STRAUSS MATLAB FUNCTIONS AND SCRIPT FILES: CONSTANTS phi - the golden proportion CREATION OF SPECIAL MATRICES design - creates GLM design matrix makegrps - compose a group-membership vector from group labels and frequencies KINDS OF MATRICES isblank - determines whether character matrix consists of all blanks iscorr - determines whether matrix is in form of a correlation matrix iscov - determines whether matrix is in form of a covariance matrix iseven - determines whether matrix elements are even isin - finds elements of matrix A contained within matrix B isintegr - determines whether matrix is all integers ismatrix - determines whether matrix is at least 2-dimensional ismonotonic - determines whether cols of matrix are monotonic isodd - determines whether matrix elements are odd isposdef - determines whether square-symmetric matrix is positive-definite isscalar - determines whether matrix is a scalar issorted - determines whether matrix cols are sorted issqsym - determines whether matrix is square-symmetric isvector - determines whether matrix is a vector; also returns size NUMERICAL OPERATIONS baseconv - convert numeric vector to single base-10 values complex - convert two-column real matrix to complex distance - convert points to distances, given specifications grpcentr - zero-center the columns of data matrix, by group prbcount - vector of counts from a vector of probabilities ranks - ranks of data by column, invoking midrank ties reassign - reassign labels of vector to maximize matches with second vector rowneab - returns column vector of row means, optionally ignoring missing data rowsum - returns column vector of row sums, optionally ignoring missing data setrange - rescales ranges, by column, given min and max values subgrpadj - adjust subgroup means to grand mean within group sumsqscale - scales columns so that the squared elements sum to unity sweep - sweep operator for symmetric matrices todegs - converts radians to degrees torads - converts degrees to radians zcenter - zero-centers data matrix by column zscore - standardizes columns of data matrix UNIVARIATE STATISTICAL ANALYSES absdev - converts data matrix to absolute deviations from mean or median anova - one-way unbalanced fixed-effects ANOVA, with variance components anovaf - objective function for 'anova' anovanst - two-level nested random-effects ANOVA, with variance components anovanstf - objective function for 'anovanst' anovanstg - design matrices for 'anovanst' anovaparam - one-way unbalanced anova, given only means, stdevs, and sample sizes anovast - one-way unbalanced ANOVA of statistic estimates & stderrs asymmeas - Palmer-Strobeck anova model for fluctuating asymmetry censoredregr - Tobit model for censored regression censoredstats - mean, stdev and their standard errors for censored data chi2comb - combines chi-squared values to give a single p-value chi2corr - chi-square distances among columns of contingency table cisignif - pairwise differences based on means and confidence intervals only contin1 - randomized 1-way chi-square goodness-of-fit test contin2 - randomized 2-way contingency-table analysis, fixed or free marginals continex - Fisher's exact test for [2x2] contingency table cummean - cumulative means and variances fratio - randomized F-ratio test for equal variances goodfit - power divergence chi-squared goodness-of-fit test goodfitp - Edgington's permutation least-squares goodness-of-fit test gtest - 2-way log-likelihood contingency-table test histplot - matrix of histograms homosub - homogeneous subsets from a symmetric binary matrix of signif diffs kruskwal - randomized Kruskal-Wallace (& Mann-Whitney) test for 2+ samples kstest1 - 1-sample randomized Kolmogorov-Smirnov test kstest1f - objective function for kstest1 kstest2 - 2-sample randomized Kolmogorov-Smirnov test kstest2f - objective function for kstest2 kwcrit - critical values for the Kruskal-Wallace statistic, given sample sizes kwstat - Kruskal-Wallace test-statistic value levene - Levene's test: anova of absolute deviations from the means logb - logarithm of x to base b mannprob - tail probability for the Mann-Whitney statistic mannwhit - 2-group 2-tailed Mann-Whitney test for group differences mannwhf - objective function for mannwhit means - means by column (even for row vectors), optionally by group meanwt - weighted mean, variance, skewness, kurtosis medians - medians by column (even for row vectors), optionally by group mode - finds mode by over-binning negbino - fits negative binomial distribution to matrix of quadrat counts normaltest - Shapiro-Francia test for normality nscores - normal (phi) scores orderstats - means and covar matrix of normal order statistics pairwise - overall and pairwise anova/Kruskal-Wallace tests, randomized prctilerange - percentile range prctiles - find percentiles of a distribution by linear interpolation probdetect - estimates prob of detecting one or more binomial events probzero - probability of observing 0 of N 'successes' propdiff - tests for difference in two proportions rankasgn - ranks of single data vector, invoking midrank ties rankits - expected normal scores for an ordered random sample ranks - ranks of data by column, optionally within-group ratioprob - tests a sex ratio against the null of unity seqbonf - sequential Bonferroni test on a set of probabilities subgrpadj - adjust subgroup means to grand mean within group subgrpmeans - tables of cell sample sizes and means for subgroups within groups sums - sums by column (even for row vectors), optionally by group trimmean - trimmed mean as function of trimming proportion truncate - truncates (fixes) a matrix to a specified number of decimal places ttest - pairwise unbalanced t-tests among two or more groups ttestpr - paired t-test, with control as covariate ttestparam - unbalanced t-test, given only means, stdevs, and sample sizes tval - 2-sample t statistic, unequal sample sizes varcomp - variance components from a nested ANOVA, unequal sample sizes univar - moment and median statistics, allowing for missing data wilcoxon - Wilcoxon 1-sample signed-ranks test REGRESSION accumcurve - accumulation curve and predicted saturation asymptote ancovpred - predicted values per group under a common-slope ancova model bilinear - fits a bilinear segmented regression model bilinearf - objective function for 'bilinear' bilintrans - fits a transitional bilinear segmented regression model bilintransf - objective function for 'bilintrans' charshape - bivariate shape scores for characters growth - fits one or more growth models growthfn - objective function for 'growth' lineeqn - slope and intercept from two points linregr - predictive bivariate linear regression logistic - logistic regression logistf - objective function for 'logistic' ltsregr - least trimmed squares bivariate regression mse - MSE and adjusted R2 for regression orthogpolyregr - orthogonal polynomial regression orthogpolyregre - sums of squares for orthogonal polynomial regression orthogpolyregrf - objective function for orthogonal polynomial regression orthogpolyregrp - plot of orthogonal polynomial regression probit - probit regression of binary response on continuous 'dose' variable probitf - objective function for 'probit' quadratic - quadratic regression r2adj - adjusted squared multiple correlation regrcompare - randomized comparison of two or more linear regression lines regrnull - significance of bivariate regressions, given null beta0 & beta1 sweepreg - multiple regression via the sweep operator, given means & covars trajectory - fits and evaluates 1-5 parameter models of segmented trajectories MULTIVARIATE STATISTICAL ANALYSES allom - convert size-vector loadings to multivariate allometric coeffs allomtst - test for heterogeneity among within-group size vectors autocorr - lagged autocorrelations along matrix columns autorank - Spearman rank autocorrelations along a vector or matrix columns brokestk - number of significant eigenvalues based on broken-stick model cancorr - canonical correlation analysis charshape - bivariate shape scores for characters classify - reclassify obs or classify unknowns, based on Mahalanobis distances corr - Pearson correlations among variables or between sets of variables corrf - objective function for 'corr' corrci - simultaneous confidence intervals for Pearson correlation corrcmpl - distances (1-corrcoef) among columns corresp - correspondence analysis of tables of counts corrplot - correlation-style matrix of bivariate plots corrpool - pooled within-group correlation matrix corrprci - individual probs and confidence intervals for correlation matrix corrprob - test of correlation matrix against H0:diagonal matrix corrz - Fisher's z-transform (w/ Hotelling's correction) for correlations covcorr - rescale covariance matrix to correlation matrix + vector of stdevs covpairwise - covariance matrix when data matrix contains missing values covpool - pooled within-group covariance matrix discrdet - determinant and rank of B matrix as function of number of vars discrim - bootstrapped discriminant analysis discrimb - bootstrap objective function for 'discrim' discrimf - calculating function for 'discrim' distdiff - test for within- vs among-group pairwise distances or similarities eigen - sorted, directed eigenvectors and eigenvalues of symmetric matrix friedraf - randomized Friedman-Rafesky test for unequal multivariate distribs geneigen - generalized eigen analysis for two square matrices henze - Henze nearest-neighbor test for unequal multivariate distribs homogen - measures the homogeneity among variables for a data matrix hullpeel - finds percentiles of 2D data from nested sets of convex hulls jaccard - Jaccard measure of association (similarity) jaccardd - Jaccard distance krige - predict missing values in a spatial matrix using universal kriging loadscrs - calculate loadings and scores mahal - bootstrapped Mahalanobis distances mahalsf - size-free Mahalanobis distances majaxis - major-axis regression manova - one-way multivariate analysis of variance manovaf - objective function for manova mantel - Mantel's test for association between symmetric distances matrices mantelb - returns bootstrapped distance matrix matcond - matrix condition based on rarification of vars or obs condfactor - modified condition factor of correlation or covariance matrix morisita - Morisita's measure of dissimilarity between communities morphint - measures and assesses morphological integration (character suites) mosimann - calculates Mossiman ratio-independent size vector partcorm - partials a covariate from a correlation matrix partcorr - calculates partial correlations, or possible ranges of correlations pcaconstr - PCA, constrained to be independent of a set of independent variables pcacorr - bootstrapped PCA using correlation matrix pcacov - bootstrapped PCA using covariance matrix pcacovb - bootstrap objective function for 'pcacov' pcoa - principal coordinates analysis of a distance matrix percdist - percent-similarity distance measure posdef - if matrix isn't positive definite, finds closest corresponding matrix rankcorr - rank correlation (Pearson correlation of ranks) renkonen - Renkenon's percent-similarity distance measure score - unstandardized factor scores for a subset of factors sfresids - size-invariant residuals sizefree - size-invariant discriminant analysis sizefref - objective function for sizefree() sizefrep - parse matrix output from sizefref sizevect - within-group size vectors (PC1 coefficients) spearman - Spearman's rank correlation, adj for ties, for two variables stepdisc - stepwise discriminant or size-free discriminant analyses lawley - objective function for stepdisc() stepmano - stepwise MANOVA probabilities of the results of 'stepdisc' steprank - finds the best subset of variables to reduce a singular matrix sumsqdiff - pairwise sum-of-squares distances, bootstrapped varcomb - with missing data, finds best combinations of vars and observations vectcorr - vector correlations among vectors or matrix columns wright - Wright-style factor analysis of covariance/correlation matrix factorp - least-squares fit of general/primary factor factorpf - objective function for 'factorp' factors - least-squares fit of secondary factors factorsp - objective function for 'factors' wright - Wright-style factor analysis partial - extracts 1 or 2 factors from a corr/cov matrix submatrx - extracts a submatrix from a corr/cov matrix wrightbt - bootstrap of Wright-style factor analysis from data matrix MISSING DATA krige - predict missing values in a spatial matrix using universal kriging misscheck - checks for missing (non-finite) values in matrices missem - estimates missing values, means, and covariances via EM algorithm missemconstr - constrained version of missem() misseval - evaluate the effect of missing-value estimation on a matrix misspc - estimates missing values via multiple regression on PCs missim - simulate effects of groups and suites on missing-value estimation randmiss - random missing values inserted into a matrix missrandmeas - measures nonrandom (binomial) distribs of missing data within matrix varcomb - with missing data, finds best combinations of vars and observations COMBINATORICS allgrps - returns a list of all possible groupings of N objects into k groups allgrpf - list all possible groupings of N objects into k grps allsizes - returns list of sample-size decompositions of N into k groups binmatno - number of possible (0,1)-element matrices, given row & col sums catalan - Catalan numbers comb - number of combinations of n objects taken r at a time combvals - returns matrix containing all combinations of nCr nndeterm - training vectors/degree of determination of FF neural network partion - returns list of partitions of N linearly-spaced objects into k groups partf - recursive function to find partitions permlist - returns matrix containing all permutations permnext - returns lexicographically next permutation TREES, GRAPHS AND CLUSTER ANALYSIS addtree - neighbor-joining additive tree from a distance matrix reroot - reroots an additive tree to a specified outgroup treeroot - reroots an additive tree by the 'min var of patristic distance' criterion treerf - finds optimal root position, given the tree and the outgroup allclade - probabilities of all possible clade sizes for rooted tree ancestorfunction - converts from one type anc fn to another, andfixes problems ancmove - move ancestor to final position in ancestor function chi2clst - chi-squared clustering of rows of 2-way contingency table cladeprb - probability of sampling a tree containing an observed clade clstsupt - finds cluster-support matrix from dendrogram topology matrix cluster - boostrap UPGMA dendrogram, giving measures of cluster support clustnum - determine number of partition clusters based on Gabriel graphs contmap - least-squares mapping of continuous chars onto a tree contmape - exact mapping (topology only, or topology + nonzero branch lengths) contmapi - iterative mapping (topology + one or more zero branch lengths) contmapf - objective function for iterative mapping contmapdists - mapping of frequency distribs of a single characters onto a tree dendline - allows the plotting of vertical lines connecting taxa on a dendrogram dendplot - plots dendrogram from topology matrix gaptest - gap test for difference between two or more convex clusters kmeangrp - vary k and evaluate k-means clustering for number of groups kmeans - k-means clustering of n points into k clusters by min(sse) knnclust - k-nearest neighbor hierarchical clustering knnplot - plots scatterplot or dendrogram for k-nearest neighbor clustering lnktoanc - coverts list of links (internodes) to ancestor function minkvary - maps continuous character onto a tree for varying Minkowski k mstree - finds and plots the minimum spanning tree mstclust - finds 'significant' clusters based on randomized min-span trees mstgrp - finds groups by deleting longest edges of min-span tree nngrp - nearest-neighbor (single-linkage) distances among groups natclust - finds "natural" clusters (Carmichael et al. 1968) patrist - calculates step-distance and patristic-distance matrices of dendrogram phyliptree - plots maximum likelihood tree based on Phylip output randindx - adjusted Rand index for comparison of different data partitions topoanc - converts dendrogram topology matrix to cladogram ancestor function topotips - finds the terminal taxa within clusters from a topology matrix treenum - number of possible unrooted binary trees for N taxa treeasym - calculates Colless' I (asymmetry) for trees specified by Rohlf's M treecoli - calculates Colless' I (asymmetry) from the ancestor function treedivd - find links and levels on tree, given the ancestor function treelen - Minkowski tree lengths treemanc - recovers ancestor function from Rohlf's M treeplot - plots a tree given an ancestor function and optional branch lengths treespace - plots a tree topology on a 2D space treetips - finds the terminal taxa within a clade from an ancestor function treevect - recovers N-tuple from Rohlf's M upgma - UPGMA hierarchical cluster analysis of a distance matrix dendhier - finds links on a dendrogram, given the topology matrix dendplot - plots a dendrogram from a topology matrix visitadj - visit connected vertices of graph via an adjacency matrix GEOMETRIC OBJECTS circcrds - returns plotting coords for a specified circle circdraw - plots a circle of specified radius circfit - fits a circle to a scatter of points circfitf - objective function for 'circfit' conic - generate plots of conics ellipsebound - generate points along boundary of an ellipse ellipsesize - area and perinmeter of an ellipse ellipsesizef - objective function for integration lgspiral - generate plots of logarithmic spirals polygon - area, perimeter, and length of side of a regular polygon BOUNDARIES & PATHS cubespln - fits a cubic-splined boundary to a closed polygon fourier - Fourier fitting of a quadratic-splined boundary hausdorf - Hausdorff fractal dimension of a path pathlen - finds length of path connecting a set of points pathmax - finds longest path connecting a set of points pathmin - finds shortest path connecting a set of points (TSP) pathnn - finds the nearest-neighbor path(s) connecting a set of points pathplot - plots a path + nodes, with equal axes pathpts - evenly distributes points along a path pathseg - finds line-segment length to exactly step of a given number of steps pathsegf - residual after stepping off a given number of steps pathsegr - residual distance after stepping off line segment along path pathstat - descriptors of a path quadspline - fits quadratic-splined (Oberhauser) boundary to an open/closed path radiusfn - finds and plots a radius function randpath - random points along a specified line-segment path steplength - step lengths along a path tangentfn - finds and plots a quadratically-smoothed tangent-angle function DISTRIBUTIONS bimodal - coefficient of bimodality of a distribution, based on kurtosis bimodalf - objective function for 'bimodal' binofit - fits binomial distribution by minimizing the mean squared error binofitf - objective function for 'binofit' boxcox - Box-Cox transformation to symmetry boxcoxb - objective function for 'boxcox' boxcoxinv - inverse of Box-Cox transformation boxcoxnorm - modified Box-Cox transformation to normality boxcoxnormf - objective function for 'boxcoxnorm' cauchyrnd - random sample from a Cauchy distribution centdist - finds limits for a specified central portion of a distribution cdfdata - produces a cumulative distribution function from a data vector cumstep - converts discrete pdf into cumulative relative cdf for KS test fdistnc - cdf for noncentral F distribution finvnc - inverse cdf for noncentral F distribution finvncob - objective function for 'finvnc' PearsonFitData - fit continuous Pearson distribution function to a histogram PearsonFitDataF - objective function for 'histfit' PearsonFitMoments - fit Pearson distribution function to first four moments kurtosis - unbiased estimate and standard error of kurtosis gammalog - log of the gamma function meanwt - weighted mean and variance minkpdf - pdf of a Minkowski distribution minksamp - random or systematic sample from a Minkowski distribution moments - first r moments, by column multnormpdf - multivariate-normal probability density function nscores - transforms data to nscores poissci - central confidence interval from Poisson distribution poisfit - fits Poisson distribution by minimizing a KS-statistic poisfitf - objective function for 'poisfit' plotnorm - draw normal distributions rankits - expected normal scores for an ordered random sample skewness - unbiased estimate of skewness and standard error unidsvar - variance of uniform interval [p,q] BOOTSTRAPPING AND RANDOMIZATION bootbal - randomized observation-indices for a balanced bootstrap bootci - confidence limits from a bootstrap distribution bootprob - probability levels from bootstrap distributions bootsamp - randomly sample rows of matrix, optionally within groups bootstrp - generalized bootstrap function iterations - min number of iterations for given confidence about p-value iterconf - confidence interval about p-value, given number of iterations randprob - right-tailed probability from a randomized distribution GENERATING RANDOM OBJECTS continrn - random contingency table with fixed or floating totals mvngrps - groups of MVN data for testing other procedures prbcount - random vector of counts from a vector of probabilities randauto - random vector of autocorrelated uniform random numbers randautp - predicts parameter c from autocorrelation coefficient randbinm - random binary matrix randcirc - random points within a circle randcnvx - random points within a specified convex polygon randcorr - random correlation/covariance matrix randcova - random points for an ANCOVA model, allowing unequal slopes randmink - random values from a Minkowski pdf with parameter k randmvn - random sample of multivariate-normal data randnt - random sample from truncated normal distribution randpath - random points along a specified line-segment path randpermg - randomly permuted matrix, optionally by groups randpoly - random points within a specified polygon randprop - random proportions randstrb - random sample from distrib with specified moment statistics kurtopt - objective function for 'randkurt' kurttran - power-transform of kurtosis of a distribution momopt - objective function for 'randstrb' randkurt - optimize kurtosis randskew - optimize skewness randsplt - plotting version of 'randstrb' skewopt - objective function for 'randskew' skewtran - power-transform of skewness of a distribution randsuit - random data matrix for multiple groups of obs and suites of vars randtree - ancestor function for random tree based on Rohlf's M walkdist - models random walk of taxa from common ancestor in 2 dimensions walkrand - random walk in p dimensions from origin of coordinate system MANIPULATION OF MATRICES bintostr - converts binary matrix to character equivalent commonsize - determines whether matrices have same size, or expand a scalar complset - given list of variables, finds obs having complete data exchange - exchanges two values extrcols - extract cols of matrix into separate col vectors findmatch - finds values in common between two vectors getobs - extract subset of observations based on group identifiers labtoval - converts character-string label matrix to numeric vector minsize - finds groups having at least a minimum sample size misscheck - checks for missing (non-finite) values in matrices padcols - pads narrower matrix with columns of zeros padrows - pads shorter matrix with rows of zeros putdiag - put diagonal elements in a square matrix randpermcols - randomly permute columns of a matrix replace - replacement of numeric values within a matrix rescale - centers and rescales data by pooled within-group stdev reshapei - maps subscripts from a matrix to a reshaped matrix (both 2D) rowtoval - converts rows of matrix to vector of scalar values samelength - determines whether matices have same number of rows; expands scalars sortmat - sorts key vector, resequences other matrices to corresponding order splitgrp - splits data matrix into separate group matrices str2int - converts strings to integers submatrows - subsets of corresponding matrices by row switchem - switches contents of two matrices trilow - extracts lower triangular matrix (w/o diag) as column vector trisqmat - stashes triangular-matrix vectors + diagonal into square matrix truncate - truncates (fixes) a matrix to a specified number of decimal places uniquef - list of unique group labels and corresponding frequencies valtolab - converts numeric values to character labels wrap - returns modified modulus for wrap-around arrays MANIPULATION OF POINT CONFIGURATIONS angl - angle made by three points angledev - signed angular deviations of points from reference ray asympoly - minimum bilateral asymmetry (area, perimeter) of a polygon refldiff - finds difference between lateral boundaries reflplot - plots mirror images reflstat - finds lateral differences in area and perimeter centroid - robust estimate of centroid and median for 2D data centsize - centroid size of a point configuration coeffdispersion - finds coefficient of dispersion of points on grid digitize - get point coordinates from image distptsline - distances from a set of points to a line eucl - euclidean distances among points gabriel - Gabriel connectivity graph among planar points geogdist - great-circle arc distance between two geographic sites (lat/long) geogkmns - modification of the k-means procedure to cluster geographic localities geomsize - geometric-mean size of a point configuration getaxes - recover axis tickmark positions from digitized scatterplot getcoord - recover point coordinates from digitized scatterplot getpolyg - get polygons from graphics window via mouse input getptid - determine point identifications from plot getpts - get points from graphics window via mouse input hull - convex hull hullpeel - finds percentiles of 2D data from nested sets of convex hulls intrsect - determines whether and where two line segments intersect isinpoly - determines whether a point lies within a polygon isonline - determines whether a point lies on a line, within tolerance linextnd - extends a line (specified by two points) by a given distance lstra - orthogonal least-squares theta-rho (Procrustes) analysis mds - multidimensional scaling mdsfunc - objective function for multidimensional scaling nearestline - finds the nearest line segment for one or more points nndist - nearest-neighbor distances ntscrds - converts point coords from NTS format (from TPSDIG) to [n x 2] matrix form plotdist - plots a set of landmarks and interpoint distances polarcrd - convert polar coordinates to rectangular, or vice versa polyangl - resample polygon boundary by equal angular deviations polyarea - area, centroid, and perimeter of a closed polygon polyaxes - major and minor axes of polygon polystrn - anisotropy and direction of a polygon project - projects points onto line ptdir - determines direction of path thru 3 points randwalk - generates and analyzes random walk in p dimensions regrot - registers and rotates a point configuration rotate - rotates point configuration about the centroid by a specified angle runavg - vectors smoothed by running average spacecls - randomized k-means clustering for spatial distributions theta - value proportional to angular deviation of a point from horizontal thinplat - thin-plate splines triallom - fits predicted triangles from regressions of sides on size triangpt - triangulate a point, given distances to two reference points trusgrow - grow a truss allometrically and plot the MDS stress function unplot - recover data values from previously imaged scatterplot MANIPULATION OF IMAGES getavgcolor - gets median color parameters within polygon imagebox - extracts rectangle within image GRAPHICS alloplot - plots allometric coefficients as a horizontal bar chart arrow - draws arrow on current plot arrowdwn - downward arrow to mark positions on histograms boxplot - box plots boxplotb - draws individual box plot circcrds - returns plotting coords for a specified circle circdraw - draws a circle of given radius colrname - returns name of color given RGB specification conic - generate plots of conics corrcirc - portrays correlation coefficient & CI in circular form corrmap - plots a color-patch representation of correlation matrix corrplot - correlation-style matrix of bivariate plots densplot - scatterplot for two discrete variables distfig - plot figures of distances among landmarks, given crds and specs ellips - computes boundary of ellipse (centered, rotated) getchild - lists handle & color of each child of current plot getptid - determine point identifications from plot histgram - histogram with continuous colored bars histarw - returns position of arrow and adjusted axis ranges histbins - puts data vector into bins for histogram histpltb - plots histogram bars histgramb - plot histogram, given midpoints and heights of bars histplot - matrix of histograms of columns (variables) of a data matrix interpt - plot landmarks and interpoint distances lgspiral - generate plots of logarithmic spirals linelabl - prints a label next to a line, based on line orientation loadfig - restores a figure from characteristics saved by savefig() lollipop - 3D lollipop scatter plot with points anchored by stem pcontour - prepares MATLAB contour output for plotting with SIGMAPLOT plotbern - plots a Bernoulli distribution, for X={0,1} plotbino - plots binomial distribution, given N,p plotgrps - plot for several groups, with optional hulls, centroids, etc. pltgrpch - plot convex hulls pltgrpcn - plot group centroids pltgrpma - plot major axes and confidence ellipses pltgrpmd - plot group medians via hull peeling pltgrpop - set option flags pltgrppp - plot points pltgrppr - plot regression lines pltgrpse - plot standard-error bars plotjoin - connect pairs of points on scatterpoints plotlabl - plot corresponding labels rather than symbols plotnorm - draw normal distributions plotnum - plot observation numbers rather than symbols plotpt - add single point to existing plot, extending axes if necessary plotrect - plots rectangle, given opposing corners plotsurface - plots a mesh or surface plot plotxyerror - scatterplot of data +/- horizontal & vertical error bars plotyerror - scatterplot of data +/- vertical error bars plotvert - plots vertical lines for multiple y's per x ptscale - scale point coordinates to proportions along current axes puttext - puts text on figure using proportional coords puttitle - puts title on figure with larger-than-default font putbnd - changes scales of both axes to 5% beyond range of data putlegnd - puts a legend of character strings onto a plot putregrline - add regression line to current plot puttick - changes the tick marks and labels of a plot putxbnd - changes min,max of x-axis without changing y-axis putybnd - changes min,max of y-axis without changing x-axis putxlab - puts xlabel on figure with larger-than-default font putylab - puts ylabel on figure with larger-than-default font putzlab - puts ylabel on figure with larger-than-default font savefig - saves figure properties for later reconstruction scatter - simple unlabeled scatter plot of first two cols of a matrix sqplot - returns axis bounds for a square plot with equal-unit axes vectplot - produces vector plots of multivariate loadings (biplots) vectplot1 - one-dimensional vector plots vectplot2 - two-dimensional vector plots wordplot - resets line widths for plots to be copied to Word documents INPUT/OUTPUT loadfig - restores a figure from characteristics saved by savefig() savefig - saves figure properties for later reconstruction tofile - writes matrix to a specified file, in ascii UTILITY boottime - elapsed time of a bootstrapped analysis degday - convert temperature measurements to accum degree-days julian - Julian date (day of year, 1-365) loadchar - loads a character matrix from an ascii text file testans - generate random answers for a multiple-choice test ECOLOGY coeffdispersion - finds coefficient of dispersion of points on grid diverdiff - significance of difference in diversity between assemblages diversity - diversity and evenness indices diversf - objective function for diversity() jaccard - Jaccard measure of association (similarity) jaccardd - Jaccard distance percdist - percent-similarity distance measure rarefact - rarefaction analysis of assemblage renkonen - Renkenon's percent-similarity distance measure GENETICS allelefreq - allele frequencies and heterozygosity estimates basediff - proportional difference in base sequences between two taxa basediffp - creates pairwise contrasts from matrix of sequence data fstat - Wright's F-statistics, bootstrapped fstatcum - accumulation curves for F-statistics across populations hetcum - heterozygosity accumulation curves among popls heterozyg - heterozygosity estimates HI, HS, HT hwexact - exact Hardy-Weinberg probabilities (1 locus, 2 alleles) hwmult - asymptotic or permutation G-test for multiple alleles hwmultll - log-likelihood G-statistic for multiple-allele test micsatfs - measures of population subdivision based on microsatellite loci micsatvs - variance statistics I,S,T micsatgd - genetic distances based on microsatellite loci micsatfr - allele frequencies from data on individuals micsatds - genetic distance matrix mindetect - minimum sample size needed to detect a given allele frequency mindetectf - randomization function for mindetect() repeats - test statistical significance of tandem repeats