spatstat v1.15-0

0

Monthly downloads

0th

Percentile

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

Last month downloads

Details

Date 02 March 2009
License GPL (>= 2)
URL http://www.spatstat.org
Packaged Tue Mar 3 02:53:41 2009; adrian

Include our badge in your README

[![Rdoc](http://www.rdocumentation.org/badges/version/spatstat)](http://www.rdocumentation.org/packages/spatstat)