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