
bei Tropical rain forest trees
MultiStraussHard The Multitype/Hard Core Strauss Point Process Model
anemones Beadlet Anemones Data
Kest K-function
ponderosa Ponderosa Pine Tree Point Pattern
diameter Diameter of a Window
clarkevans Clark and Evans Aggregation Index
ants Harkness-Isham ants' nests data
Gest Nearest Neighbour Distance Function G
dummy.ppm Extract Dummy Points Used to Fit a Point Process Model
crossdist.default Pairwise distances between two different sets of points
eval.im Evaluate Expression Involving Pixel Images
distmap.owin Distance Map of Window
spatstat The Spatstat Package
spatstat-deprecated Deprecated spatstat functions
alltypes Calculate Summary Statistic for All Types in a Multitype Point Pattern
Linhom L-function
levelset Level Set of a Pixel Image
as.rectangle Window Frame
kppm Fit cluster point process model
default.dummy Generate a Default Pattern of Dummy Points
distmap.ppp Distance Map of Point Pattern
nncorr Nearest-Neighbour Correlation of Marked Point Pattern
chorley Chorley-Ribble Cancer Data
LennardJones The Lennard-Jones Potential
distmap Distance Map
crossdist.psp Pairwise distances between two different line segment patterns
angles.psp Orientation Angles of Line Segments
bramblecanes Hutchings' Bramble Canes data
Saturated Saturated Pairwise Interaction model
Kmeasure Reduced Second Moment Measure
Jmulti Marked J Function
duplicated.ppp Determine Duplicated Points in a Spatial Point Pattern
concatxy Concatenate x,y Coordinate Vectors
print.owin Print Brief Details of a Spatial Window
as.mask Pixel Image Approximation of a Window
Kdot Multitype K Function (i-to-any)
plot.quad plot a Spatial Quadrature Scheme
bounding.box.xy Convex Hull of Points
applynbd Apply Function to Every Neighbourhood in a Point Pattern
BadGey Hybrid Geyer Point Process Model
Fest Estimate the empty space function F
ewcdf Weighted Empirical Cumulative Distribution Function
cut.ppp Classify Points in a Point Pattern
pairwise.family Pairwise Interaction Process Family
crossdist Pairwise distances
Geyer Geyer's Saturation Point Process Model
Gcross Multitype Nearest Neighbour Distance Function (i-to-j)
nnwhich Nearest neighbour
identify.ppp Identify Points in a Point Pattern
density.psp Kernel Smoothing of Line Segment Pattern
Jdot Multitype J Function (i-to-any)
intersect.owin Intersection or Union of Two Windows
quad.object Class of Quadrature Schemes
density.splitppp Kernel Smoothed Intensity of Split Point Pattern
data.ppm Extract Original Data from a Fitted Point Process Model
compatible.fv Test Whether Two Function Objects Are Compatible
ganglia Beta Ganglion Cells in Cat Retina, Old Version
as.matrix.im Convert Pixel Image to Matrix
pairdist.ppp Pairwise distances
matclust.estK Fit the Matern Cluster Point Process by Minimum Contrast
predict.kppm Prediction from a Fitted Cluster Point Process Model
is.im Test Whether An Object Is A Pixel Image
km.rs Kaplan-Meier and Reduced Sample Estimator using Histograms
localK Neighbourhood density function
as.ppp Convert Data To Class ppp
expand.owin Expand Window By Factor
compatible.im Test Whether Two Pixel Images Are Compatible
print.ppp Print Brief Details of a Point Pattern Dataset
hamster Aherne's hamster tumour data
mean.im Mean Pixel Value in an Image
AreaInter The Area Interaction Point Process Model
bounding.box Bounding Box of a Window or Point Pattern
append.psp Combine Two Line Segment Patterns
erode.owin Erode a Window
clickppp Interactively Add Points
hist.im Histogram of Pixel Values in an Image
Kinhom Inhomogeneous K-function
centroid.owin Centroid of a window
is.multitype.ppm Test Whether A Point Process Model is Multitype
japanesepines Japanese Pines Point Pattern
plot.psp plot a Spatial Line Segment Pattern
area.owin Area of a Window
pairdist.psp Pairwise distances between line segments
plot.fasp Plot a Function Array
Ldot Multitype L-function (i-to-any)
density.ppp Kernel Smoothed Intensity of Point Pattern
blur Apply Gaussian Blur to a Pixel Image
eval.hyper Evaluate an Expression in Each Row of a Hyperframe
psp Create a Line Segment Pattern
lgcp.estK Fit a Log-Gaussian Cox Point Process by Minimum Contrast
runifpoint Generate N Uniform Random Points
bdist.points Distance to Boundary of Window
areadiff Difference of Disc Areas
nncross Nearest Neighbour in Another Point Pattern
inforder.family Infinite Order Interaction Family
kstest.ppm Kolmogorov-Smirnov Test for Point Process Model
demopat Artificial Data Point Pattern
as.psp Convert Data To Class psp
gpc2owin Convert Polygonal Region into Different Format
spruces Spruces Point Pattern
Poisson Poisson Point Process Model
Iest Estimate the I-function
Lest L-function
lurking Lurking variable plot
discretise Safely Convert Point Pattern Window to Binary Mask
finpines Pine saplings in Finland.
eval.fasp Evaluate Expression Involving Function Arrays
Kcross Multitype K Function (Cross-type)
multiplicity.ppp Count Multiplicity of Duplicate Points
lansing Lansing Woods Point Pattern
Kcross.inhom Inhomogeneous Cross K Function
pcf.fasp Pair Correlation Function obtained from array of K functions
model.matrix.ppm Extract Design Matrix from Point Process Model
affine.owin Apply Affine Transformation To Window
affine.ppp Apply Affine Transformation To Point Pattern
amacrine Hughes' Amacrine Cell Data
pcf Pair Correlation Function
SatPiece Piecewise Constant Saturated Pairwise Interaction Point Process Model
plot.tess Plot a tessellation
logLik.ppm Log Likelihood for Poisson Point Process Model
ppm.object Class of Fitted Point Process Models
spokes Spokes pattern of dummy points
fasp.object Function Arrays for Spatial Patterns
plot.hyperframe Plot Entries in a Hyperframe
convexhull.xy Convex Hull of Points
Kmulti Marked K-Function
interp.im Interpolate a Pixel Image
dilate.owin Dilate a Window
diagnose.ppm Diagnostic Plots for Fitted Point Process Model
affine.psp Apply Affine Transformation To Line Segment Pattern
model.images Compute Images of Constructed Covariates
print.psp Print Brief Details of a Line Segment Pattern Dataset
as.data.frame.ppp Coerce Point Pattern to a Data Frame
summary.quad Summarizing a Quadrature Scheme
psp.object Class of Line Segment Patterns
ppp.object Class of Point Patterns
is.ppp Test Whether An Object Is A Point Pattern
crossing.psp Crossing Points of Two Line Segment Patterns
quadscheme Generate a Quadrature Scheme from a Point Pattern
rotate.owin Rotate a Window
rmhmodel.list Define Point Process Model for Metropolis-Hastings Simulation.
pppdist Distance Between Two Point Patterns
predict.ppm Prediction from a Fitted Point Process Model
fv.object Data Frames of Function Values
pppmatching.object Class of Point Matchings
rotate.psp Rotate a Line Segment Pattern
print.quad Print a Quadrature Scheme
print.im Print Brief Details of an Image
rMatClust Simulate Matern Cluster Process
is.ppm Test Whether An Object Is A Fitted Point Process Model
summary.ppm Summarizing a Fitted Point Process Model
Jcross Multitype J Function (i-to-j)
plot.ppm plot a Fitted Point Process Model
owin.object Class owin
im Create a Pixel Image Object
qqplot.ppm Q-Q Plot of Residuals from Fitted Point Process Model
eem Exponential Energy Marks
letterR Window in Shape of Letter R
subset.im Extract Subset of Image
profilepl Profile Maximum Pseudolikelihood
simulate.kppm Simulate a fitted cluster point process model.
progressreport Print Progress Reports
nearest.raster.point Find Pixel Nearest to a Given Point
rmh.ppm Simulate from a Fitted Point Process Model
shift.psp Apply Vector Translation To Line Segment Pattern
as.owin Convert Data To Class owin
nndist Nearest neighbour distances
coef.ppm Coefficients of Fitted Point Process Model
is.multitype Test whether Object is Multitype
pppmatching Create a Point Matching
setcov Set Covariance of a Window
rotate.ppp Rotate a Point Pattern
summary.im Summarizing a Pixel Image
gridweights Compute Quadrature Weights Based on Grid Counts
bdist.pixels Distance to Boundary of Window
cut.im Convert Pixel Image from Numeric to Factor
trim.rectangle Cut margins from rectangle
Kdot.inhom Inhomogeneous Multitype K Dot Function
smooth.ppp Spatial smoothing of observations at irregular points
ord.family Ord Interaction Process Family
Softcore The Soft Core Point Process Model
shift.ppp Apply Vector Translation To Point Pattern
corners Corners of a rectangle
Strauss The Strauss Point Process Model
rthin Random Thinning
rNeymanScott Simulate Neyman-Scott Process
spatstat-internal Internal spatstat functions
plot.listof Plot a List of Things
ppp Create a Point Pattern
compatible.fasp Test Whether Two Function Arrays Are Compatible
MultiStrauss The Multitype Strauss Point Process Model
owin Create a Window
nztrees New Zealand Trees Point Pattern
vertices Vertices of a Window
eval.fv Evaluate Expression Involving Functions
marktable Tabulate Marks in Neighbourhood of Every Point in a Point Pattern
tiles Extract List of Tiles in a Tessellation
rmhmodel.ppm Interpret Fitted Model for Metropolis-Hastings Simulation.
quadrat.test Chi-Squared Dispersion Test for Spatial Point Pattern Based on Quadrat Counts
PairPiece The Piecewise Constant Pairwise Interaction Point Process Model
effectfun Compute Fitted Effect of a Spatial Covariate in a Point Process Model
plot.ppp plot a Spatial Point Pattern
Pairwise Generic Pairwise Interaction model
rstrat Simulate Stratified Random Point Pattern
pairsat.family Saturated Pairwise Interaction Point Process Family
distmap.psp Distance Map of Line Segment Pattern
rmpoint Generate N Random Multitype Points
Ord Generic Ord Interaction model
plot.fv Plot Function Valuesn
subset.splitppp Extract or Replace Sub-Patterns
is.marked Test Whether Marks Are Present
residuals.ppm Residuals for Fitted Point Process Model
Jest Estimate the J-function
eroded.areas Areas of Morphological Erosions
split.ppp Divide Point Pattern into Sub-patterns
reduced.sample Reduced Sample Estimator using Histogram Data
affine Apply Affine Transformation
shift.im Apply Vector Translation To Pixel Image
cells Biological Cells Point Pattern
fitin.ppm Extract the Interaction from a Fitted Point Process Model
reach Interaction Distance of a Point Process
rshift.splitppp Randomly Shift a List of Point Patterns
pairdist.default Pairwise distances
as.im Convert to Pixel Image
complement.owin Take Complement of a Window
is.marked.ppm Test Whether A Point Process Model is Marked
dirichlet.weights Compute Quadrature Weights Based on Dirichlet Tessellation
crossdist.ppp Pairwise distances between two different point patterns
fitted.ppm Fitted Conditional Intensity for Point Process Model
print.ppm Print a Fitted Point Process Model
quantile.im Sample Quantiles of Pixel Image
plot.plotppm Plot a plotppm Object Created by plot.ppm
union.quad Union of Data and Dummy Points
betacells Beta Ganglion Cells in Cat Retina
summary.ppp Summary of a Point Pattern Dataset
Gdot Multitype Nearest Neighbour Distance Function (i-to-any)
mincontrast Method of Minimum Contrast
rThomas Simulate Thomas Process
rshift Random Shift
stieltjes Compute Integral of Function Against Cumulative Distribution
rmhstart Determine Initial State for Metropolis-Hastings Simulation.
envelope Simulation envelopes of summary function
runifdisc Generate N Uniform Random Points in a Disc
setmarks Set or Reset the Marks in a Point Pattern
redwoodfull California Redwoods Point Pattern (Entire Dataset)
rmhmodel.default Build Point Process Model for Metropolis-Hastings Simulation.
summary.listof Summary of a List of Things
rshift.ppp Randomly Shift a Point Pattern
simdat Simulated Point Pattern
kaplan.meier Kaplan-Meier Estimator using Histogram Data
rescale.ppp Convert Point Pattern to Another Unit of Length
Lcross Multitype L-function (cross-type)
solutionset Evaluate Logical Expression Involving Pixel Images and Return Region Where Expression is True
longleaf Longleaf Pines Point Pattern
[.tess Extract or Replace Subset of Tessellation
summary.psp Summary of a Line Segment Pattern Dataset
rescale.psp Convert Line Segment Pattern to Another Unit of Length
persp.im Perspective Plot of Pixel Image
plot.im Plot a Pixel Image
markcorr Mark Correlation Function
rpoispp Generate Poisson Point Pattern
is.owin Test Whether An Object Is A Window
square Square Window
endpoints.psp Endpoints of Line Segment Pattern
subset.fasp Extract Subset of Function Array
contour.im Contour plot of pixel image
StraussHard The Strauss / Hard Core Point Process Model
rSSI Simulate Simple Sequential Inhibition
DiggleGratton Diggle-Gratton model
rmhcontrol Set Control Parameters for Metropolis-Hastings Algorithm.
rGaussPoisson Simulate Gauss-Poisson Process
rmh Simulate point patterns using the Metropolis-Hastings algorithm.
is.subset.owin Determine Whether One Window is Contained In Another
anova.ppm ANOVA for Fitted Point Process Models
rpoint Generate N Random Points
update.kppm Update a Fitted Cluster Point Process Model
swedishpines Swedish Pines Point Pattern
update.ppm Update a Fitted Point Process Model
rmpoispp Generate Multitype Poisson Point Pattern
superimpose Superimpose Several Point Patterns
matchingdist Distance for a Point Pattern Matching
ripras Estimate window from points alone
rlinegrid Generate grid of parallel lines with random displacement
markstat Summarise Marks in Every Neighbourhood in a Point Pattern
lengths.psp Lengths of Line Segments
quad.ppm Extract Quadrature Scheme Used to Fit a Point Process Model
gridcentres Rectangular grid of points
im.object Class of Images
rlabel Random Re-Labelling of Point Pattern
unmark Remove Marks from a Marked Point Pattern
allstats Calculate four standard summary functions of a point pattern.
inside.owin Test Whether Points Are Inside A Window
redwood California Redwoods Point Pattern (Ripley's Subset)
disc Circular Window
thomas.estK Fit the Thomas Point Process by Minimum Contrast
midpoints.psp Midpoints of Line Segment Pattern
shift.owin Apply Vector Translation To Window
rescale Convert dataset to another unit of length
rMaternI Simulate Matern Model I
plot.splitppp Plot a List of Point Patterns
summary.owin Summary of a Spatial Window
Kest.fft K-function using FFT
rescale.owin Convert Window to Another Unit of Length
rsyst Simulate systematic random point pattern
rshift.psp Randomly Shift a Line Segment Pattern
rcell Simulate Baddeley-Silverman Cell Process
subset.ppp Extract or Replace Subset of Point Pattern
quadratcount Quadrat counting for a point pattern
suffstat Sufficient Statistic of Point Process Model
spatstat.options Internal Options in Spatstat Package
scanpp Read Point Pattern From Data File
rStrauss Perfect Simulation of the Strauss Process
raster.x Cartesian Coordinates for a Pixel Raster
dirichlet Dirichlet Tessellation of Point Pattern
subset.psp Extract Subset of Line Segment Pattern
ppm Fit Point Process Model to Data
rpoisline Generate Poisson Random Line Process
selfcrossing.psp Crossing Points in a Line Segment Pattern
nbfires Point Patterns of New Brunswick Forest Fires
subset.listof Extract or Replace Subset of a List of Things
tess Create a Tessellation
rescue.rectangle Convert Window Back To Rectangle
humberside Humberside Data on Childhood Leukaemia and Lymphoma
rmhmodel Define Point Process Model for Metropolis-Hastings Simulation.
hyperframe Hyper Data Frame
with.fv Evaluate an Expression in a Function Table
nndist.psp Nearest neighbour distances between line segments
plot.kppm Plot a fitted cluster point process
residualspaper Data and Code From JRSS Discussion Paper on Residuals
rMaternII Simulate Matern Model II
pairdist Pairwise distances
subsetget.im Reset Values in Subset of Image
rotate Rotate
urkiola Urkiola Woods Point Pattern
unitname Name for Unit of Length
rmh.default Simulate Point Process Models using the Metropolis-Hastings Algorithm.
is.marked.ppp Test Whether A Point Pattern is Marked
pcf.fv Pair Correlation Function obtained from K Function
plot.owin Plot a Spatial Window
pcf.ppp Pair Correlation Function of Point Pattern
Gmulti Marked Nearest Neighbour Distance Function
is.multitype.ppp Test Whether A Point Pattern is Multitype
subset.fv Extract Subset of Function Values
vcov.ppm Variance-Covariance Matrix for a Fitted Point Process Model
shift Apply Vector Translation
unique.ppp Extract Unique Points from a Spatial Point Pattern
harmonic Basis for Harmonic Functions
rjitter Random Perturbation of a Point Pattern
summary.splitppp Summary of a Split Point Pattern
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Date 22 July 2008
License GPL (>= 2)
URL http://www.spatstat.org
Packaged Wed Jul 23 13:29:25 2008; adrian

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