spatstat v1.10-3

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

Last month downloads

Details

Date 20 November 2006
License GPL version 2 or newer
URL http://www.spatstat.org
Packaged Mon Nov 20 16:03:00 2006; adrian

Include our badge in your README

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