Nearest Neighbor Methods for Spatial Patterns

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Documentation for package ‘nnspat’ version 0.1.2

• DESCRIPTION file.

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A B C D E F I K L M N O P Q R S T V W X Z misc

nnspat-package

nnspat: A package for NN Methods and Their Use in Testing Spatial Patterns

-- A --

aij.mat	Aij matrices for computation of Moments of Cuzick and Edwards T_k Test statistic
aij.nonzero	Aij matrices for computation of Moments of Cuzick and Edwards T_k Test statistic
aij.theta	Closeness or Proximity Matrix for Tango's Spatial Clustering Tests
asycovTkTl	Asymptotic Covariance between T_k and T_l Values
asyvarTk	Asymptotic Variance of Cuzick and Edwards T_k Test statistic

-- B --

base.class.spec	Base Class-specific Chi-square Tests based on NNCTs
base.class.spec.ct	Base Class-specific Chi-square Tests based on NNCTs
bvnorm.pdf	pdf of the Bivariate Normal Distribution

-- C --

cell.spec	Cell-specific Z Tests of Segregation for NNCTs
cell.spec.ct	Cell-specific Z Tests of Segregation for NNCTs
cell.spec.ss	Pielou's Cell-specific Segregation Test with Normal Approximation (for Sparse Sampling)
cell.spec.ss.ct	Pielou's Cell-specific Segregation Test with Normal Approximation (for Sparse Sampling)
cellsTij	Entries for the Types I-IV cell-specific tests
ceTk	Cuzick and Edwards T_k Test statistic
ceTkinv	Cuzick and Edwards T_k^{inv} Test statistic
ceTrun	Cuzick and Edwards T_{run} Test statistic
class.spec	Class-specific Chi-square Tests based on NNCTs
class.spec.ct	Class-specific Chi-square Tests based on NNCTs
classirest	Functions for one versus rest type labeling
col.sum	Functions for row and column sums of a matrix
correct.cf1	Correction Matrices for the Covariance Matrix of NNCT entries
correct.cf2	Correction Matrices for the Covariance Matrix of NNCT entries
cov.2cells	Auxiliary Functions for Computing Covariances Between Cell Counts in the TCT
cov.2cols	Auxiliary Functions for Computing Covariances Between Cell Counts in the TCT
cov.cell.col	Auxiliary Functions for Computing Covariances Between Cell Counts in the TCT
cov.nnct	Covariance Matrix of the Cell Counts in an NNCT
cov.nnsym	Covariance Matrix of the Differences of the Off-Diagonal Cell Counts in an NNCT
cov.seg.coeff	Covariance Matrix of Segregation Coefficients in a Multi-class Case
cov.tct	Covariance Matrix of the Entries of the Type I-IV TCTs
cov.tct3	Functions for Covariances of the Entries of the Types I, III and IV TCTs
cov.tctI	Functions for Covariances of the Entries of the Types I, III and IV TCTs
cov.tctIII	Functions for Covariances of the Entries of the Types I, III and IV TCTs
cov.tctIV	Functions for Covariances of the Entries of the Types I, III and IV TCTs
covCiCj	Auxiliary Functions for Computing Covariances Between Cell Counts in the TCT
covNii	Covariance Matrix of the Self Entries in a Species Correspondence Contingency Table (SCCT)
covNii.ct	Covariance Matrix of the Self Entries in a Species Correspondence Contingency Table (SCCT)
covNijCk	Auxiliary Functions for Computing Covariances Between Cell Counts in the TCT
covNrow2col	Conversion of the Covariance Matrix of the Row-wise Vectorized Cell Counts to Column-wise Vectorized Cell Counts in an NNCT
covTcomb	Covariance matrix for T_k values in 'Tcomb'
covTkTl	Finite Sample Covariance between T_k and T_l Values

-- D --

dist.std.data	Interpoint Distance Matrix for Standardized Data
dist2full	Converts a lower triangular distance matrix to a full distance matrix

-- E --

euc.dist	The Euclidean distance between two vectors, matrices, or data frames
EV.Nii	Expected Values of the Self Entries in a Species Correspondence Contingency Table (SCCT)
EV.nnct	Expected Values of the Cell Counts in NNCT
EV.rct	Expected Values of the Cell Counts in RCT
EV.Tcomb	Expected Value for Cuzick & Edwards T_{comb} Test Statistic
EV.tct	Expected Values of the Types I-IV cell-specific tests
EV.tctI	Expected Values of the Type I cell-specific tests
EV.Tk	Expected Value for Cuzick and Edwards T_k Test statistic
EV.Tkaij	Expected Value for Cuzick and Edwards T_k Test statistic
EV.Tkinv	Expected Value of Cuzick and Edwards T_k^{inv} Test statistic
EV.Trun	Expected Value for Cuzick and Edwards T_{run} Test statistic
EV.Trun.alt	Expected Value for Cuzick and Edwards T_{run} Test statistic
exact.nnct	Exact version of Pearson's chi-square test on NNCTs
exact.pval1s	p-value correction to the one-sided version of exact NNCT test
exact.pval2s	p-value correction to the two-sided version of exact NNCT test

-- F --

funs.auxcovtct	Auxiliary Functions for Computing Covariances Between Cell Counts in the TCT
funs.base.class.spec	Base Class-specific Chi-square Tests based on NNCTs
funs.cell.spec.ss	Pielou's Cell-specific Segregation Test with Normal Approximation (for Sparse Sampling)
funs.class.spec	Class-specific Chi-square Tests based on NNCTs
funs.covNii	Covariance Matrix of the Self Entries in a Species Correspondence Contingency Table (SCCT)
funs.covtct	Functions for Covariances of the Entries of the Types I, III and IV TCTs
funs.kNNdist	Functions for the k^{th} and 'k' NN distances
funs.kNNdist2cl	Functions for the k^{th} and 'k' NN distances
funs.overall.nnct	Dixon's Overall Test of Segregation for NNCT
funs.overall.seg	Overall Segregation Tests for NNCTs
funs.overall.tct	Types I-IV Overall Tests of Segregation for NNCT
funs.pijPij	The functions for probability of selecting a number of points from respective classes
funs.scct	Species Correspondence Contingency Table (SCCT)
funs.seg.coeff	Pielou's Segregation Coefficients for NNCTs
funs.varNii	Variances of the Self Entries in a Species Correspondence Contingency Table (SCCT)
funs.vartct	Functions for Variances of Cell Counts in the Types I, III and IV TCTs
funsAijmat	Aij matrices for computation of Moments of Cuzick and Edwards T_k Test statistic
funsC_MI_II	Correction Matrices for the Covariance Matrix of NNCT entries
funsExpTk	Expected Value for Cuzick and Edwards T_k Test statistic
funsExpTrun	Expected Value for Cuzick and Edwards T_{run} Test statistic
funsNNclass.spec	NN Class-specific Chi-square Tests based on NNCTs
funsN_I_II	Correction Matrices for the NNCT entries
funsOnevsRest	Functions for one versus rest type labeling
funsPseg.ss	Pielou's Overall Test of Segregation for NNCT (for Sparse Sampling)
funsQandR	Functions for the number of shared NNs, shared NN vector, and the number of reflexive NNs
funsRowColSums	Functions for row and column sums of a matrix
funsVarTk	Variance of Cuzick and Edwards T_k Test statistic
funsVarTrun	Variance of Cuzick and Edwards T_{run} Test statistic
funsW345values	W_k values for Tango's T test statistic
funsXsq.nnref	Reflexivity Test with Chi-square Approximation
funsXsq.nnsym.dx	Dixon's NN Symmetry Test with Chi-square Approximation for multiple classes
funsXsq.nnsym.ss	Pielou's First Type of NN Symmetry Test with Chi-square Approximation for multiple classes (for Sparse Sampling)
funsXsq.seg.coeff	Chi-square Test for Segregation Coefficients
funsXsq.spec.cor	Overall Species Correspondence Test with Chi-square Approximation
funsZcell.nnct	Dixon's Cell-specific Z Tests of Segregation for NNCT
funsZcell.nnct.pval	p-values for Cell-specific Z Test Statistics for NNCT
funsZcell.spec	Cell-specific Z Tests of Segregation for NNCTs
funsZcell.tct	Types I-IV Cell-specific Z Tests of Segregation based on NNCTs
funsZdir.nnct	Directional Segregation Test for Two Classes with Normal Approximation
funsZdir.nnct.ss	Directional Segregation Test for Two Classes with Normal Approximation (for Sparse Sampling)
funsZmixed.nonref	Mixed-Non-Reflexivity Test with Normal Approximation
funsZnnref	Z Tests for NN Reflexivity
funsZnnself	Self-Reflexivity Tests with Normal Approximation
funsZnnself.sum	Cumulative Species Correspondence Test with Normal Approximation
funsZnnsym.dx	Dixon's Pairwise NN Symmetry Test with Normal Approximation
funsZnnsym.ss	Pielou's Pairwise NN Symmetry Test with Normal Approximation (for Sparse Sampling)
funsZnnsym2cl.dx	Dixon's NN Symmetry Test with Normal Approximation for Two Classes
funsZnnsym2cl.ss	Pielou's First Type of NN Symmetry Test with Normal Approximation for Two Classes (for Sparse Sampling)
funsZseg.coeff	Z Tests for Segregation Coefficients
funsZsegind	Z Tests for Segregation Indices
funsZself.ref	Self-Reflexivity Test with Normal Approximation
funsZTkinv	Z-Test for Cuzick and Edwards T_k^{inv} statistic

-- I --

ind.nnsym	Index Matrix for Computing the Covariance of Dixon's Overall NN Symmetry Test
ind.seg.coeff	Index Matrix for Computing the Covariance of Segregation Coefficients
ipd.mat	Interpoint Distance Matrix
ipd.mat.euc	Euclidean Interpoint Distance Matrix

-- K --

kNN	Finding the indices of the 'k' NNs of a given point
kNNdist	Functions for the k^{th} and 'k' NN distances
kNNdist2cl	Functions for the k^{th} and 'k' NN distances
kthNNdist	Functions for the k^{th} and 'k' NN distances
kthNNdist2cl	Functions for the k^{th} and 'k' NN distances

-- L --

lab.onevsrest

Functions for one versus rest type labeling

-- M --

mat2vec	Conversion of a Matrix to a Vector
matrix.sqrt	Square root of a matrix

-- N --

Ninv	Vector of Shared NNs and Number of Reflexive NNs
NN	Finding the index of the NN of a given point
NN.class.spec	NN Class-specific Chi-square Tests based on NNCTs
NN.class.spec.ct	NN Class-specific Chi-square Tests based on NNCTs
nnct	Nearest Neighbor Contingency Table (NNCT)
nnct.boot.dis	Bootstrap Nearest Neighbor Contingency Table (NNCT)
nnct.cr1	Correction Matrices for the NNCT entries
nnct.cr2	Correction Matrices for the NNCT entries
nnct.sub	Nearest Neighbor Contingency Table (NNCT) with (only) base points restricted to a subsample
NNdist	Distances between subjects and their NNs
NNdist2cl	Distances between subjects from class i and their NNs from class j
nnspat	nnspat: A package for NN Methods and Their Use in Testing Spatial Patterns
NNsub	Finding the index of the NN of a given point among a subset of points
Nt.def	N_t Value (found with the definition formula)
Ntkl	N_{tkl} Value

-- O --

overall.nnct	Dixon's Overall Test of Segregation for NNCT
overall.nnct.ct	Dixon's Overall Test of Segregation for NNCT
overall.seg	Overall Segregation Tests for NNCTs
overall.seg.ct	Overall Segregation Tests for NNCTs
overall.tct	Types I-IV Overall Tests of Segregation for NNCT
overall.tct.ct	Types I-IV Overall Tests of Segregation for NNCT

-- P --

P11	The functions for probability of selecting a number of points from respective classes
p11	The functions for probability of selecting a number of points from respective classes
P111	The functions for probability of selecting a number of points from respective classes
p111	The functions for probability of selecting a number of points from respective classes
P1111	The functions for probability of selecting a number of points from respective classes
p1111	The functions for probability of selecting a number of points from respective classes
P1112	The functions for probability of selecting a number of points from respective classes
p1112	The functions for probability of selecting a number of points from respective classes
P112	The functions for probability of selecting a number of points from respective classes
p112	The functions for probability of selecting a number of points from respective classes
P1122	The functions for probability of selecting a number of points from respective classes
p1122	The functions for probability of selecting a number of points from respective classes
P1123	The functions for probability of selecting a number of points from respective classes
p1123	The functions for probability of selecting a number of points from respective classes
P12	The functions for probability of selecting a number of points from respective classes
p12	The functions for probability of selecting a number of points from respective classes
p122	The functions for probability of selecting a number of points from respective classes
p1223	The functions for probability of selecting a number of points from respective classes
P123	The functions for probability of selecting a number of points from respective classes
p123	The functions for probability of selecting a number of points from respective classes
P1234	The functions for probability of selecting a number of points from respective classes
p1234	The functions for probability of selecting a number of points from respective classes
pairwise.lab	Keeping the pair of the specified labels in the data
pick.min.max	Smallest and Largest Distances in a Distance Matrix
pk	Probability of 'k' items selected from the class with size n_1
plot.Clusters	Plot a 'Clusters' object
plot.SpatPatterns	Plot a 'SpatPatterns' object
print.cellhtest	Print a summary of a 'cellhtest' object
print.Chisqtest	Print a summary of a 'Chisqtest' object
print.classhtest	Print a summary of a 'classhtest' object
print.Clusters	Print a 'Clusters' object
print.refhtest	Print a summary of a 'refhtest' object
print.SpatPatterns	Print a 'SpatPatterns' object
print.summary.Clusters	Print a summary of a 'Clusters' object
print.summary.SpatPatterns	Print a summary of a 'SpatPatterns' object
prob.nnct	Probability of the current nearest neighbor contingency table
Pseg.coeff	Pielou's Segregation Coefficients for NNCTs
Pseg.ss	Pielou's Overall Test of Segregation for NNCT (for Sparse Sampling)
Pseg.ss.ct	Pielou's Overall Test of Segregation for NNCT (for Sparse Sampling)

-- Q --

QRval	Number of Shared and Reflexive NNs
Qsym.ct	Q-symmetry Contingency Table (QCT)
Qsym.test	Pielou's Second Type of NN Symmetry Test with Chi-square Approximation
Qval	Functions for the number of shared NNs, shared NN vector, and the number of reflexive NNs
Qvec	Functions for the number of shared NNs, shared NN vector, and the number of reflexive NNs

-- R --

rassoc	Generation of Points Associated with a Given Set of Points
rassocC	Generation of Points Associated in the Type C Sense with a Given Set of Points
rassocG	Generation of Points Associated in the Type G Sense with a Given Set of Points
rassocI	Generation of Points Associated in the Type I Sense with a Given Set of Points
rassocU	Generation of Points Associated in the Type U Sense with a Given Set of Points
rct	Reflexivity Contingency Table (RCT)
rdiag.clust	Generation of Points with Clusters along the First Diagonal
rhor.clust	Generation of Points with Clusters along the Horizontal Axis
rnonRL	Non-Random Labeling of a Given Set of Points
rnonRLI	Type I Non-Random Labeling of a Given Set of Points
rnonRLII	Type II Non-Random Labeling of a Given Set of Points
rnonRLIII	Type III Non-Random Labeling of a Given Set of Points
rnonRLIV	Type IV Non-Random Labeling of a Given Set of Points
row.sum	Functions for row and column sums of a matrix
rrot.clust	Generation of Points with Rotational Clusters
rseg	Generation of Points under Segregation of Two Classes
rself.ref	Generation of Points from Self Correspondence Pattern
runif.circ	Generation of Uniform Points in a Circle
Rval	Functions for the number of shared NNs, shared NN vector, and the number of reflexive NNs

-- S --

scct	Species Correspondence Contingency Table (SCCT)
scct.ct	Species Correspondence Contingency Table (SCCT)
seg.coeff	Pielou's Segregation Coefficients for NNCTs
seg.ind	Dixon's Segregation Indices for NNCTs
sharedNN	Functions for the number of shared NNs, shared NN vector, and the number of reflexive NNs
sharedNNmc	The Shared NN Vectors for Multiple Classes
SkewTk	Skewness of Cuzick and Edwards T_k Test statistic
summary.Clusters	Return a summary of a 'Clusters' object
summary.SpatPatterns	Return a summary of a 'SpatPatterns' object
swamptrees	Tree Species in a Swamp Forest

-- T --

Tcomb	Cuzick & Edwards Tcomb Test Statistic
tct	T Contingency Table (TCT)
tocher.cor	Tocher's randomized correction to the exact p-value
Tval	T value in NN structure

-- V --

var.nnct	Variances of Cell Counts in an NNCT
var.nnsym	Variances of Differences of Off-Diagonal Entries in an NNCT
var.seg.coeff	Variances of Segregation Coefficients in a Multi-class Case
var.tct	Variances of Entries in a TCT
var.tctI	Functions for Variances of Cell Counts in the Types I, III and IV TCTs
var.tctIII	Functions for Variances of Cell Counts in the Types I, III and IV TCTs
var.tctIV	Functions for Variances of Cell Counts in the Types I, III and IV TCTs
varNii	Variances of the Self Entries in a Species Correspondence Contingency Table (SCCT)
varNii.ct	Variances of the Self Entries in a Species Correspondence Contingency Table (SCCT)
varPseg.coeff	Variance of Pielou's Segregation Coefficient for 2 Classes
varTk	Variance of Cuzick and Edwards T_k Test statistic
varTkaij	Variance of Cuzick and Edwards T_k Test statistic
varTkinv.sim	Simulated Variance of Cuzick and Edwards T_k^{inv} Test statistic
varTrun	Variance of Cuzick and Edwards T_{run} Test statistic
varTrun.sim	Variance of Cuzick and Edwards T_{run} Test statistic

-- W --

W3val	W_k values for Tango's T test statistic
W4val	W_k values for Tango's T test statistic
W5val	W_k values for Tango's T test statistic
Wmat	The incidence matrix 'W' for the NN digraph

-- X --

Xsq.ceTk	Chi-square Approximation to Cuzick and Edwards T_k Test statistic
Xsq.nnref	Reflexivity Test with Chi-square Approximation
Xsq.nnref.ct	Reflexivity Test with Chi-square Approximation
Xsq.nnsym	Overall NN Symmetry Test with Chi-square Approximation
Xsq.nnsym.dx	Dixon's NN Symmetry Test with Chi-square Approximation for multiple classes
Xsq.nnsym.dx.ct	Dixon's NN Symmetry Test with Chi-square Approximation for multiple classes
Xsq.nnsym.ss	Pielou's First Type of NN Symmetry Test with Chi-square Approximation for multiple classes (for Sparse Sampling)
Xsq.nnsym.ss.ct	Pielou's First Type of NN Symmetry Test with Chi-square Approximation for multiple classes (for Sparse Sampling)
Xsq.seg.coeff	Chi-square Test for Segregation Coefficients
Xsq.seg.coeff.ct	Chi-square Test for Segregation Coefficients
Xsq.spec.cor	Overall Species Correspondence Test with Chi-square Approximation
Xsq.spec.cor.ct	Overall Species Correspondence Test with Chi-square Approximation

-- Z --

Zcell.nnct	Dixon's Cell-specific Z Tests of Segregation for NNCT
Zcell.nnct.2s	p-values for Cell-specific Z Test Statistics for NNCT
Zcell.nnct.ct	Dixon's Cell-specific Z Tests of Segregation for NNCT
Zcell.nnct.ls	p-values for Cell-specific Z Test Statistics for NNCT
Zcell.nnct.pval	p-values for Cell-specific Z Test Statistics for NNCT
Zcell.nnct.rs	p-values for Cell-specific Z Test Statistics for NNCT
Zcell.tct	Types I-IV Cell-specific Z Tests of Segregation based on NNCTs
Zcell.tct.ct	Types I-IV Cell-specific Z Tests of Segregation based on NNCTs
ZceTk	Z-test for Cuzick and Edwards T_k statistic
Zdir.nnct	Directional Segregation Test for Two Classes with Normal Approximation
Zdir.nnct.ct	Directional Segregation Test for Two Classes with Normal Approximation
Zdir.nnct.ss	Directional Segregation Test for Two Classes with Normal Approximation (for Sparse Sampling)
Zdir.nnct.ss.ct	Directional Segregation Test for Two Classes with Normal Approximation (for Sparse Sampling)
Zmixed.nonref	Mixed-Non-Reflexivity Test with Normal Approximation
Zmixed.nonref.ct	Mixed-Non-Reflexivity Test with Normal Approximation
Znnref	Z Tests for NN Reflexivity
Znnref.ct	Z Tests for NN Reflexivity
Znnself	Self-Reflexivity Tests with Normal Approximation
Znnself.ct	Self-Reflexivity Tests with Normal Approximation
Znnself.sum	Cumulative Species Correspondence Test with Normal Approximation
Znnself.sum.ct	Cumulative Species Correspondence Test with Normal Approximation
Znnsym	NN Symmetry Test with Normal Approximation
Znnsym.dx	Dixon's Pairwise NN Symmetry Test with Normal Approximation
Znnsym.dx.ct	Dixon's Pairwise NN Symmetry Test with Normal Approximation
Znnsym.ss	Pielou's Pairwise NN Symmetry Test with Normal Approximation (for Sparse Sampling)
Znnsym.ss.ct	Pielou's Pairwise NN Symmetry Test with Normal Approximation (for Sparse Sampling)
Znnsym2cl	NN Symmetry Test with Normal Approximation for Two Classes
Znnsym2cl.dx	Dixon's NN Symmetry Test with Normal Approximation for Two Classes
Znnsym2cl.dx.ct	Dixon's NN Symmetry Test with Normal Approximation for Two Classes
Znnsym2cl.ss	Pielou's First Type of NN Symmetry Test with Normal Approximation for Two Classes (for Sparse Sampling)
Znnsym2cl.ss.ct	Pielou's First Type of NN Symmetry Test with Normal Approximation for Two Classes (for Sparse Sampling)
Zseg.coeff	Z Tests for Segregation Coefficients
Zseg.coeff.ct	Z Tests for Segregation Coefficients
Zseg.ind	Z Tests for Segregation Indices
Zseg.ind.ct	Z Tests for Segregation Indices
Zself.ref	Self-Reflexivity Test with Normal Approximation
Zself.ref.ct	Self-Reflexivity Test with Normal Approximation
ZTcomb	Z-test for Cuzick and Edwards T_{comb} statistic
ZTkinv	Z-Test for Cuzick and Edwards T_k^{inv} statistic
ZTkinv.sim	Z-Test for Cuzick and Edwards T_k^{inv} statistic
ZTrun	Z-test for Cuzick and Edwards T_{run} statistic

-- misc --

.onAttach	.onAttach start message
.onLoad	.onLoad getOption package settings