spatstat v1.11-7

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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 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
Kmeasure Reduced Second Moment Measure
affine Apply Affine Transformation
ganglia Beta Ganglion Cells in Cat Retina, Old Version
as.matrix.im Convert Pixel Image to Matrix
allstats Calculate four standard summary functions of a point pattern.
hist.im Histogram of Pixel Values in an Image
fv.object Data Frames of Function Values
Kmulti Marked K-Function
ewcdf Weighted Empirical Cumulative Distribution Function
Geyer Geyer's Saturation Point Process Model
spatstat The Spatstat Package
alltypes Calculate Statistic for All Types in a Multitype Point Pattern
Gest Nearest Neighbour Distance Function G
PairPiece The Piecewise Constant Pairwise Interaction Point Process Model
cells Biological Cells Point Pattern
data.ppm Extract Original Data from a Fitted Point Process Model
Kcross Multitype K Function (Cross-type)
append.psp Combine Two Line Segment Patterns
cut.ppp Convert Point Pattern Marks from Numeric to Factor
area.owin Area of a Window
affine.owin Apply Affine Transformation To Window
Iest Estimate the I-function
bounding.box.xy Convex Hull of Points
gridcentres Rectangular grid of points
anova.ppm ANOVA for Fitted Point Process Models
as.ppp Convert Data To Class ppp
DiggleGratton Diggle-Gratton model
is.marked.ppp Test Whether A Point Pattern is Marked
diameter Diameter of a Window
default.dummy Generate a Default Pattern of Dummy Points
quad.object Class of Quadrature Schemes
is.multitype.ppp Test Whether A Point Pattern is Multitype
disc Circular Window
is.ppm Test Whether An Object Is A Fitted Point Process Model
owin Create a Window
rMaternI Simulate Matern Model I
clickppp Interactively Add Points
identify.ppp Identify Points in a Point Pattern
dummy.ppm Extract Dummy Points Used to Fit a Point Process Model
interp.im Interpolate a Pixel Image
spatstat-deprecated Deprecated spatstat functions
plot.ppp plot a Spatial Point Pattern
betacells Beta Ganglion Cells in Cat Retina
redwoodfull California Redwoods Point Pattern (Entire Dataset)
distmap Distance Map
eem Exponential Energy Marks
inside.owin Test Whether Points Are Inside A Window
copper Berman-Huntington points and lines data
im.object Class of Images
plot.plotppm Plot a plotppm Object Created by plot.ppm
redwood California Redwoods Point Pattern (Ripley's Subset)
Saturated Saturated Pairwise Interaction model
is.owin Test Whether An Object Is A Window
gridweights Compute Quadrature Weights Based on Grid Counts
rcell Simulate Baddeley-Silverman Cell Process
rMaternII Simulate Matern Model II
bounding.box Bounding Box of a Window or Point Pattern
im Create a Pixel Image Object
rMatClust Simulate Matern Cluster Process
rotate.ppp Rotate a Point Pattern
intersect.owin Intersection or Union of Two Windows
residuals.ppm Residuals for Fitted Point Process Model
nearest.raster.point Find Pixel Nearest to a Given Point
rThomas Simulate Thomas Process
ripras Estimate window from points alone
rsyst Simulate systematic random point pattern
rshift.splitppp Randomly Shift a List of Point Patterns
rStrauss Perfect Simulation of the Strauss Process
is.im Test Whether An Object Is A Pixel Image
split.ppp Divide Point Pattern into Sub-patterns
ppm Fit Point Process Model to Data
rSSI Simulate Simple Sequential Inhibition
mean.im Mean Pixel Value in an Image
plot.splitppp Plot a List of Point Patterns
simdat Simulated Point Pattern
is.multitype.ppm Test Whether A Point Process Model is Multitype
rshift Random Shift
is.marked Test Whether Marks Are Present
pairdist Pairwise distances
print.owin Print Brief Details of a Spatial Window
setmarks Set or Reset the Marks in a Point Pattern
summary.listof Summary of a List of Things
pairwise.family Pairwise Interaction Process Family
pairdist.ppp Pairwise distances
ord.family Ord Interaction Process Family
pppdist Optimal Match Between Two Point Patterns
psp.object Class of Line Segment Patterns
print.psp Print Brief Details of a Line Segment Pattern Dataset
Jest Estimate the J-function
rmhmodel.default Build Point Process Model for Metropolis-Hastings Simulation.
quadscheme Generate a Quadrature Scheme from a Point Pattern
plot.im Plot a Pixel Image
psp Create a Line Segment Pattern
levelset Level Set of a Pixel Image
rescue.rectangle Convert Window Back To Rectangle
plot.quad plot a Spatial Quadrature Scheme
Kest K-function
subset.ppp Extract or Replace Subset of Point Pattern
thomas.estK Fit the Thomas Point Process by Minimum Contrast
residualspaper Data and Code From JRSS Discussion Paper on Residuals
rmh.ppm Simulate from a Fitted Point Process Model
rotate.psp Rotate a Line Segment Pattern
subset.listof Extract or Replace Subset of a List of Things
spruces Spruces Point Pattern
rpoisline Generate Poisson Random Line Process
shift.psp Apply Vector Translation To Line Segment Pattern
Kest.fft K-function using FFT
square Square Window
clickpoly Interactively Define a Polygon
rmpoispp Generate Multitype Poisson Point Pattern
summary.splitppp Summary of a Split Point Pattern
summary.psp Summary of a Line Segment Pattern Dataset
as.mask Pixel Image Approximation of a Window
angles.psp Orientation Angles of Line Segments
owin.object Class owin
print.quad Print a Quadrature Scheme
applynbd Apply Function to Every Neighbourhood in a Point Pattern
quad.ppm Extract Quadrature Scheme Used to Fit a Point Process Model
pcf.fasp Pair Correlation Function obtained from array of K functions
compatible.im Test Whether Two Pixel Images Are Compatible
crossdist.default Pairwise distances between two different sets of points
compatible.fv Test Whether Two Function Objects Are Compatible
affine.psp Apply Affine Transformation To Line Segment Pattern
rescale.psp Convert Line Segment Pattern to Another Unit of Length
Kdot Multitype K Function (i-to-any)
density.ppp Kernel Smoothed Intensity of Point Pattern
persp.im Perspective Plot of Pixel Image
Pairwise Generic Pairwise Interaction model
crossdist Pairwise distances
expand.owin Expand Window By Factor
corners Corners of a rectangle
multiplicity.ppp Count Multiplicity of Duplicate Points
midpoints.psp Midpoints of Line Segment Pattern
MultiStraussHard The Multitype/Hard Core Strauss Point Process Model
dirichlet.weights Compute Quadrature Weights Based on Dirichlet Tessellation
endpoints.psp Endpoints of Line Segment Pattern
ks.test.ppm Kolmogorov-Smirnov Test for Point Process Model
lengths.psp Lengths of Line Segments
japanesepines Japanese Pines Point Pattern
pcf Pair Correlation Function
nztrees New Zealand Trees Point Pattern
centroid.owin Centroid of a window
subset.fv Extract Subset of Function Values
reach Interaction Distance of a Point Process
rshift.ppp Randomly Shift a Point Pattern
convexhull.xy Convex Hull of Points
subset.im Extract Subset of Image
rmh.default Simulate Point Process Models using the Metropolis-Hastings Algorithm.
markstat Summarise Marks in Every Neighbourhood in a Point Pattern
mincontrast Method of Minimum Contrast
is.subset.owin Determine Whether One Window is Contained In Another
rpoispp Generate Poisson Point Pattern
density.splitppp Kernel Smoothed Intensity of Split Point Pattern
nndist.psp Nearest neighbour distances between line segments
envelope Simulation envelopes of summary function
shift.ppp Apply Vector Translation To Point Pattern
discretise Safely Convert Point Pattern Window to Binary Mask
print.ppp Print Brief Details of a Point Pattern Dataset
runifpoint Generate N Uniform Random Points
plot.owin Plot a Spatial Window
rescale.ppp Convert Point Pattern to Another Unit of Length
subset.psp Extract Subset of Line Segment Pattern
union.quad Union of Data and Dummy Points
is.multitype Test whether Object is Multitype
trim.rectangle Cut margins from rectangle
rlinegrid Generate grid of parallel lines with random displacement
quadrat.test Chi-Squared Dispersion Test for Spatial Point Pattern Based on Quadrat Counts
rescale Convert dataset to another unit of length
rotate Rotate
subset.fasp Extract Subset of Function Array
rthin Random Thinning
rstrat Simulate Stratified Random Point Pattern
vertices Vertices of a Window
swedishpines Swedish Pines Point Pattern
crossdist.psp Pairwise distances between two different line segment patterns
as.im Convert to Pixel Image
humberside Humberside Data on Childhood Leukaemia and Lymphoma
km.rs Kaplan-Meier and Reduced Sample Estimator using Histograms
lansing Lansing Woods Point Pattern
plot.fasp Plot a Function Array
ppp Create a Point Pattern
Gmulti Marked Nearest Neighbour Distance Function
Jmulti Marked J Function
plot.ppm plot a Fitted Point Process Model
rmhstart Determine Initial State for Metropolis-Hastings Simulation.
solutionset Evaluate Logical Expression Involving Pixel Images and Return Region Where Expression is True
vcov.ppm Variance-Covariance Matrix for a Fitted Point Process Model
Kinhom Inhomogeneous K-function
LennardJones The Lennard-Jones Potential
distmap.owin Distance Map of Window
contour.im Contour plot of pixel image
duplicated.ppp Determine Duplicated Points in a Spatial Point Pattern
scanpp Read Point Pattern From Data File
affine.ppp Apply Affine Transformation To Point Pattern
as.owin Convert Data To Class owin
demopat Artificial Data Point Pattern
crossing.psp Crossing Points of Two Line Segment Patterns
concatxy Concatenate x,y Coordinate Vectors
distmap.ppp Distance Map of Point Pattern
ants Harkness-Isham ants' nests data
fitin.ppm Extract the Interaction from a Fitted Point Process Model
longleaf Longleaf Pines Point Pattern
predict.ppm Prediction from a Fitted Point Process Model
hamster Aherne's hamster tumour data
profilepl Profile Maximum Pseudolikelihood
reduced.sample Reduced Sample Estimator using Histogram Data
letterR Window in Shape of Letter R
selfcrossing.psp Crossing Points in a Line Segment Pattern
lurking Lurking variable plot
pcf.ppp Pair Correlation Function of Point Pattern
shift Apply Vector Translation
superimpose Superimpose Several Point Patterns
update.ppm Update a Fitted Point Process Model
setcov Set Covariance of a Window
progressreport Print Progress Reports
raster.x Cartesian Coordinates for a Pixel Raster
spatstat.options Internal Options in Spatstat Package
qqplot.ppm Q-Q Plot of Residuals from Fitted Point Process Model
rshift.psp Randomly Shift a Line Segment Pattern
shift.owin Apply Vector Translation To Window
unmark Remove Marks from a Marked Point Pattern
Strauss The Strauss Point Process Model
bdist.points Distance to Boundary of Window
erode.owin Erode a Window
markcorr Mark Correlation Function
dilate.owin Dilate a Window
eval.fv Evaluate Expression Involving Functions
harmonic Basis for Harmonic Functions
logLik.ppm Log Likelihood for Poisson Point Process Model
lgcp.estK Fit a Log-Gaussian Cox Point Process by Minimum Contrast
nncross Nearest Neighbour in Another Point Pattern
rNeymanScott Simulate Neyman-Scott Process
nnwhich Nearest neighbour
runifdisc Generate N Uniform Random Points in a Disc
rmhmodel.list Define Point Process Model for Metropolis-Hastings Simulation.
summary.ppp Summary of a Point Pattern Dataset
subsetget.im Reset Values in Subset of Image
summary.owin Summary of a Spatial Window
as.psp Convert Data To Class psp
crossdist.ppp Pairwise distances between two different point patterns
eval.im Evaluate Expression Involving Pixel Images
plot.listof Plot a List of Things
rmpoint Generate N Random Multitype Points
rmhmodel.ppm Interpret Fitted Model for Metropolis-Hastings Simulation.
units Name for Unit of Length
subset.splitppp Extract or Replace Sub-Patterns
Fest Estimate the empty space function F
Jdot Multitype J Function (i-to-any)
Jcross Multitype J Function (i-to-j)
Kdot.inhom Inhomogeneous Multitype K Dot Function
Softcore The Soft Core Point Process Model
distmap.psp Distance Map of Line Segment Pattern
fitted.ppm Fitted Conditional Intensity for Point Process Model
spatstat-internal Internal spatstat functions
pairdist.default Pairwise distances
pcf.fv Pair Correlation Function obtained from K Function
plot.fv Plot Function Valuesn
print.im Print Brief Details of an Image
rlabel Random Re-Labelling of Point Pattern
rpoint Generate N Random Points
summary.ppm Summarizing a Fitted Point Process Model
unique.ppp Extract Unique Points from a Spatial Point Pattern
rmhcontrol Set Control Parameters for Metropolis-Hastings Algorithm.
rmhmodel Define Point Process Model for Metropolis-Hastings Simulation.
bei Tropical rain forest trees
Kcross.inhom Inhomogeneous Cross K Function
density.psp Kernel Smoothing of Line Segment Pattern
nncorr Nearest-Neighbour Correlation of Marked Point Pattern
amacrine Hughes' Amacrine Cell Data
ppm.object Class of Fitted Point Process Models
matclust.estK Fit the Matern Cluster Point Process by Minimum Contrast
Poisson Poisson Point Process Model
rotate.owin Rotate a Window
kaplan.meier Kaplan-Meier Estimator using Histogram Data
diagnose.ppm Diagnostic Plots for Fitted Point Process Model
anemones Beadlet Anemones Data
Gdot Multitype Nearest Neighbour Distance Function (i-to-any)
is.ppp Test Whether An Object Is A Point Pattern
cut.im Convert Pixel Image from Numeric to Factor
rescale.owin Convert Window to Another Unit of Length
as.rectangle Window Frame
shift.im Apply Vector Translation To Pixel Image
summary.im Summarizing a Pixel Image
pairsat.family Saturated Pairwise Interaction Point Process Family
quantile.im Sample Quantiles of Pixel Image
Ord Generic Ord Interaction model
chorley Chorley-Ribble Cancer Data
MultiStrauss The Multitype Strauss Point Process Model
pairdist.psp Pairwise distances between line segments
bdist.pixels Distance to Boundary of Window
nbfires Point Patterns of New Brunswick Forest Fires
fasp.object Function Arrays for Spatial Patterns
plot.psp plot a Spatial Line Segment Pattern
coef.ppm Coefficients of Fitted Point Process Model
spokes Spokes pattern of dummy points
OrdThresh Ord's Interaction model
StraussHard The Strauss / Hard Core Point Process Model
Gcross Multitype Nearest Neighbour Distance Function (i-to-j)
finpines Pine saplings in Finland.
clarkevans Clark and Evans Aggregation Index
is.marked.ppm Test Whether A Point Process Model is Marked
eroded.areas Areas of Morphological Erosions
nndist Nearest neighbour distances
print.ppm Print a Fitted Point Process Model
rmh Simulate point patterns using the Metropolis-Hastings algorithm.
ppp.object Class of Point Patterns
summary.quad Summarizing a Quadrature Scheme
suffstat Sufficient Statistic of Point Process Model
bramblecanes Hutchings' Bramble Canes data
complement.owin Take Complement of a Window
quadratcount Quadrat counting for a point pattern
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Date 9 June 2007
License GPL version 2 or newer
URL http://www.spatstat.org
Packaged Tue Jun 12 02:00:25 2007; adrian

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