R: Exploratory Data Analysis for the 'spatstat' Family

# Exploratory Data Analysis for the 'spatstat' Family

## Documentation for package ‘spatstat.explore’ version 3.8-1

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS

## Help Pages

A B C D E F G H I J K L M N O P Q R S T U V W Y misc

spatstat.explore-package | The spatstat.explore Package

## -- A --

adaptive.density | Adaptive Estimate of Intensity of Point Pattern
allstats | Calculate four standard summary functions of a point pattern.
alltypes | Calculate Summary Statistic for All Types in a Multitype Point Pattern
apply.ssf | Evaluate Expression in a Spatially Sampled Function
as.data.frame.envelope | Coerce Envelope to Data Frame
as.function.fv | Convert Function Value Table to Function
as.function.rhohat | Convert Function Table to Function
as.function.ssf | Methods for Spatially Sampled Functions
as.fv | Convert Data To Class fv
as.fv.bw.optim | Convert Data To Class fv
as.fv.data.frame | Convert Data To Class fv
as.fv.density | Convert Data To Class fv
as.fv.fasp | Convert Data To Class fv
as.fv.fv | Convert Data To Class fv
as.fv.matrix | Convert Data To Class fv
as.im.scan.test | Plot Result of Scan Test
as.im.ssf | Methods for Spatially Sampled Functions
as.owin.quadrattest | Convert Data To Class owin
as.ppp.ssf | Methods for Spatially Sampled Functions
as.tess.quadrattest | Convert Data To Tessellation
auc | Area Under ROC Curve for Point Pattern Data
auc.bermantest | Area Under ROC Curve for Point Pattern Data
auc.cdftest | Area Under ROC Curve for Point Pattern Data
auc.im | Area Under ROC Curve for Point Pattern Data
auc.ppp | Area Under ROC Curve for Point Pattern Data
auc.roc | Area Under ROC Curve for Point Pattern Data

## -- B --

berman.test | Berman's Tests for Point Process Model
berman.test.ppp | Berman's Tests for Point Process Model
bias.envelope | Pointwise Statistics on an Envelope Object
bind.fv | Combine Function Value Tables
bits.envelope | Global Envelopes for Balanced Independent Two-Stage Test
bits.test | Balanced Independent Two-Stage Monte Carlo Test
blur | Apply Gaussian Blur to a Pixel Image
blurHeat | Diffusion Blur
blurHeat.im | Diffusion Blur
boyce | Boyce Index
bw.abram.ppp | Abramson's Adaptive Bandwidths For Spatial Point Pattern
bw.bdh | Adjust Bandwidth Selection Rule to Account for Inhomogeneity
bw.CvL | Cronie and van Lieshout's Criterion for Bandwidth Selection for Kernel Density
bw.CvL.adaptive | Select Adaptive Bandwidth for Kernel Estimation Using Cronie-Van Lieshout Criterion
bw.CvLHeat | Bandwidth Selection for Diffusion Smoother by Cronie-van Lieshout Rule
bw.diggle | Cross Validated Bandwidth Selection for Kernel Density
bw.fiksel | Stoyan's and Fiksel's Rules of Thumb for Bandwidth for Estimating Pair Correlation
bw.frac | Bandwidth Selection Based on Window Geometry
bw.optim.object | Class of Optimized Bandwidths
bw.pcf | Cross Validated Bandwidth Selection for Pair Correlation Function
bw.pcfinhom | Cross Validated Bandwidth Selection for Inhomogeneous Pair Correlation Function
bw.ppl | Likelihood Cross Validation Bandwidth Selection for Kernel Density
bw.pplHeat | Bandwidth Selection for Diffusion Smoother by Likelihood Cross-Validation
bw.relrisk | Cross Validated Bandwidth Selection for Relative Risk Estimation
bw.relrisk.ppp | Cross Validated Bandwidth Selection for Relative Risk Estimation
bw.relriskHeatppp | Bandwidth Selection for Relative Risk using Diffusion
bw.scott | Scott's Rule for Bandwidth Selection for Kernel Density
bw.scott.iso | Scott's Rule for Bandwidth Selection for Kernel Density
bw.smoothppp | Cross Validated Bandwidth Selection for Spatial Smoothing
bw.stoyan | Stoyan's and Fiksel's Rules of Thumb for Bandwidth for Estimating Pair Correlation

## -- C --

cbind.fv | Combine Function Value Tables
cdf.test | Spatial Distribution Test for Point Pattern or Point Process Model
cdf.test.ppp | Spatial Distribution Test for Point Pattern or Point Process Model
circdensity | Density Estimation for Circular Data
clarkevans | Clark and Evans Aggregation Index
clarkevans.test | Clark and Evans Test
clusterset | Allard-Fraley Estimator of Cluster Feature
collapse.anylist | Collapse Several Function Tables into One
collapse.fv | Collapse Several Function Tables into One
compatible.fasp | Test Whether Function Arrays Are Compatible
compatible.fv | Test Whether Function Objects Are Compatible
compileCDF | Generic Calculation of Cumulative Distribution Function of Distances
compileK | Generic Calculation of K Function and Pair Correlation Function
compilepcf | Generic Calculation of K Function and Pair Correlation Function
Complex.fasp | S3 Group Generic Methods for Function Arrays
Complex.fv | S3 Group Generic Methods for Function Tables
contour.ssf | Plot a Spatially Sampled Function
cor.im | Covariance and Correlation between Images
cov.im | Covariance and Correlation between Images
coxmap | Identify Dense and Sparse Regions in a Point Pattern
coxmap.ppp | Identify Dense and Sparse Regions in a Point Pattern

## -- D --

dclf.progress | Progress Plot of Test of Spatial Pattern
dclf.sigtrace | Significance Trace of Cressie-Loosmore-Ford or Maximum Absolute Deviation Test
dclf.test | Diggle-Cressie-Loosmore-Ford and Maximum Absolute Deviation Tests
density.ppp | Kernel Smoothed Intensity of Point Pattern
density.ppplist | Kernel Smoothed Intensity of Split Point Pattern
density.psp | Kernel Smoothing of Line Segment Pattern
density.splitppp | Kernel Smoothed Intensity of Split Point Pattern
densityAdaptiveKernel.ppp | Adaptive Kernel Estimate of Intensity of Point Pattern
densityAdaptiveKernel.ppplist | Adaptive Kernel Estimate of Intensity for Split Point Pattern
densityAdaptiveKernel.splitppp | Adaptive Kernel Estimate of Intensity for Split Point Pattern
densityfun | Kernel Estimate of Intensity as a Spatial Function
densityfun.ppp | Kernel Estimate of Intensity as a Spatial Function
densityHeat | Diffusion Estimate of Point Pattern Intensity
densityHeat.ppp | Diffusion Estimate of Point Pattern Intensity
densityVoronoi | Intensity Estimate of Point Pattern Using Voronoi-Dirichlet Tessellation
densityVoronoi.ppp | Intensity Estimate of Point Pattern Using Voronoi-Dirichlet Tessellation
deriv.fv | Calculate Derivative of Function Values
dg.envelope | Global Envelopes for Dao-Genton Test
dg.progress | Progress Plot of Dao-Genton Test of Spatial Pattern
dg.sigtrace | Significance Trace of Dao-Genton Test
dg.test | Dao-Genton Adjusted Goodness-Of-Fit Test
dimhat | Estimate Dimension of Central Subspace
distcdf | Distribution Function of Interpoint Distance
domain.quadrattest | Extract the Domain of any Spatial Object

## -- E --

edge.Ripley | Ripley's Isotropic Edge Correction
edge.Trans | Translation Edge Correction
Emark | Diagnostics for random marking
envelope | Simulation Envelopes of Summary Function
envelope.envelope | Recompute Envelopes
envelope.pp3 | Simulation Envelopes of Summary Function for 3D Point Pattern
envelope.ppp | Simulation Envelopes of Summary Function
envelopeArray | Array of Simulation Envelopes of Summary Function
eval.fasp | Evaluate Expression Involving Function Arrays
eval.fv | Evaluate Expression Involving Functions

## -- F --

F3est | Empty Space Function of a Three-Dimensional Point Pattern
fasp.object | Function Arrays for Spatial Patterns
Fest | Estimate the Empty Space Function or its Hazard Rate
Fhazard | Estimate the Empty Space Function or its Hazard Rate
Finhom | Inhomogeneous Empty Space Function
Fmulti.inhom | Inhomogeneous Marked F-Function
FmultiInhom | Inhomogeneous Marked F-Function
formula.fv | Extract or Change the Plot Formula for a Function Value Table
formula<- | Extract or Change the Plot Formula for a Function Value Table
formula<-.fv | Extract or Change the Plot Formula for a Function Value Table
fryplot | Fry Plot of Point Pattern
frypoints | Fry Plot of Point Pattern
fv | Create a Function Value Table
fv.object | Function Value Table
fvnames | Abbreviations for Groups of Columns in Function Value Table
fvnames<- | Abbreviations for Groups of Columns in Function Value Table

## -- G --

G3est | Nearest Neighbour Distance Distribution Function of a Three-Dimensional Point Pattern
Gcross | Multitype Nearest Neighbour Distance Function (i-to-j)
Gcross.inhom | Inhomogeneous Multitype G Cross Function
Gdot | Multitype Nearest Neighbour Distance Function (i-to-any)
Gdot.inhom | Inhomogeneous Multitype G Dot Function
Gest | Nearest Neighbour Distance Function G
Gfox | Foxall's Distance Functions
Ginhom | Inhomogeneous Nearest Neighbour Function
Gmulti | Marked Nearest Neighbour Distance Function
Gmulti.inhom | Inhomogeneous Marked G-Function
GmultiInhom | Inhomogeneous Marked G-Function

## -- H --

harmonise.fv | Make Function Tables Compatible
harmonize.fv | Make Function Tables Compatible
Hest | Spherical Contact Distribution Function
hopskel | Hopkins-Skellam Test
hopskel.test | Hopkins-Skellam Test
hotbox | Heat Kernel for a Two-Dimensional Rectangle

## -- I --

idw | Inverse-distance weighted smoothing of observations at irregular points
Iest | Estimate the I-function
image.ssf | Plot a Spatially Sampled Function
increment.fv | Increments of a Function
integral.fv | Compute Integral of Function Object
integral.ssf | Methods for Spatially Sampled Functions
ISB.envelope | Mean Integrated Squared Error on an Envelope Object
ISE.envelope | Integrated Squared Error on an Envelope Object
IV.envelope | Mean Integrated Squared Error on an Envelope Object

## -- J --

Jcross | Multitype J Function (i-to-j)
Jcross.inhom | Inhomogeneous Multitype J function (i-to-j)
Jdot | Multitype J Function (i-to-any)
Jdot.inhom | Inhomogeneous Multitype J function (i-to-any)
Jest | Estimate the J-function
Jfox | Foxall's Distance Functions
Jinhom | Inhomogeneous J-function
Jmulti | Marked J Function
Jmulti.inhom | Inhomogeneous Marked J-Function

## -- K --

K3est | K-function of a Three-Dimensional Point Pattern
Kcross | Multitype K Function (Cross-type)
Kcross.inhom | Inhomogeneous Cross K Function
Kdot | Multitype K Function (i-to-any)
Kdot.inhom | Inhomogeneous Multitype K Dot Function
Kest | K-function
Kest.fft | K-function using FFT
Kinhom | Inhomogeneous K-function
Kmark | Mark-Weighted K Function
Kmeasure | Reduced Second Moment Measure
Kmulti | Marked K-Function
Kmulti.inhom | Inhomogeneous Marked K-Function
Kscaled | Locally Scaled K-function
Ksector | Sector K-function

## -- L --

laslett | Laslett's Transform
Lcross | Multitype L-function (cross-type)
Lcross.inhom | Inhomogeneous Cross Type L Function
Ldot | Multitype L-function (i-to-any)
Ldot.inhom | Inhomogeneous Multitype L Dot Function
Lest | L-function
Linhom | Inhomogeneous L-function
localK | Neighbourhood density function
localKcross | Local Multitype K Function (Cross-Type)
localKcross.inhom | Inhomogeneous Multitype K Function
localKdot | Local Multitype K Function (Dot-Type)
localKinhom | Inhomogeneous Neighbourhood Density Function
localL | Neighbourhood density function
localLcross | Local Multitype K Function (Cross-Type)
localLcross.inhom | Inhomogeneous Multitype K Function
localLdot | Local Multitype K Function (Dot-Type)
localLinhom | Inhomogeneous Neighbourhood Density Function
localpcf | Local pair correlation function
localpcfinhom | Local pair correlation function
lohboot | Bootstrap Confidence Bands for Summary Function
Lscaled | Locally Scaled K-function

## -- M --

mad.progress | Progress Plot of Test of Spatial Pattern
mad.sigtrace | Significance Trace of Cressie-Loosmore-Ford or Maximum Absolute Deviation Test
mad.test | Diggle-Cressie-Loosmore-Ford and Maximum Absolute Deviation Tests
markconnect | Mark Connection Function
markcorr | Mark Correlation Function
markcorrint | Mark-Weighted K Function
markcrosscorr | Mark Cross-Correlation Function
markequal | Mark Equality Function
markmarkscatter | Mark-Mark Scatter Plot
markmean | Spatial smoothing of observations at irregular points
marks.ssf | Methods for Spatially Sampled Functions
marks<-.ssf | Methods for Spatially Sampled Functions
marktable | Tabulate Marks in Neighbourhood of Every Point in a Point Pattern
markvar | Spatial smoothing of observations at irregular points
markvario | Mark Variogram
Math.fasp | S3 Group Generic Methods for Function Arrays
Math.fv | S3 Group Generic Methods for Function Tables
max.ssf | Methods for Spatially Sampled Functions
mctest.progress | Progress Plot of Test of Spatial Pattern
mctest.sigtrace | Significance Trace of Cressie-Loosmore-Ford or Maximum Absolute Deviation Test
methods.rho2hat | Methods for Intensity Functions of Two Spatial Covariates
methods.rhohat | Methods for Intensity Functions of Spatial Covariate
methods.ssf | Methods for Spatially Sampled Functions
min.ssf | Methods for Spatially Sampled Functions
miplot | Morisita Index Plot
MISE.envelope | Mean Integrated Squared Error on an Envelope Object

## -- N --

nearest.neighbour | Nearest Neighbour Distance Function G
nnclean | Nearest Neighbour Clutter Removal
nnclean.pp3 | Nearest Neighbour Clutter Removal
nnclean.ppp | Nearest Neighbour Clutter Removal
nncorr | Nearest-Neighbour Correlation Indices of Marked Point Pattern
nncount | Nearest Neighbour Cross-Type Occurrence Count Function
nndensity | Estimate Intensity of Point Pattern Using Nearest Neighbour Distances
nndensity.ppp | Estimate Intensity of Point Pattern Using Nearest Neighbour Distances
nnequal | Nearest Neighbour Type-Equality Function
nnmean | Nearest-Neighbour Correlation Indices of Marked Point Pattern
nnorient | Nearest Neighbour Orientation Distribution
nnvario | Nearest-Neighbour Correlation Indices of Marked Point Pattern

## -- O --

Ops.fasp | S3 Group Generic Methods for Function Arrays
Ops.fv | S3 Group Generic Methods for Function Tables

## -- P --

pairMean | Mean of a Function of Interpoint Distance
pairorient | Point Pair Orientation Distribution
pairs.im | Scatterplot Matrix for Pixel Images
panel.contour | Panel Plots using Colour Image or Contour Lines
panel.histogram | Panel Plots using Colour Image or Contour Lines
panel.image | Panel Plots using Colour Image or Contour Lines
pcf | Pair Correlation Function
pcf.fasp | Pair Correlation Function obtained from array of K functions
pcf.fv | Pair Correlation Function obtained from K Function
pcf.ppp | Pair Correlation Function of Point Pattern
pcf3est | Pair Correlation Function of a Three-Dimensional Point Pattern
pcfcross | Multitype pair correlation function (cross-type)
pcfcross.inhom | Inhomogeneous Multitype Pair Correlation Function (Cross-Type)
pcfdot | Multitype pair correlation function (i-to-any)
pcfdot.inhom | Inhomogeneous Multitype Pair Correlation Function (Type-i-To-Any-Type)
pcfinhom | Inhomogeneous Pair Correlation Function
pcfmulti | Marked pair correlation function
pcfmulti.inhom | Inhomogeneous Multitype Pair Correlation Function
plot.bermantest | Plot Result of Berman Test
plot.cdftest | Plot a Spatial Distribution Test
plot.envelope | Plot a Simulation Envelope
plot.fasp | Plot a Function Array
plot.fv | Plot Function Values
plot.laslett | Plot Laslett Transform
plot.quadrattest | Display the result of a quadrat counting test.
plot.rho2hat | Methods for Intensity Functions of Two Spatial Covariates
plot.rhohat | Methods for Intensity Functions of Spatial Covariate
plot.scan.test | Plot Result of Scan Test
plot.ssf | Plot a Spatially Sampled Function
plot.studpermutest | Plot a Studentised Permutation Test
pool | Pool Data
pool.anylist | Pool Data from a List of Objects
pool.envelope | Pool Data from Several Envelopes
pool.fasp | Pool Data from Several Function Arrays
pool.fv | Pool Several Functions
pool.quadrattest | Pool Several Quadrat Tests
pool.rat | Pool Data from Several Ratio Objects
PPversion | Transform a Function into its P-P or Q-Q Version
predict.rho2hat | Methods for Intensity Functions of Two Spatial Covariates
predict.rhohat | Methods for Intensity Functions of Spatial Covariate
print.rho2hat | Methods for Intensity Functions of Two Spatial Covariates
print.rhohat | Methods for Intensity Functions of Spatial Covariate
print.ssf | Methods for Spatially Sampled Functions
ptwise.envelope | Pointwise Statistics on an Envelope Object

## -- Q --

QQversion | Transform a Function into its P-P or Q-Q Version
quadrat.test | Dispersion Test for Spatial Point Pattern Based on Quadrat Counts
quadrat.test.ppp | Dispersion Test for Spatial Point Pattern Based on Quadrat Counts
quadrat.test.quadratcount | Dispersion Test for Spatial Point Pattern Based on Quadrat Counts
quadrat.test.splitppp | Dispersion Test of CSR for Split Point Pattern Based on Quadrat Counts

## -- R --

radcumint | Radial Cumulative Integral
range.ssf | Methods for Spatially Sampled Functions
rat | Ratio object
rectcontact | Contact Distribution Function using Rectangular Structuring Element
reload.or.compute | Perform Computations or Retrieve Results From File
relrisk | Estimate of Spatially-Varying Relative Risk
relrisk.ppp | Nonparametric Estimate of Spatially-Varying Relative Risk
relriskHeat | Diffusion Estimate of Conditional Probabilities
relriskHeat.ppp | Diffusion Estimate of Conditional Probabilities
rho2hat | Smoothed Relative Density of Pairs of Covariate Values
rhohat | Nonparametric Estimate of Intensity as Function of a Covariate
rhohat.ppp | Nonparametric Estimate of Intensity as Function of a Covariate
rhohat.quad | Nonparametric Estimate of Intensity as Function of a Covariate
rmax.Ripley | Ripley's Isotropic Edge Correction
rmax.Trans | Translation Edge Correction
RMSE.envelope | Pointwise Statistics on an Envelope Object
roc | Receiver Operating Characteristic
roc.bermantest | Receiver Operating Characteristic
roc.cdftest | Receiver Operating Characteristic
roc.im | Receiver Operating Characteristic
roc.ppp | Receiver Operating Characteristic
roc.rhohat | Receiver Operating Characteristic
rose | Rose Diagram
rose.default | Rose Diagram
rose.density | Rose Diagram
rose.fv | Rose Diagram
rose.histogram | Rose Diagram
rotmean | Rotational Average of a Pixel Image

## -- S --

scan.test | Spatial Scan Test
scanLRTS | Likelihood Ratio Test Statistic for Scan Test
sdr | Sufficient Dimension Reduction
sdr.ppp | Sufficient Dimension Reduction
sdrPredict | Compute Predictors from Sufficient Dimension Reduction
segregation.test | Test of Spatial Segregation of Types
segregation.test.ppp | Test of Spatial Segregation of Types
sharpen | Data Sharpening of Point Pattern
sharpen.ppp | Data Sharpening of Point Pattern
simulate.rhohat | Methods for Intensity Functions of Spatial Covariate
Smooth | Spatial smoothing of data
Smooth.fv | Apply Smoothing to Function Values
Smooth.im | Apply Gaussian Blur to a Pixel Image
Smooth.ppp | Spatial smoothing of observations at irregular points
Smooth.ssf | Smooth a Spatially Sampled Function
Smoothfun | Smooth Interpolation of Marks as a Spatial Function
Smoothfun.ppp | Smooth Interpolation of Marks as a Spatial Function
SmoothHeat | Spatial Smoothing of Data by Diffusion
SmoothHeat.im | Diffusion Blur
SmoothHeat.ppp | Spatial Smoothing of Observations using Diffusion Estimate of Density
spatcov | Estimate the Spatial Covariance Function of a Random Field
spatialcdf | Spatial Cumulative Distribution Function
SpatialMedian | Spatially Weighted Median or Quantile
SpatialMedian.ppp | Spatially Weighted Median of Values at Points
SpatialQuantile | Spatially Weighted Median or Quantile
SpatialQuantile.ppp | Spatially Weighted Quantile of Values at Points
spatstat.explore | The spatstat.explore Package
ssf | Spatially Sampled Function
stienen | Stienen Diagram
stienenSet | Stienen Diagram
studpermu.test | Studentised Permutation Test
subspaceDistance | Distance Between Linear Spaces
Summary.fasp | S3 Group Generic Methods for Function Arrays
Summary.fv | S3 Group Generic Methods for Function Tables
summary.ssf | Methods for Spatially Sampled Functions

## -- T --

thresholdCI | Confidence Interval for Threshold of Numerical Predictor
thresholdSelect | Select Threshold to Convert Numerical Predictor to Binary Predictor
tolcon | Tolerance Contours for Relative Risk
transect.im | Pixel Values Along a Transect
Tstat | Third order summary statistic

## -- U --

unmark.ssf | Methods for Spatially Sampled Functions

## -- V --

varblock | Estimate Variance of Summary Statistic by Subdivision
Vmark | Diagnostics for random marking

## -- W --

Window.quadrattest | Extract Window of Spatial Object
with.fv | Evaluate an Expression in a Function Table
with.ssf | Evaluate Expression in a Spatially Sampled Function

## -- Y --

youden | Youden Statistic

## -- misc --

$<-.fv | Extract or Replace Subset of Function Values
[.fasp | Extract Subset of Function Array
[.fv | Extract or Replace Subset of Function Values
[.ssf | Subset of spatially sampled function
[<-.fv | Extract or Replace Subset of Function Values