| .onAttach start message | .onAttach |
| .onLoad getOption package settings | .onLoad |
| Closeness or Proximity Matrix for Tango's Spatial Clustering Tests | aij.theta |
| Asymptotic Covariance between T_k and T_l Values | asycovTkTl |
| Asymptotic Variance of Cuzick and Edwards T_k Test statistic | asyvarTk |
| pdf of the Bivariate Normal Distribution | bvnorm.pdf |
| Entries for the Types I-IV cell-specific tests | cellsTij |
| Cuzick and Edwards T_k Test statistic | ceTk |
| Cuzick and Edwards T_k^{inv} Test statistic | ceTkinv |
| Cuzick and Edwards T_{run} Test statistic | ceTrun |
| Covariance Matrix of the Cell Counts in an NNCT | cov.nnct |
| Covariance Matrix of the Differences of the Off-Diagonal Cell Counts in an NNCT | cov.nnsym |
| Covariance Matrix of Segregation Coefficients in a Multi-class Case | cov.seg.coeff |
| Covariance Matrix of the Entries of the Type I-IV TCTs | cov.tct |
| Conversion of the Covariance Matrix of the Row-wise Vectorized Cell Counts to Column-wise Vectorized Cell Counts in an NNCT | covNrow2col |
| Covariance matrix for T_k values in 'Tcomb' | covTcomb |
| Finite Sample Covariance between T_k and T_l Values | covTkTl |
| Interpoint Distance Matrix for Standardized Data | dist.std.data |
| Converts a lower triangular distance matrix to a full distance matrix | dist2full |
| The Euclidean distance between two vectors, matrices, or data frames | euc.dist |
| Expected Values of the Self Entries in a Species Correspondence Contingency Table (SCCT) | EV.Nii |
| Expected Values of the Cell Counts in NNCT | EV.nnct |
| Expected Values of the Cell Counts in RCT | EV.rct |
| Expected Value for Cuzick & Edwards T_{comb} Test Statistic | EV.Tcomb |
| Expected Values of the Types I-IV cell-specific tests | EV.tct |
| Expected Values of the Type I cell-specific tests | EV.tctI |
| Expected Value of Cuzick and Edwards T_k^{inv} Test statistic | EV.Tkinv |
| Exact version of Pearson's chi-square test on NNCTs | exact.nnct |
| p-value correction to the one-sided version of exact NNCT test | exact.pval1s |
| p-value correction to the two-sided version of exact NNCT test | exact.pval2s |
| Auxiliary Functions for Computing Covariances Between Cell Counts in the TCT | cov.2cells cov.2cols cov.cell.col covCiCj covNijCk funs.auxcovtct |
| Base Class-specific Chi-square Tests based on NNCTs | base.class.spec base.class.spec.ct funs.base.class.spec |
| Pielou's Cell-specific Segregation Test with Normal Approximation (for Sparse Sampling) | cell.spec.ss cell.spec.ss.ct funs.cell.spec.ss |
| Class-specific Chi-square Tests based on NNCTs | class.spec class.spec.ct funs.class.spec |
| Covariance Matrix of the Self Entries in a Species Correspondence Contingency Table (SCCT) | covNii covNii.ct funs.covNii |
| Functions for Covariances of the Entries of the Types I, III and IV TCTs | cov.tct3 cov.tctI cov.tctIII cov.tctIV funs.covtct |
| Functions for the k^{th} and 'k' NN distances | funs.kNNdist kNNdist kthNNdist |
| Functions for the k^{th} and 'k' NN distances | funs.kNNdist2cl kNNdist2cl kthNNdist2cl |
| Dixon's Overall Test of Segregation for NNCT | funs.overall.nnct overall.nnct overall.nnct.ct |
| Overall Segregation Tests for NNCTs | funs.overall.seg overall.seg overall.seg.ct |
| Types I-IV Overall Tests of Segregation for NNCT | funs.overall.tct overall.tct overall.tct.ct |
| The functions for probability of selecting a number of points from respective classes | funs.pijPij P11 p11 P111 p111 P1111 p1111 P1112 p1112 P112 p112 P1122 p1122 P1123 p1123 P12 p12 p122 p1223 P123 p123 P1234 p1234 |
| Species Correspondence Contingency Table (SCCT) | funs.scct scct scct.ct |
| Pielou's Segregation Coefficients for NNCTs | funs.seg.coeff Pseg.coeff seg.coeff |
| Variances of the Self Entries in a Species Correspondence Contingency Table (SCCT) | funs.varNii varNii varNii.ct |
| Functions for Variances of Cell Counts in the Types I, III and IV TCTs | funs.vartct var.tctI var.tctIII var.tctIV |
| Aij matrices for computation of Moments of Cuzick and Edwards T_k Test statistic | aij.mat aij.nonzero funsAijmat |
| Correction Matrices for the Covariance Matrix of NNCT entries | correct.cf1 correct.cf2 funsC_MI_II |
| Expected Value for Cuzick and Edwards T_k Test statistic | EV.Tk EV.Tkaij funsExpTk |
| Expected Value for Cuzick and Edwards T_{run} Test statistic | EV.Trun EV.Trun.alt funsExpTrun |
| Correction Matrices for the NNCT entries | funsN_I_II nnct.cr1 nnct.cr2 |
| NN Class-specific Chi-square Tests based on NNCTs | funsNNclass.spec NN.class.spec NN.class.spec.ct |
| Functions for one versus rest type labeling | classirest funsOnevsRest lab.onevsrest |
| Pielou's Overall Test of Segregation for NNCT (for Sparse Sampling) | funsPseg.ss Pseg.ss Pseg.ss.ct |
| Functions for the Number of Shared NNs, Shared NN vector and the number of reflexive NNs | funsQandR Qval Qvec Rval sharedNN |
| Functions for row and column sums of a matrix | col.sum funsRowColSums row.sum |
| Variance of Cuzick and Edwards T_k Test statistic | funsVarTk varTk varTkaij |
| Variance of Cuzick and Edwards T_{run} Test statistic | funsVarTrun varTrun varTrun.sim |
| W_k values for Tango's T test statistic | funsW345values W3val W4val W5val |
| Reflexivity Test with Chi-square Approximation | funsXsq.nnref Xsq.nnref Xsq.nnref.ct |
| Dixon's NN Symmetry Test with Chi-square Approximation for multiple classes | funsXsq.nnsym.dx Xsq.nnsym.dx Xsq.nnsym.dx.ct |
| Pielou's First Type of NN Symmetry Test with Chi-square Approximation for multiple classes (for Sparse Sampling) | funsXsq.nnsym.ss Xsq.nnsym.ss Xsq.nnsym.ss.ct |
| Chi-square Test for Segregation Coefficients | funsXsq.seg.coeff Xsq.seg.coeff Xsq.seg.coeff.ct |
| Overall Species Correspondence Test with Chi-square Approximation | funsXsq.spec.cor Xsq.spec.cor Xsq.spec.cor.ct |
| Dixon's Cell-specific Z Tests of Segregation for NNCT | funsZcell.nnct Zcell.nnct Zcell.nnct.ct |
| p-values for Cell-specific Z Test Statistics for NNCT | funsZcell.nnct.pval Zcell.nnct.2s Zcell.nnct.ls Zcell.nnct.pval Zcell.nnct.rs |
| Cell-specific Z Tests of Segregation for NNCTs | cell.spec cell.spec.ct funsZcell.spec |
| Types I-IV Cell-specific Z Tests of Segregation based on NNCTs | funsZcell.tct Zcell.tct Zcell.tct.ct |
| Directional Segregation Test for Two Classes with Normal Approximation | funsZdir.nnct Zdir.nnct Zdir.nnct.ct |
| Directional Segregation Test for Two Classes with Normal Approximation (for Sparse Sampling) | funsZdir.nnct.ss Zdir.nnct.ss Zdir.nnct.ss.ct |
| Mixed-Non-Reflexivity Test with Normal Approximation | funsZmixed.nonref Zmixed.nonref Zmixed.nonref.ct |
| Z Tests for NN Reflexivity | funsZnnref Znnref Znnref.ct |
| Self-Reflexivity Tests with Normal Approximation | funsZnnself Znnself Znnself.ct |
| Cumulative Species Correspondence Test with Normal Approximation | funsZnnself.sum Znnself.sum Znnself.sum.ct |
| Dixon's Pairwise NN Symmetry Test with Normal Approximation | funsZnnsym.dx Znnsym.dx Znnsym.dx.ct |
| Pielou's Pairwise NN Symmetry Test with Normal Approximation (for Sparse Sampling) | funsZnnsym.ss Znnsym.ss Znnsym.ss.ct |
| Dixon's NN Symmetry Test with Normal Approximation for Two Classes | funsZnnsym2cl.dx Znnsym2cl.dx Znnsym2cl.dx.ct |
| Pielou's First Type of NN Symmetry Test with Normal Approximation for Two Classes (for Sparse Sampling) | funsZnnsym2cl.ss Znnsym2cl.ss Znnsym2cl.ss.ct |
| Z Tests for Segregation Coefficients | funsZseg.coeff Zseg.coeff Zseg.coeff.ct |
| Z Tests for Segregation Indices | funsZsegind Zseg.ind Zseg.ind.ct |
| Self-Reflexivity Test with Normal Approximation | funsZself.ref Zself.ref Zself.ref.ct |
| Z-Test for Cuzick and Edwards T_k^{inv} statistic | funsZTkinv ZTkinv ZTkinv.sim |
| Index Matrix for Computing the Covariance of Dixon's Overall NN Symmetry Test | ind.nnsym |
| Index Matrix for Computing the Covariance of Segregation Coefficients | ind.seg.coeff |
| Interpoint Distance Matrix | ipd.mat |
| Euclidean Interpoint Distance Matrix | ipd.mat.euc |
| Finding the indices of the 'k' NNs of a given point | kNN |
| Conversion of a Matrix to a Vector | mat2vec |
| Square root of a matrix | matrix.sqrt |
| Vector of Shared NNs and Number of Reflexive NNs | Ninv |
| Finding the index of the NN of a given point | NN |
| Nearest Neighbor Contingency Table (NNCT) | nnct |
| Bootstrap Nearest Neighbor Contingency Table (NNCT) | nnct.boot.dis |
| Nearest Neighbor Contingency Table (NNCT) with (only) base points restricted to a subsample | nnct.sub |
| Distances between subjects and their NNs | NNdist |
| Distances between subjects from class i and their NNs from class j | NNdist2cl |
| nnspat: A package for NN Methods and Their Use in Testing Spatial Patterns | nnspat |
| Finding the index of the NN of a given point among a subset of points | NNsub |
| N_t Value (found with the definition formula) | Nt.def |
| N_{tkl} Value | Ntkl |
| Keeping the pair of the specified labels in the data | pairwise.lab |
| Smallest and Largest Distances in a Distance Matrix | pick.min.max |
| Probability of 'k' items selected from the class with size n_1 | pk |
| Plot a 'Clusters' object | plot.Clusters |
| Plot a 'SpatPatterns' object | plot.SpatPatterns |
| Print a summary of a 'cellhtest' object | print.cellhtest |
| Print a summary of a 'Chisqtest' object | print.Chisqtest |
| Print a summary of a 'classhtest' object | print.classhtest |
| Print a 'Clusters' object | print.Clusters |
| Print a summary of a 'refhtest' object | print.refhtest |
| Print a 'SpatPatterns' object | print.SpatPatterns |
| Print a summary of a 'Clusters' object | print.summary.Clusters |
| Print a summary of a 'SpatPatterns' object | print.summary.SpatPatterns |
| Probability of the current nearest neighbor contingency table | prob.nnct |
| Number of Shared and Reflexive NNs | QRval |
| Q-symmetry Contingency Table (QCT) | Qsym.ct |
| Pielou's Second Type of NN Symmetry Test with Chi-square Approximation | Qsym.test |
| Generation of Points Associated with a Given Set of Points | rassoc |
| Generation of Points Associated in the Type C Sense with a Given Set of Points | rassocC |
| Generation of Points Associated in the Type G Sense with a Given Set of Points | rassocG |
| Generation of Points Associated in the Type I Sense with a Given Set of Points | rassocI |
| Generation of Points Associated in the Type U Sense with a Given Set of Points | rassocU |
| Reflexivity Contingency Table (RCT) | rct |
| Generation of Points with Clusters along the First Diagonal | rdiag.clust |
| Generation of Points with Clusters along the Horizontal Axis | rhor.clust |
| Non-Random Labeling of a Given Set of Points | rnonRL |
| Type I Non-Random Labeling of a Given Set of Points | rnonRLI |
| Type II Non-Random Labeling of a Given Set of Points | rnonRLII |
| Type III Non-Random Labeling of a Given Set of Points | rnonRLIII |
| Type IV Non-Random Labeling of a Given Set of Points | rnonRLIV |
| Generation of Points with Rotational Clusters | rrot.clust |
| Generation of Points under Segregation of Two Classes | rseg |
| Generation of Points from Self Correspondence Pattern | rself.ref |
| Generation of Uniform Points in a Circle | runif.circ |
| Dixon's Segregation Indices for NNCTs | seg.ind |
| The Shared NN Vectors for Multiple Classes | sharedNNmc |
| Skewness of Cuzick and Edwards T_k Test statistic | SkewTk |
| Return a summary of a 'Clusters' object | summary.Clusters |
| Return a summary of a 'SpatPatterns' object | summary.SpatPatterns |
| Tree Species in a Swamp Forest | swamptrees |
| Cuzick & Edwards Tcomb Test Statistic | Tcomb |
| T Contingency Table (TCT) | tct |
| Tocher's randomized correction to the exact p-value | tocher.cor |
| T value in NN structure | Tval |
| Variances of Cell Counts in an NNCT | var.nnct |
| Variances of Differences of Off-Diagonal Entries in an NNCT | var.nnsym |
| Variances of Segregation Coefficients in a Multi-class Case | var.seg.coeff |
| Variances of Entries in a TCT | var.tct |
| Variance of Pielou's Segregation Coefficient for 2 Classes | varPseg.coeff |
| Simulated Variance of Cuzick and Edwards T_k^{inv} Test statistic | varTkinv.sim |
| The incidence matrix 'W' for the NN digraph | Wmat |
| Chi-square Approximation to Cuzick and Edwards T_k Test statistic | Xsq.ceTk |
| Overall NN Symmetry Test with Chi-square Approximation | Xsq.nnsym |
| Z-test for Cuzick and Edwards T_k statistic | ZceTk |
| NN Symmetry Test with Normal Approximation | Znnsym |
| NN Symmetry Test with Normal Approximation for Two Classes | Znnsym2cl |
| Z-test for Cuzick and Edwards T_{comb} statistic | ZTcomb |
| Z-test for Cuzick and Edwards T_{run} statistic | ZTrun |
