spatstat v1.14-2

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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
rStrauss Perfect Simulation of the Strauss Process
persp.im Perspective Plot of Pixel Image
rotate.owin Rotate a Window
plot.splitppp Plot a List of Point Patterns
rthin Random Thinning
rshift.ppp Randomly Shift a Point Pattern
pairdist Pairwise distances
quad.object Class of Quadrature Schemes
pcf.fasp Pair Correlation Function obtained from array of K functions
shift.im Apply Vector Translation To Pixel Image
plot.tess Plot a tessellation
quadscheme Generate a Quadrature Scheme from a Point Pattern
rNeymanScott Simulate Neyman-Scott Process
subset.im Extract Subset of Image
rescale.psp Convert Line Segment Pattern to Another Unit of Length
rlinegrid Generate grid of parallel lines with random displacement
plot.psp plot a Spatial Line Segment Pattern
redwoodfull California Redwoods Point Pattern (Entire Dataset)
plot.ppm plot a Fitted Point Process Model
pairdist.psp Pairwise distances between line segments
ponderosa Ponderosa Pine Tree Point Pattern
rjitter Random Perturbation of a Point Pattern
[.tess Extract or Replace Subset of Tessellation
pixelquad Quadrature Scheme Based on Pixel Grid
spruces Spruces Point Pattern
print.quad Print a Quadrature Scheme
runifpoint Generate N Uniform Random Points
summary.im Summarizing a Pixel Image
progressreport Print Progress Reports
subset.ppp Extract or Replace Subset of Point Pattern
unique.ppp Extract Unique Points from a Spatial Point Pattern
psp Create a Line Segment Pattern
predict.kppm Prediction from a Fitted Cluster Point Process Model
print.ppm Print a Fitted Point Process Model
rMaternII Simulate Matern Model II
subset.listof Extract or Replace Subset of a List of Things
rescue.rectangle Convert Window Back To Rectangle
summary.listof Summary of a List of Things
reduced.sample Reduced Sample Estimator using Histogram Data
ripras Estimate window from points alone
rescale.ppp Convert Point Pattern to Another Unit of Length
plot.quad plot a Spatial Quadrature Scheme
rescale.im Convert Pixel Image to Another Unit of Length
rmh.default Simulate Point Process Models using the Metropolis-Hastings Algorithm.
plot.listof Plot a List of Things
update.ppm Update a Fitted Point Process Model
rmhmodel.ppm Interpret Fitted Model for Metropolis-Hastings Simulation.
rmhmodel.default Build Point Process Model for Metropolis-Hastings Simulation.
plot.plotppm Plot a plotppm Object Created by plot.ppm
summary.splitppp Summary of a Split Point Pattern
rshift Random Shift
plot.fasp Plot a Function Array
plot.owin Plot a Spatial Window
pcf Pair Correlation Function
thomas.estK Fit the Thomas Point Process by Minimum Contrast
residualspaper Data and Code From JRSS Discussion Paper on Residuals
psp.object Class of Line Segment Patterns
rmhstart Determine Initial State for Metropolis-Hastings Simulation.
print.psp Print Brief Details of a Line Segment Pattern Dataset
[.quad Subset of Quadrature Scheme
shift.psp Apply Vector Translation To Line Segment Pattern
rpoint Generate N Random Points
unmark Remove Marks from a Marked Point Pattern
rSSI Simulate Simple Sequential Inhibition
rMatClust Simulate Matern Cluster Process
pcf.fv Pair Correlation Function obtained from K Function
pairwise.family Pairwise Interaction Process Family
shift.ppp Apply Vector Translation To Point Pattern
rThomas Simulate Thomas Process
rescale Convert dataset to another unit of length
rotate.ppp Rotate a Point Pattern
urkiola Urkiola Woods Point Pattern
subsetget.im Reset Values in Subset of Image
plot.ppp plot a Spatial Point Pattern
rpoispp Generate Poisson Point Pattern
plot.hyperframe Plot Entries in a Hyperframe
pairsat.family Saturated Pairwise Interaction Point Process Family
vcov.ppm Variance-Covariance Matrix for a Fitted Point Process Model
ppm.object Class of Fitted Point Process Models
spatstat.options Internal Options in Spatstat Package
rmpoispp Generate Multitype Poisson Point Pattern
simdat Simulated Point Pattern
pairdist.ppp Pairwise distances
plot.kppm Plot a fitted cluster point process
reach Interaction Distance of a Point Process
subset.psp Extract Subset of Line Segment Pattern
summary.ppm Summarizing a Fitted Point Process Model
pppdist Distance Between Two Point Patterns
summary.psp Summary of a Line Segment Pattern Dataset
superimpose Superimpose Several Point Patterns
rescale.owin Convert Window to Another Unit of Length
runifdisc Generate N Uniform Random Points in a Disc
simulate.kppm Simulate a fitted cluster point process model.
trim.rectangle Cut margins from rectangle
print.ppp Print Brief Details of a Point Pattern Dataset
ppp.object Class of Point Patterns
scanpp Read Point Pattern From Data File
residuals.ppm Residuals for Fitted Point Process Model
pppmatching Create a Point Matching
plot.fv Plot Function Valuesn
unitname Name for Unit of Length
rshift.splitppp Randomly Shift a List of Point Patterns
profilepl Profile Maximum Pseudolikelihood
rmhmodel Define Point Process Model for Metropolis-Hastings Simulation.
setcov Set Covariance of a Window
print.owin Print Brief Details of a Spatial Window
setmarks Set or Reset the Marks in a Point Pattern
rstrat Simulate Stratified Random Point Pattern
plot.im Plot a Pixel Image
rsyst Simulate systematic random point pattern
rGaussPoisson Simulate Gauss-Poisson Process
qqplot.ppm Q-Q Plot of Residuals from Fitted Point Process Model
print.im Print Brief Details of an Image
with.fv Evaluate an Expression in a Function Table
suffstat Sufficient Statistic of Point Process Model
ppm Fit Point Process Model to Data
swedishpines Swedish Pines Point Pattern
quantile.im Sample Quantiles of Pixel Image
shift.owin Apply Vector Translation To Window
rMaternI Simulate Matern Model I
rmpoint Generate N Random Multitype Points
union.quad Union of Data and Dummy Points
tiles Extract List of Tiles in a Tessellation
redwood California Redwoods Point Pattern (Ripley's Subset)
smooth.ppp Spatial smoothing of observations at irregular points
stieltjes Compute Integral of Function Against Cumulative Distribution
rmhmodel.list Define Point Process Model for Metropolis-Hastings Simulation.
subset.fv Extract Subset of Function Values
rshift.psp Randomly Shift a Line Segment Pattern
rcell Simulate Baddeley-Silverman Cell Process
predict.ppm Prediction from a Fitted Point Process Model
rmhcontrol Set Control Parameters for Metropolis-Hastings Algorithm.
quadratcount Quadrat counting for a point pattern
rlabel Random Re-Labelling of Point Pattern
rotate.psp Rotate a Line Segment Pattern
rpoisline Generate Poisson Random Line Process
Geyer Geyer's Saturation Point Process Model
summary.quad Summarizing a Quadrature Scheme
shift Apply Vector Translation
update.kppm Update a Fitted Cluster Point Process Model
spokes Spokes pattern of dummy points
summary.ppp Summary of a Point Pattern Dataset
pcf.ppp Pair Correlation Function of Point Pattern
vertices Vertices of a Window
square Square Window
selfcrossing.psp Crossing Points in a Line Segment Pattern
subset.splitppp Extract or Replace Sub-Patterns
Kmulti Marked K-Function
raster.x Cartesian Coordinates for a Pixel Raster
Strauss The Strauss Point Process Model
Jdot Multitype J Function (i-to-any)
rmh.ppm Simulate from a Fitted Point Process Model
ppp Create a Point Pattern
density.splitppp Kernel Smoothed Intensity of Split Point Pattern
solutionset Evaluate Logical Expression Involving Pixel Images and Return Region Where Expression is True
Lest L-function
blur Apply Gaussian Blur to a Pixel Image
subset.fasp Extract Subset of Function Array
dilate.owin Dilate a Window
bdist.pixels Distance to Boundary of Window
rotate Rotate
bdist.points Distance to Boundary of Window
Jcross Multitype J Function (i-to-j)
harmonic Basis for Harmonic Functions
kppm Fit cluster point process model
pcfcross Multitype pair correlation function
is.multitype Test whether Object is Multitype
is.owin Test Whether An Object Is A Window
nnwhich Nearest neighbour
Fest Estimate the empty space function F
clickppp Interactively Add Points
AreaInter The Area Interaction Point Process Model
pppmatching.object Class of Point Matchings
quad.ppm Extract Quadrature Scheme Used to Fit a Point Process Model
kstest.ppm Kolmogorov-Smirnov Test for Point Process Model
as.im Convert to Pixel Image
PairPiece The Piecewise Constant Pairwise Interaction Point Process Model
disc Circular Window
distmap.psp Distance Map of Line Segment Pattern
Kmeasure Reduced Second Moment Measure
lansing Lansing Woods Point Pattern
ewcdf Weighted Empirical Cumulative Distribution Function
as.matrix.im Convert Pixel Image to Matrix
affine.owin Apply Affine Transformation To Window
Gdot Multitype Nearest Neighbour Distance Function (i-to-any)
default.dummy Generate a Default Pattern of Dummy Points
Poisson Poisson Point Process Model
longleaf Longleaf Pines Point Pattern
allstats Calculate four standard summary functions of a point pattern.
OrdThresh Ord's Interaction model
nearest.raster.point Find Pixel Nearest to a Given Point
Kinhom Inhomogeneous K-function
eroded.areas Areas of Morphological Erosions
affine.ppp Apply Affine Transformation To Point Pattern
compatible.fasp Test Whether Two Function Arrays Are Compatible
by.ppp Apply a Function to a Point Pattern Broken Down by Factor
as.ppp Convert Data To Class ppp
corners Corners of a rectangle
nbfires Point Patterns of New Brunswick Forest Fires
Jmulti Marked J Function
bramblecanes Hutchings' Bramble Canes data
as.rectangle Window Frame
as.data.frame.ppp Coerce Point Pattern to a Data Frame
nndist Nearest neighbour distances
Linhom L-function
owin.object Class owin
Ord Generic Ord Interaction model
quadrat.test Chi-Squared Dispersion Test for Spatial Point Pattern Based on Quadrat Counts
rmh Simulate point patterns using the Metropolis-Hastings algorithm.
Saturated Saturated Pairwise Interaction model
concatxy Concatenate x,y Coordinate Vectors
spatstat-deprecated Deprecated spatstat functions
anemones Beadlet Anemones Data
cut.im Convert Pixel Image from Numeric to Factor
cut.ppp Classify Points in a Point Pattern
levelset Level Set of a Pixel Image
data.ppm Extract Original Data from a Fitted Point Process Model
ord.family Ord Interaction Process Family
split.ppp Divide Point Pattern into Sub-patterns
eval.fasp Evaluate Expression Involving Function Arrays
diameter Diameter of a Window
markstat Summarise Marks in Every Neighbourhood in a Point Pattern
eval.hyper Evaluate an Expression in Each Row of a Hyperframe
hamster Aherne's hamster tumour data
inforder.family Infinite Order Interaction Family
affine Apply Affine Transformation
is.marked.ppp Test Whether A Point Pattern is Marked
nndist.psp Nearest neighbour distances between line segments
density.psp Kernel Smoothing of Line Segment Pattern
bounding.box Bounding Box of a Window or Point Pattern
summary.owin Summary of a Spatial Window
cells Biological Cells Point Pattern
tess Create a Tessellation
eem Exponential Energy Marks
Kest.fft K-function using FFT
is.marked Test Whether Marks Are Present
StraussHard The Strauss / Hard Core Point Process Model
bei Tropical rain forest trees
dummy.ppm Extract Dummy Points Used to Fit a Point Process Model
coef.ppm Coefficients of Fitted Point Process Model
Jest Estimate the J-function
expand.owin Expand Window By Factor
ganglia Beta Ganglion Cells in Cat Retina, Old Version
fv.object Data Frames of Function Values
spatstat-internal Internal spatstat functions
logLik.ppm Log Likelihood for Poisson Point Process Model
Kest K-function
finpines Pine saplings in Finland.
identify.ppp Identify Points in a Point Pattern
multiplicity.ppp Count Multiplicity of Duplicate Points
marktable Tabulate Marks in Neighbourhood of Every Point in a Point Pattern
lgcp.estK Fit a Log-Gaussian Cox Point Process by Minimum Contrast
is.multitype.ppm Test Whether A Point Process Model is Multitype
area.owin Area of a Window
gridweights Compute Quadrature Weights Based on Grid Counts
applynbd Apply Function to Every Neighbourhood in a Point Pattern
Gcross Multitype Nearest Neighbour Distance Function (i-to-j)
angles.psp Orientation Angles of Line Segments
Kdot Multitype K Function (i-to-any)
erode.owin Erode a Window
is.marked.ppm Test Whether A Point Process Model is Marked
spatstat The Spatstat Package
compatible.fv Test Whether Two Function Objects Are Compatible
contour.im Contour plot of pixel image
envelope Simulation envelopes of summary function
demopat Artificial Data Point Pattern
MultiStraussHard The Multitype/Hard Core Strauss Point Process Model
eval.fv Evaluate Expression Involving Functions
Lcross Multitype L-function (cross-type)
lurking Lurking variable plot
letterR Window in Shape of Letter R
duplicated.ppp Determine Duplicated Points in a Spatial Point Pattern
dirichlet Dirichlet Tessellation of Point Pattern
MultiStrauss The Multitype Strauss Point Process Model
DiggleGratton Diggle-Gratton model
affine.psp Apply Affine Transformation To Line Segment Pattern
is.im Test Whether An Object Is A Pixel Image
gridcentres Rectangular grid of points
as.psp Convert Data To Class psp
alltypes Calculate Summary Statistic for All Types in a Multitype Point Pattern
model.matrix.ppm Extract Design Matrix from Point Process Model
anova.ppm ANOVA for Fitted Point Process Models
crossdist.default Pairwise distances between two different sets of points
amacrine Hughes' Amacrine Cell Data
as.mask Pixel Image Approximation of a Window
ants Harkness-Isham ants' nests data
humberside Humberside Data on Childhood Leukaemia and Lymphoma
pairdist.default Pairwise distances
gpc2owin Convert Polygonal Region into Different Format
append.psp Combine Two Line Segment Patterns
Softcore The Soft Core Point Process Model
areadiff Difference of Disc Areas
endpoints.psp Endpoints of Line Segment Pattern
Iest Estimate the I-function
clickpoly Interactively Define a Polygon
SatPiece Piecewise Constant Saturated Pairwise Interaction Point Process Model
clarkevans Clark and Evans Aggregation Index
Pairwise Generic Pairwise Interaction model
is.subset.owin Determine Whether One Window is Contained In Another
fitted.ppm Fitted Conditional Intensity for Point Process Model
dirichlet.weights Compute Quadrature Weights Based on Dirichlet Tessellation
betacells Beta Ganglion Cells in Cat Retina
convexhull.xy Convex Hull of Points
bounding.box.xy Convex Hull of Points
fasp.object Function Arrays for Spatial Patterns
copper Berman-Huntington points and lines data
crossdist Pairwise distances
interp.im Interpolate a Pixel Image
nztrees New Zealand Trees Point Pattern
matclust.estK Fit the Matern Cluster Point Process by Minimum Contrast
BadGey Hybrid Geyer Point Process Model
chorley Chorley-Ribble Cancer Data
distmap Distance Map
discretise Safely Convert Point Pattern Window to Binary Mask
is.multitype.ppp Test Whether A Point Pattern is Multitype
diagnose.ppm Diagnostic Plots for Fitted Point Process Model
im Create a Pixel Image Object
hyperframe Hyper Data Frame
compatible.im Test Whether Two Pixel Images Are Compatible
hist.im Histogram of Pixel Values in an Image
distmap.ppp Distance Map of Point Pattern
distmap.owin Distance Map of Window
km.rs Kaplan-Meier and Reduced Sample Estimator using Histograms
crossdist.ppp Pairwise distances between two different point patterns
density.ppp Kernel Smoothed Intensity of Point Pattern
intersect.owin Intersection or Union of Two Windows
Gest Nearest Neighbour Distance Function G
inside.owin Test Whether Points Are Inside A Window
Kdot.inhom Inhomogeneous Multitype K Dot Function
midpoints.psp Midpoints of Line Segment Pattern
Ldot Multitype L-function (i-to-any)
complement.owin Take Complement of a Window
kaplan.meier Kaplan-Meier Estimator using Histogram Data
lengths.psp Lengths of Line Segments
effectfun Compute Fitted Effect of a Spatial Covariate in a Point Process Model
owin Create a Window
im.object Class of Images
LennardJones The Lennard-Jones Potential
crossing.psp Crossing Points of Two Line Segment Patterns
nncorr Nearest-Neighbour Correlation of Marked Point Pattern
markcorr Mark Correlation Function
nncross Nearest Neighbour in Another Point Pattern
Gmulti Marked Nearest Neighbour Distance Function
mean.im Mean Pixel Value in an Image
as.owin Convert Data To Class owin
Kcross.inhom Inhomogeneous Cross K Function
Kcross Multitype K Function (Cross-type)
centroid.owin Centroid of a window
model.images Compute Images of Constructed Covariates
crossdist.psp Pairwise distances between two different line segment patterns
eval.im Evaluate Expression Involving Pixel Images
delaunay Delaunay Triangulation of Point Pattern
is.ppp Test Whether An Object Is A Point Pattern
localK Neighbourhood density function
fitin.ppm Extract the Interaction from a Fitted Point Process Model
matchingdist Distance for a Point Pattern Matching
is.ppm Test Whether An Object Is A Fitted Point Process Model
japanesepines Japanese Pines Point Pattern
murchison Murchison gold deposits
mincontrast Method of Minimum Contrast
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Date 8 September 2008
License GPL (>= 2)
URL http://www.spatstat.org
Packaged Tue Sep 9 07:16:02 2008; adrian

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