spatstat v1.19-2


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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. Also supports three-dimensional point patterns, and space-time point patterns in any number of dimensions. 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, pixel images and tessellations. 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
Fiksel The Fiksel Interaction
Gmulti Marked Nearest Neighbour Distance Function
DiggleGratton Diggle-Gratton model
Gfox Foxall's Distance Functions
Iest Estimate the I-function
StraussHard The Strauss / Hard Core Point Process Model
Hest Spherical Contact Distribution Function
areaGain Difference of Disc Areas
applynbd Apply Function to Every Neighbourhood in a Point Pattern
Saturated Saturated Pairwise Interaction model
PairPiece The Piecewise Constant Pairwise Interaction Point Process Model
as.tess Convert Data To Tessellation
Jcross Multitype J Function (i-to-j) Coerce Hyperframe to Data Frame Reset Values in Subset of Image
Kinhom Inhomogeneous K-function
bdist.points Distance to Boundary of Window
Kest K-function Convert Pixel Image from Numeric to Factor
bei Tropical rain forest trees
Strauss The Strauss Point Process Model
boxx Multi-Dimensional Box
SatPiece Piecewise Constant Saturated Pairwise Interaction Point Process Model
demopat Artificial Data Point Pattern
Lcross.inhom Inhomogeneous Cross Type L Function
Extract.fasp Extract Subset of Function Array
anemones Beadlet Anemones Data
data.ppm Extract Original Data from a Fitted Point Process Model
affine.psp Apply Affine Transformation To Line Segment Pattern
Extract.splitppp Extract or Replace Sub-Patterns Extract Subset of Image
Kest.fft K-function using FFT
as.owin Convert Data To Class owin
Gdot Multitype Nearest Neighbour Distance Function (i-to-any)
crossdist.default Pairwise distances between two different sets of points
Gcross Multitype Nearest Neighbour Distance Function (i-to-j)
Kmeasure Reduced Second Moment Measure Coerce Line Segment Pattern to a Data Frame
bdist.pixels Distance to Boundary of Window
clickppp Interactively Add Points
hamster Aherne's hamster tumour data
K3est K-function of a Three-Dimensional Point Pattern
distmap.owin Distance Map of Window
border Border Region of a Window
dilated.areas Areas of Morphological Dilations
allstats Calculate four standard summary functions of a point pattern.
crossdist.psp Pairwise distances between two different line segment patterns
ants Harkness-Isham ants' nests data
compatible.fasp Test Whether Two Function Arrays Are Compatible
Softcore The Soft Core Point Process Model
closing Morphological Closing
as.rectangle Window Frame
append.psp Combine Two Line Segment Patterns Convert Pixel Image to Matrix
Kcross Multitype K Function (Cross-type)
crossdist.ppp Pairwise distances between two different point patterns
area.owin Area of a Window
diameter Diameter of an Object
is.marked.ppm Test Whether A Point Process Model is Marked
Emark Diagnostics for random marking
Fest Estimate the empty space function F
diagnose.ppm Diagnostic Plots for Fitted Point Process Model
gridweights Compute Quadrature Weights Based on Grid Counts
Kdot.inhom Inhomogeneous Multitype K Dot Function
fitin.ppm Extract the Interaction from a Fitted Point Process Model
areaLoss Difference of Disc Areas
Extract.listof Extract or Replace Subset of a List of Things
AreaInter The Area Interaction Point Process Model
G3est Nearest Neighbour Distance Distribution Function of a Three-Dimensional Point Pattern
bronzefilter Bronze gradient filter data
as.polygonal Convert a Window to a Polygonal Window
japanesepines Japanese Pines Point Pattern
affine.ppp Apply Affine Transformation To Point Pattern
Ldot Multitype L-function (i-to-any)
colourmap Colour Lookup Tables
as.psp Convert Data To Class psp
F3est Empty Space Function of a Three-Dimensional Point Pattern
spatstat-internal Internal spatstat functions
by.ppp Apply a Function to a Point Pattern Broken Down by Factor Bounding Box of a Window or Point Pattern
endpoints.psp Endpoints of Line Segment Pattern
Hardcore The Hard Core Point Process Model
kaplan.meier Kaplan-Meier Estimator using Histogram Data
chop.tess Subdivide a Window or Tessellation using a Set of Lines
kppm Fit cluster point process model
Linhom L-function Coerce Point Pattern to a Data Frame
distfun Distance Map as a Function
MultiStrauss The Multitype Strauss Point Process Model
Kdot Multitype K Function (i-to-any)
Gest Nearest Neighbour Distance Function G
dummy.ppm Extract Dummy Points Used to Fit a Point Process Model
as.hyperframe.ppx Extract coordinates and marks of multidimensional point pattern
eem Exponential Energy Marks
gridcentres Rectangular grid of points
as.ppp Convert Data To Class ppp
Extract.tess Extract or Replace Subset of Tessellation
Extract.fv Extract Subset of Function Values
betacells Beta Ganglion Cells in Cat Retina
Pairwise Generic Pairwise Interaction model
istat Point and Click Interface for Exploratory Analysis of Point Pattern
OrdThresh Ord's Interaction model
BadGey Hybrid Geyer Point Process Model
Jmulti Marked J Function
density.splitppp Kernel Smoothed Intensity of Split Point Pattern
markconnect Mark Connection Function
incircle Find Largest Circle Inside Window
Ldot.inhom Inhomogeneous Multitype L Dot Function
dilation Morphological Dilation
Jdot Multitype J Function (i-to-any)
crossdist.pp3 Pairwise distances between two different three-dimensional point patterns
bermantest Berman's Tests for Point Process Model
Extract.ppp Extract or Replace Subset of Point Pattern
infline Infinite Straight Lines
is.owin Test Whether An Object Is A Window
amacrine Hughes' Amacrine Cell Data
duplicated.ppp Determine Duplicated Points in a Spatial Point Pattern
box3 Three-Dimensional Box
Kmulti Marked K-Function
Extract.psp Extract Subset of Line Segment Pattern
anova.ppm ANOVA for Fitted Point Process Models
Extract.quad Subset of Quadrature Scheme
lansing Lansing Woods Point Pattern
connected Connected components of an image or window
pcf.ppp Pair Correlation Function of Point Pattern
bind.fv Combine Function Value Tables
adaptive.density Intensity Estimate of Point Pattern Using Tessellation
fitted.ppm Fitted Conditional Intensity for Point Process Model Convert Pixel Image to Data Frame
Kcross.inhom Inhomogeneous Cross K Function
clarkevans Clark and Evans Aggregation Index
alltypes Calculate Summary Statistic for All Types in a Multitype Point Pattern
kstest.ppm Kolmogorov-Smirnov Test for Point Process Model
as.hyperframe Convert Data to Hyperframe
crossing.psp Crossing Points of Two Line Segment Patterns
Geyer Geyer's Saturation Point Process Model
eval.fasp Evaluate Expression Involving Function Arrays
collapse.fv Collapse Several Function Tables into One
diameter.box3 Geometrical Calculations for Three-Dimensional Box
Jest Estimate the J-function
discretise Safely Convert Point Pattern Window to Binary Mask
iplot Point and Click Interface for Displaying a Point Pattern
distmap Distance Map
marktable Tabulate Marks in Neighbourhood of Every Point in a Point Pattern
fasp.object Function Arrays for Spatial Patterns
pairdist.ppx Pairwise Distances in Any Dimensions
ganglia Beta Ganglion Cells in Cat Retina, Old Version
is.multitype.ppp Test Whether A Point Pattern is Multitype
Lest L-function
heather Diggle's Heather Data
is.subset.owin Determine Whether One Window is Contained In Another
LennardJones The Lennard-Jones Potential
markvario Mark Variogram
disc Circular Window
expand.owin Expand Window By Factor Saturated Pairwise Interaction Point Process Family
Ord Generic Ord Interaction model
affine.owin Apply Affine Transformation To Window
lengths.psp Lengths of Line Segments
is.ppm Test Whether An Object Is A Fitted Point Process Model
deltametric Delta Metric
Lcross Multitype L-function (cross-type)
angles.psp Orientation Angles of Line Segments
methods.boxx Methods for Multi-Dimensional Box
ppx Multidimensional Space-Time Point Pattern
blur Apply Gaussian Blur to a Pixel Image
psp Create a Line Segment Pattern
crossdist Pairwise distances
concatxy Concatenate x,y Coordinate Vectors
ewcdf Weighted Empirical Cumulative Distribution Function
nnwhich.pp3 Nearest neighbours in three dimensions
convexhull Convex Hull
fv.object Data Frames of Function Values
gpc2owin Convert Polygonal Region into Different Format
compatible.fv Test Whether Two Function Objects Are Compatible
envelope.pp3 Simulation Envelopes of Summary Function for 3D Point Pattern
dirichlet Dirichlet Tessellation of Point Pattern
owin.object Class owin
nbfires Point Patterns of New Brunswick Forest Fires
clip.infline Intersect Infinite Straight Lines with a Window
copper Berman-Huntington points and lines data
as.mask Pixel Image Approximation of a Window Apply Function to Image Broken Down by Factor
pairdist.default Pairwise distances
humberside Humberside Data on Childhood Leukaemia and Lymphoma
harmonic Basis for Harmonic Functions
MultiStraussHard The Multitype/Hard Core Strauss Point Process Model Interpolate a Pixel Image
as.box3 Convert Data to Three-Dimensional Box
Poisson Poisson Point Process Model
erosion Morphological Erosion
chorley Chorley-Ribble Cancer Data
affine Apply Affine Transformation
diameter.owin Diameter of a Window
is.multitype Test whether Object is Multitype
nnclean Nearest Neighbour Clutter Removal
rMosaicSet Mosaic Random Set
plot.pp3 Plot a three-dimensional point pattern Integral of a Pixel Image Convex Hull of Points
model.frame.ppm Extract the Environment of a Point Process Model
marks Marks of a Point Pattern
cbind.hyperframe Combine Hyperframes by Rows or by Columns Plot a Pixel Image
finpines Pine saplings in Finland.
distmap.psp Distance Map of Line Segment Pattern
coords Extract Coordinates of a Spatial or Spatiotemporal Point Pattern
rcell Simulate Baddeley-Silverman Cell Process
coef.ppm Coefficients of Fitted Point Process Model
convexhull.xy Convex Hull of Points
rmh.ppm Simulate from a Fitted Point Process Model
bdist.tiles Distance to Boundary of Window Print News About Latest Version of Package
identify.ppp Identify Points in a Point Pattern
matclust.estK Fit the Matern Cluster Point Process by Minimum Contrast Kaplan-Meier and Reduced Sample Estimator using Histograms
is.ppp Test Whether An Object Is A Point Pattern
progressreport Print Progress Reports
crossdist.ppx Pairwise Distances Between Two Different Multi-Dimensional Point Patterns
delaunay Delaunay Triangulation of Point Pattern
default.dummy Generate a Default Pattern of Dummy Points
is.marked Test Whether Marks Are Present
density.psp Kernel Smoothing of Line Segment Pattern
plot.colourmap Plot a Colour Map
localK Neighbourhood density function
as.mask.psp Convert Line Segment Pattern to Binary Pixel Mask Convert to Pixel Image
centroid.owin Centroid of a window
density.ppp Kernel Smoothed Intensity of Point Pattern
is.marked.ppp Test Whether A Point Pattern is Marked
eval.fv Evaluate Expression Involving Functions
methods.box3 Methods for Three-Dimensional Box
spatstat-deprecated Deprecated spatstat functions
methods.ppx Methods for Multidimensional Space-Time Point Patterns
diameter.boxx Geometrical Calculations for Multi-Dimensional Box
nearest.raster.point Find Pixel Nearest to a Given Point
residuals.ppm Residuals for Fitted Point Process Model
lut Lookup Tables
distmap.ppp Distance Map of Point Pattern
murchison Murchison gold deposits
rknn Theoretical Distribution of Nearest Neighbour Distance
pointsOnLines Place Points Evenly Along Specified Lines
pcf.fasp Pair Correlation Function obtained from array of K functions
plot.ppm plot a Fitted Point Process Model
markcorrint Mark Correlation Integral
rotate.owin Rotate a Window
pairdist.ppp Pairwise distances
plot.splitppp Plot a List of Point Patterns
markcorr Mark Correlation Function
model.matrix.ppm Extract Design Matrix from Point Process Model
miplot Morishita Index Plot
dirichlet.weights Compute Quadrature Weights Based on Dirichlet Tessellation
nndist.psp Nearest neighbour distances between line segments
cells Biological Cells Point Pattern
bramblecanes Hutchings' Bramble Canes data Print Brief Details of an Image
nncross Nearest Neighbours Between Two Patterns
levelset Level Set of a Pixel Image
rmpoispp Generate Multitype Poisson Point Pattern
summary.ppm Summarizing a Fitted Point Process Model
runifpointx Generate N Uniform Random Points in Any Dimensions
is.empty Test Whether An Object Is Empty Evaluate Expression Involving Pixel Images
matchingdist Distance for a Point Pattern Matching
clickpoly Interactively Define a Polygon
rMaternI Simulate Matern Model I
quad.ppm Extract Quadrature Scheme Used to Fit a Point Process Model
nnwhich Nearest neighbour
rshift.psp Randomly Shift a Line Segment Pattern
fv Create a Function Value Table
nztrees New Zealand Trees Point Pattern
rescale.owin Convert Window to Another Unit of Length
hyperframe Hyper Data Frame
psp.object Class of Line Segment Patterns
rotate.psp Rotate a Line Segment Pattern
pixellate.owin Convert Window to Pixel Image
is.multitype.ppm Test Whether A Point Process Model is Multitype
longleaf Longleaf Pines Point Pattern
rmhmodel.ppm Interpret Fitted Model for Metropolis-Hastings Simulation. Test Whether An Object Is A Pixel Image
plot.hyperframe Plot Entries in a Hyperframe
cut.ppp Classify Points in a Point Pattern
rGaussPoisson Simulate Gauss-Poisson Process
logLik.ppm Log Likelihood for Poisson Point Process Model
midpoints.psp Midpoints of Line Segment Pattern Test Whether Two Pixel Images Are Compatible
nndist Nearest neighbour distances
lurking Lurking variable plot
plot.fasp Plot a Function Array
predict.kppm Prediction from a Fitted Cluster Point Process Model
rmhmodel.list Define Point Process Model for Metropolis-Hastings Simulation.
smooth.fv Apply Smoothing to Function Values
intersect.tess Intersection of Two Tessellations
npoints Number of Points in a Point Pattern
model.images Compute Images of Constructed Covariates
spruces Spruces Point Pattern
rmhcontrol Set Control Parameters for Metropolis-Hastings Algorithm.
discpartarea Area of Part of Disc
perimeter Perimeter Length of Window
rsyst Simulate systematic random point pattern
markstat Summarise Marks in Every Neighbourhood in a Point Pattern
ripras Estimate window from points alone
complement.owin Take Complement of a Window
eroded.areas Areas of Morphological Erosions
pcfcross Multitype pair correlation function (cross-type)
rmhstart Determine Initial State for Metropolis-Hastings Simulation.
fryplot Fry Plot of Point Pattern
rmhmodel.default Build Point Process Model for Metropolis-Hastings Simulation.
update.ppm Update a Fitted Point Process Model
pixellate Convert Spatial Object to Pixel Image Contour plot of pixel image
plot.psp plot a Spatial Line Segment Pattern
nnwhich.ppx Nearest Neighbours in Any Dimensions
ponderosa Ponderosa Pine Tree Point Pattern
simdat Simulated Point Pattern
pairdist.psp Pairwise distances between line segments
rpoisppOnLines Generate Poisson Point Pattern on Line Segments Infinite Order Interaction Family Histogram of Pixel Values in an Image
plot.ppp plot a Spatial Point Pattern
letterR Window in Shape of Letter R
lgcp.estK Fit a Log-Gaussian Cox Point Process by Minimum Contrast
pixellate.psp Convert Line Segment Pattern to Pixel Image
pcf.fv Pair Correlation Function obtained from K Function
nncorr Nearest-Neighbour Correlation Indices of Marked Point Pattern Perspective Plot of Pixel Image
pairdist.pp3 Pairwise distances in Three Dimensions
pcfinhom Inhomogeneous Pair Correlation Function
plot.owin Plot a Spatial Window
summary.owin Summary of a Spatial Window
rshift Random Shift Summarizing a Pixel Image
envelope Simulation Envelopes of Summary Function
rotate.ppp Rotate a Point Pattern
nndist.pp3 Nearest neighbour distances in three dimensions
pcfcross.inhom Inhomogeneous Multitype Pair Correlation Function (Cross-Type)
quadrats Divide Region into Quadrats
plot.tess Plot a tessellation
rThomas Simulate Thomas Process
plot.quad plot a Spatial Quadrature Scheme
plot.fv Plot Function Values
rthin Random Thinning
nndist.ppx Nearest Neighbour Distances in Any Dimensions
multiplicity.ppp Count Multiplicity of Duplicate Points
rshift.ppp Randomly Shift a Point Pattern
rshift.splitppp Randomly Shift a List of Point Patterns
runifdisc Generate N Uniform Random Points in a Disc
plot.kstest Plot a Spatial Kolmogorov-Smirnov Test
corners Corners of a rectangle
spatstat.options Internal Options in Spatstat Package
shift.owin Apply Vector Translation To Window Pairwise Interaction Process Family
inside.owin Test Whether Points Are Inside A Window
swedishpines Swedish Pines Point Pattern
effectfun Compute Fitted Effect of a Spatial Covariate in a Point Process Model
pppdist Distance Between Two Point Patterns
square Square Window
pairdist Pairwise distances
print.psp Print Brief Details of a Line Segment Pattern Dataset
opening Morphological Opening
with.fv Evaluate an Expression in a Function Table
rpoislinetess Poisson Line Tessellation
simulate.kppm Simulate a Fitted Cluster Point Process Model
quadrat.test.splitppp Chi-Squared Test of CSR for Split Point Pattern
raster.x Cartesian Coordinates for a Pixel Raster
update.kppm Update a Fitted Cluster Point Process Model
pp3 Three Dimensional Point Pattern
pppmatching Create a Point Matching
quadratcount Quadrat counting for a point pattern
im Create a Pixel Image Object
mincontrast Method of Minimum Contrast Scatterplot Matrix for Pixel Images
pixelquad Quadrature Scheme Based on Pixel Grid
qqplot.ppm Q-Q Plot of Residuals from Fitted Point Process Model
nearestsegment Find Line Segment Nearest to Each Point
is.convex Test Whether a Window is Convex
runifpoint3 Generate N Uniform Random Points in Three Dimensions
im.object Class of Images
owin Create a Window Ord Interaction Process Family
runifpoint Generate N Uniform Random Points
osteo Osteocyte Lacunae Data: Replicated Three-Dimensional Point Patterns
spatstat-package The Spatstat Package
predict.ppm Prediction from a Fitted Point Process Model
shift.ppp Apply Vector Translation To Point Pattern
rMatClust Simulate Matern Cluster Process
ppp.object Class of Point Patterns
unmark Remove Marks
project2segment Move Point To Nearest Line
summary.ppp Summary of a Point Pattern Dataset
summary.splitppp Summary of a Split Point Pattern
summary.quad Summarizing a Quadrature Scheme
rpoispp Generate Poisson Point Pattern
summary.listof Summary of a List of Things
suffstat Sufficient Statistic of Point Process Model
rStrauss Perfect Simulation of the Strauss Process
rMaternII Simulate Matern Model II
print.quad Print a Quadrature Scheme
runifpointOnLines Generate N Uniform Random Points On Line Segments
quad.object Class of Quadrature Schemes
pcfdot.inhom Inhomogeneous Multitype Pair Correlation Function (Type-i-To-Any-Type)
rjitter Random Perturbation of a Point Pattern
rescale.ppp Convert Point Pattern to Another Unit of Length
print.ppm Print a Fitted Point Process Model
rpoisppx Generate Poisson Point Pattern in Any Dimensions
quadscheme Generate a Quadrature Scheme from a Point Pattern
rNeymanScott Simulate Neyman-Scott Process
ppm Fit Point Process Model to Data
rlinegrid Generate grid of parallel lines with random displacement
scanpp Read Point Pattern From Data File
residualspaper Data and Code From JRSS Discussion Paper on Residuals
stieltjes Compute Integral of Function Against Cumulative Distribution
rotate Rotate
solutionset Evaluate Logical Expression Involving Pixel Images and Return Region Where Expression is True
reduced.sample Reduced Sample Estimator using Histogram Data
shift Apply Vector Translation
rescue.rectangle Convert Window Back To Rectangle
rescale Convert dataset to another unit of length
rmh.default Simulate Point Process Models using the Metropolis-Hastings Algorithm.
union.quad Union of Data and Dummy Points
redwoodfull California Redwoods Point Pattern (Entire Dataset)
urkiola Urkiola Woods Point Pattern
rescale.psp Convert Line Segment Pattern to Another Unit of Length
plot.kppm Plot a fitted cluster point process
intersect.owin Intersection, Union or Set Subtraction of Two Windows
plot.listof Plot a List of Things
smooth.ppp Spatial smoothing of observations at irregular points
ppp Create a Point Pattern
print.owin Print Brief Details of a Spatial Window
thomas.estK Fit the Thomas Point Process by Minimum Contrast Maximum, Minimum, Mean, Median, Range or Sum of Pixel Values in an Image
pcf Pair Correlation Function
quadrat.test Chi-Squared Dispersion Test for Spatial Point Pattern Based on Quadrat Counts
redwood California Redwoods Point Pattern (Ripley's Subset)
split.ppp Divide Point Pattern into Sub-patterns
plot.plotppm Plot a plotppm Object Created by plot.ppm
reach Interaction Distance of a Point Process
print.ppp Print Brief Details of a Point Pattern Dataset
methods.pp3 Methods for three-dimensional point patterns
pixellate.ppp Convert Point Pattern to Pixel Image Divide Image Into Sub-images
rmhmodel Define Point Process Model for Metropolis-Hastings Simulation.
periodify Make Periodic Copies of a Spatial Pattern
superimposePSP Superimpose Several Line Segment Patterns
trim.rectangle Cut margins from rectangle
quadratresample Resample a Point Pattern by Resampling Quadrats
vertices Vertices of a Window
vcov.ppm Variance-Covariance Matrix for a Fitted Point Process Model
spokes Spokes pattern of dummy points
rpoint Generate N Random Points
superimpose Superimpose Several Point Patterns
profilepl Profile Maximum Pseudolikelihood
with.hyperframe Evaluate an Expression in Each Row of a Hyperframe
rpoisline Generate Poisson Random Line Process
whist Weighted Histogram
rpoispp3 Generate Poisson Point Pattern in Three Dimensions Apply Vector Translation To Pixel Image
setcov Set Covariance of a Window Sample Quantiles of Pixel Image
selfcrossing.psp Crossing Points in a Line Segment Pattern
shift.psp Apply Vector Translation To Line Segment Pattern
summary.psp Summary of a Line Segment Pattern Dataset
rSSI Simulate Simple Sequential Inhibition
pcfdot Multitype pair correlation function (i-to-any)
simulate.ppm Simulate a Fitted Gibbs Point Process Model Convert Pixel Image to Another Unit of Length
plot.bermantest Plot Result of Berman Test
pppmatching.object Class of Point Matchings
rMosaicField Mosaic Random Field
ppm.object Class of Fitted Point Process Models
rstrat Simulate Stratified Random Point Pattern
rlabel Random Re-Labelling of Point Pattern
tiles Extract List of Tiles in a Tessellation
tess Create a Tessellation
unitname Name for Unit of Length
shapley Galaxies in the Shapley Supercluster
rmpoint Generate N Random Multitype Points
rmh Simulate point patterns using the Metropolis-Hastings algorithm.
unique.ppp Extract Unique Points from a Spatial Point Pattern
volume Volume of an Object
simplify.owin Approximate a Polygon by a Simpler Polygon
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Last month downloads


Date 2010-06-09
License GPL (>= 2)
Packaged 2010-06-09 04:47:42 UTC; adrian
Repository CRAN
Date/Publication 2010-06-09 12:29:20

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