% cl - same as clc % clz - same as clear + clc + close all % f_AIC - compute AIC (or BIC) for least-squares based methods or classifiers % f_CCorA - canonical correlation analysis (CCorA) % f_CCorA_PL - CCorA based on P. Legendre's vegan code % f_CCorAplot - plot results from a CCorA analysis % f_NSIDCimport - import a National Snow & Ice Data Center (NSIDC) sea ice coverage binary file % f_NSIDCinterp - interpolate sea ice coverage values for a specific location % f_adjustP - adjust p-values for multiple comparison tests % f_ancova - nonparametric (permutation-based) 1-way ANCOVA % f_ancovaPW - a posteriori, multiple-comparison tests for Homogeneous Slopes in ANCOVA % f_anosim - 1-way Analysis of Similarity (ANOSIM) % f_anosim2 - 2-way crossed ANOSIM with no replication % f_arrow - draw an arrow % f_author - display author and license information for the 'Fathom Toolbox for Matlab' % f_balance - get indices of elements to create a balanced design % f_bartlett - Bartlett's test for Homogeneity of Variances % f_beep - play a custom sound file % f_betainc - incomplete beta function ('non-regularized') % f_bioenv - correlation between distance matrix and all subsets of X (BEST or BIOENV) % f_biplot - eigenvector-based 2-d distance biplot % f_biplotEnv2 - create environmental vectors for 2-d nMDS ordination distance biplot % f_biplotEnv3 - create environmental vectors for 3-d nMDS ordination distance biplot % f_biplotPca2 - create 2-d PCA distance biplot % f_biplotSpecies - create species vectors for ordination distance biplot % f_boot - bootstrap resampling with replacement % f_bootCI - bootstrapped confidence interval of the mean for univariate data % f_braycurtis - legacy Bray-Curtis symmetric distance matrix function % f_brokenstick - determine # of significant ordination dimensions via "Broken-Stick model" % f_brush2idx - create index to rows of data currently selected by 'brushing' % f_bubble - create B&W bubble plots % f_butter - smooth columns of time series data via Butterworth lowpass filter % f_cap - Canonical Analysis of Principal Coordinates (CAP) using ANY distance matrix % f_capMLE - maximum likelihood estimator of mixture proportions based on CAP % f_capOptimal - get optimal value of m for f_cap % f_capPlot - plot results from a CAP analysis % f_cda - Canonical Discriminant Analysis % f_cda632 - estimate CDA error rate using bootstrap .632+ rule % f_cdaBCV - bootstrap cross-validation for Canonical Discriminant Analysis % f_cdaCV - leave-one-out cross validation for Canonical Discriminant Analysis % f_cdaClass - classify unknown observations for f_cda % f_cdaPlot - plot results from a Canonical Discriminant Analysis % f_cellstr2cat - convert a cell array of strings to a single categorical variable % f_cellstr2num - convert a cell array of strings to a single categorical variable % f_center - center data on column mean % f_central - central tendency (mean, median, or mode) % f_centroid - returns coordinates of the centroid of X, optionally partitioned into groups % f_chanceClass - classification success expected by chance (= proportional chance criterion) % f_chisqIndep - Chi-square test of independence (= homogeneity of proportions) % f_clock - current date and time as hyphen ('-') delimited character string % f_cluster - UPGMA-based cluster analysis of a symmetric dissimilarity matrix % f_colormap - create a custom colormap % f_compet - get index of column containing the maximum value of each row % f_confEllipse - parametric or bootstrapped confidence ellipse for bivariate data % f_convHull - convex hull for bivariate data % f_copy - copies a numerical-array to the clipboard % f_corr - Pearson's, Spearman's, or Kendall's correlation between 2 vectors % f_corrSign - determine if a correlation b/n 2 vectors is positive or negative % f_correlogram - multivariate Mantel correlogram % f_cov - returns covariance (= dispersion) matrix from X % f_covPool - covariance matrix pooled across groups % f_cv - coefficient of variation % f_deg2utm - convert lat/lon vectors into UTM coordinates (WGS84) % f_delaunay - create a Delaunay triangulation from 2-D spatial coordinates % f_depthCM - 'Depth of Center of Mass' for plankton survey data % f_depthMean - weighted 'Mean Depth of Occurrence' for plankton survey data % f_designMatrix - create ANOVA design matrix using dummy variables % f_diag - replace diagonals of a square matrix % f_dis - create symmetric dissimilarity (or distance) matrix % f_dis2sim - convert square symmetric distance matrix to a similarity matrix % f_disprof - dissimilarity profile analysis (DISPROF, SIMPROF) % f_disprof_clust - dissimilarity profile analysis (DISPROF) of a cluster analysis dendrogram % f_disprof_clustPlot - plot dendrogram of a DISPROF-based custer analysis % f_disprof_clust_bin - compare 2 DISPROF binary connectivity matrices % f_dnn - distance-based Nearest Neighbor Graph from 2-D spatial coordinates % f_dummy - dummy coding of categorical variables % f_dummy2cat - convert dummy codes to a single categorical variable % f_eig - eigenanalysis of a square matrix % f_eigenMaps - create Moran's eigenvector maps from spatial coordinates % f_eigenMapsStepwise - stepwise selection of Moran's Eigenvector Maps (MEM's) % f_ekmanDepth - depth of the Ekman layer % f_empPDF - empirical probability density function % f_errRate - error rate for a classifier % f_euclid - legacy Euclidean distance matrix function % f_export - write ASCII delimited file. % f_exportDods - export DODS bathymetry for import into Surfer % f_exportR - export data for import into R % f_extractFields - extract structure fields & combine into a single matrix % f_figArea - finds the area of figure objects % f_filterMA - smooth columns of a matrix using a Moving Average (or Median) % f_filterSinclair - filter/smooth columns of a matrix via 11-point Moving Median + Average % f_findCell - index to rows of Y that match X % f_firstOccur - returns indices of the first occurrence of unique elements of input vector % f_gabriel - create a Gabriel graph from 2-D spatial coordinates % f_getNLOM - download Navy Layered Ocean Model SSH Nowcast imagery % f_gower - Gower's centered matrix % f_graphviz_mds - create a Graphviz DOT file to perform multidimensional scaling (MDS) % f_graphviz_mst - export a minimal spanning tree to Graphviz DOT format % f_graphviz_neato - create an undirected graph using Graphviz % f_greenwood - Greenwood's statistic % f_greenwood_cdf - cumulative probability density function for Greenwood's statistic % f_greenwood_par - get parameters of the distribution of Greenwood's statistic for n>2 % f_greenwood_pdf - probability density function for Greenwood's statistic % f_greenwood_plt - plot the PDF or CDF for Greenwood's statistic % f_greenwood_rnd - randomized distribution of Greenwood's statistic % f_gregorian - convert Julian date to Gregorian % f_grpBoot - within-group bootstrap sampling (fixed size) % f_grpBootMix - within-group bootstrap sampling (variable size), with mixing among columns % f_grpMean - returns the mean/stdv/se of X (column-wise) separately for groups % f_grpOutlier - logical index identifying outliers, separately for each group % f_grpPlot - group plotting function % f_grpRel - returns the relative proportion of X (column-wise) separately for groups % f_grpResample - within-group resampling or bootstrapping (variable size) % f_grpSize - get the number of observations in each category for a grouping variable % f_gshhs2Shp - export a shapefile from the GSHHS database for use in Surfer/Arcview % f_halfchange - scale nMDS configuration to half-change % f_hellinger - Hellinger transform data or create a symmetric dissimilarity matrix % f_helmert - Helmert orthogonal contrast codes for an ANOVA design matrix % f_hist - create a normalized histogram plot of a column vector % f_ibc - indicator-species based cluster analysis % f_importCSV - import numeric data from a comma-separated-values (*.csv) file % f_importShapefile - import ArcView shapefile for M_Map Mapping Toolbox % f_importSurfer - import Surfer *.bln blanking file for M_Map % f_importSurferBln - import Surfer *.bln blanking file for M_Map % f_importSurferGrd - import Surfer GRID (*.grd) file % f_indVal - species indicator values % f_inv - matrix inversion via "\" (left division) % f_isAbsent - determine which rows of A are absent from B % f_isDST - determine if dates occur during Daylight Savings Time % f_isOdd - determine if integer is odd or even % f_isPresent - determine which rows of A are present in B % f_isScalar - determine if input is a scalar % f_issymSim - determine if input is square symmetric similarity matrix % f_issymdis - determine if input is square symmetric distance matrix % f_julian - convert date vector to Julian date % f_julianSub - get indices to subsample a series of Julian dates % f_kde - Botev's nonparametric kernel density estimator for univariate data % f_labelplot - create 2-d label plot % f_latlong - compute terrestrial distance matrix % f_leapYear - determine if a year is a leap year % f_lenfreq - length-frequency plot (adjusted for sampling effort) % f_ll2utm - legacy function (use f_deg2utm instead) % f_lowpass - smooth columns of a matrix via a lowpass filter % f_lowpass40 - smooth columns of a matrix via a 6th order, 40-hr lowpass filter % f_mad - median absolute deviation % f_mantel - standardized Mantel statistic for 2 symmetric distance matrices % f_mle - maximum likelihood estimator of mixture proportions via an EM algorithm % f_mleCook - maximum likelihood estimation via Cook's constrained corrected classification % f_mocnessAb - returns abundance (# under 10 m^2 of sea surface) % f_modelMatrix - create model matrix for a Mantel Test % f_month2num - convert month string to number % f_moran - Moran's coefficient of spatial autocorrelation % f_mregress - Multiple Linear Regression via Least Squares Estimation % f_mst - Minimum Spanning Tree from a symmetric distance matrix % f_mst_mex - create a minimal spanning tree (MEX version) % f_mst_old - legacy version of f_mst % f_multicomb - generate permutation distribution of grouping labels % f_nan2ave - replace missing values (NaN's) with average value (columnwise) by group % f_ncap - Nonlinear Canonical Analysis of Principal Coordinates (NCAP) % f_ncapOptimal - evaluate a range of values of m for f_ncap % f_nmds - Nonmetric Multidimensional Scaling (nMDS) % f_nmdsPlot - plot results from a nonmetric Multidimensional Scaling (nMDS) % f_nnMLP - feedforward multilayer perceptron neural network for classification % f_nnMLP632 - estimate MLP error rate using bootstrap .632+ rule % f_nnMLPcv - leave-one-out cross validation for f_nnMLP % f_normal - normalize values of X % f_npDisp - distance-based measures of multivariate dispersion % f_npDispAll - similar to f_npDisp, but returns distance to all centroids % f_npDispPlot - plot distance-based measures of Homogeneity in Multivariate Dispersion % f_npMLE - distance-based, maximum likelihood estimator % f_npManova - nonparametric (permutation-based) MANOVA for ANY distance matrix % f_npManovaPW - a posteriori, multiple-comparison tests % f_num2cell - convert a vector of numbers to a cell array of strings % f_numAtLength - estimate number of fish within length classes for visual survey data % f_origin - mark the origin of a graph with horizontal/vertical line(s) % f_outlier - calculate outlier measures for a symmetric proximity (similarity) matrix % f_outlyingness - normalized measure of outlyingness % f_outlyingness_test - permutation test of maximum outlyingness % f_parse - parse matrix to structure % f_pca - Principal Component Analysis of a data matrix % f_pcaPlot - plot results from a Principal Components Analysis % f_pcnm - Principal Coordinates of Neighbor Matrices (PCNM) from spatial coordinates % f_pcoa - Principal Coordinates Analysis (PCoA) % f_pcoaPlot - plot results from a Principal Coordinates Analysis % f_pdf - export current figure to PDF file % f_pdfCrop - crop a PDF file to its bounding box % f_pdfDistill - distill Postscript files to PDF using Acrobat Distiller % f_pdfLatex - typeset a LaTeX file % f_pdfMerge - merge a series of PS (or PDF) files into a single PDF % f_pdfSplit - split a multipage PDF file into separate single-page PDF's % f_perError - percent error between measured and accepted values % f_permtest - two sample permutation test of means % f_perturb - randomly perturb the values of a matrix, separately for each column % f_plotBarsH - horizontal bar graphs % f_plotBarsV - vertical bar graphs % f_plotError - add error bars to current figure % f_plotNeigh - plotting function for f_delaunay, f_dnn, f_gabriel, f_mst, & f_relNeigh % f_plotUSGS - plot USGS Coastwatch SST image with M_Map Toolbox % f_pnn - Probabilistic Neural Network % f_pnn632 - estimate PNN error using bootstrap .632+ rule % f_pnnAIC - stepwise selection of explanatory variables in PNN using AIC (or BIC) % f_pnnCV - leave-one-out cross validation for PNN % f_pnnSm - determine optimal smoothing factor for a PNN % f_poly - create a matrix of polynomials of degree d % f_prd - percent relative difference between 2 sets of values % f_procrustes - Procrustes rotation of Y to X % f_qSort - quick sort elements i:j of a vector, ascending % f_randDir - draw random numbers from a Dirichlet distribution % f_randRange - returns n random integers ranging from min to max % f_randSub - extract a random subset of N rows from matrix X % f_randWH - Wichmann & Hill's (2006) good pseudo-random number generator % f_range - return the min and max values of a vector % f_ranging - scale columns of x to range [0 to 1] or [-1 to 1] % f_ranks - ranks data in X (column-wise) with averaging of ties % f_rda - Redundancy Analysis (RDA) % f_rdaAIC - stepwise forward selection of explanatory variables in RDA using AIC (or BIC) % f_rdaAnova - permutation-based (M)ANOVA via RDA % f_rdaDB - distance-based Redundancy Analysis (db-RDA) % f_rdaDB_AIC - stepwise forward selection of explanatory variables in db-RDA using AIC (or BIC) % f_rdaDB_Stepwise - stepwise selection of explanatory variables in db-RDA based on F-stat % f_rdaDB_manova - nonparametric (permutation-based) MANOVA via db-RDA % f_rdaPlot - ordination distance biplot for a Redundancy Analysis (RDA) % f_rdaStepwise - stepwise selection of explanatory variables in RDA based on F-stat % f_readcwf - import a Coastwatch Satellite SST file % f_recode - recode elements of vector as consecutive integers % f_relNeigh - create a Relative Neighbor graph from 2-D spatial coordinates % f_rename - rename variable without memory reallocation % f_renameBatch - rename variables across multiple files % f_renameField - rename a structure field % f_rewrap - wraps vector into symmetric distance matrix (reverses f_unwrap) % f_rgb - utility program for selecting color of plot symbols % f_round - round data to specified number of decimal places % f_rsd - percent relative standard deviation % f_selectW - AIC-based selection of optimal spatial weighting matrices % f_shadeBox - shade subsets of a time series plot % f_shuffle - randomly sorts vector, matrix, or symmetric distance matrix % f_simper - similarity percentages (SIMPER) & species contributions among 2 groups % f_smooth - smooth columns of a matrix using a Moving Average filter % f_sort - sort elements of X (ascending) and create sorting/unsorting indices % f_stdErr - returns the standard error % f_stnd - standardize values of a matrix, column-wise (= z-scores) % f_struct2flat - turn a structure into a flat table & optionally export % f_style - utility program for selecting line styles % f_sub - subsample data every 6 hrs % f_subsetDisPW - extract subsets of distance matrix based on all pairs of a grouping factor % f_subsetPW - extract subsets of column vector based on all pairs of a grouping factor % f_svd - singular value decomposition of a matrix % f_swapInt - swap 2 integer values % f_symb - utility program for selecting plot symbols % f_table - display a matrix X in the command window % f_trajectory - get distance along a trajectory % f_transform - several methods for data transformation % f_unique - returns unsorted list of unique values % f_unwrap - unwrap lower tri-diagonal (w/o diag) of symmetric distance matrix into a column vector % f_utm2deg - convert vectors of UTM coordinates into Lat/Lon vectors (WGS84) % f_variogram - multivariate empirical variogram % f_vecAngle - counter-clockwise angle between 2 points % f_vecDiagram - plot progressive vector diagrams % f_vecMagDir - get magnitude & direction from u,v vector components % f_vecPlot - plot time series of velocity vectors % f_vecRot - rotate vectors (U,V) by angle THETA % f_vecRotAngle - determine the angle of an isobath % f_vecTrans - transform 2d vector coordinates % f_vecTrans3d - transform 3d vector coordinates % f_vecUV - returns U,V components of a vector given its magnitude & direction % f_vectorfit - plot environmental ordination vectors via multiple linear regression % f_vonBert - von Bertalanffy growth function % f_vonBertAge - age a fish of known length with the von Bertalanffy growth equation % f_vonBertModel - fit a von Bertalanffy growth model using nonlinear regression % f_vonBertModelInit - initial parameter estimate of a von Bertalanffy growth model % f_vonBert_La - calculate La parameter for the von Bertalanffy growth function % f_vonBert_t0 - calculate t0 parameter for the von Bertalanffy growth function % f_wascores - weighted-averages scores of species for a site ordination % f_windCMAN - process CMAN (or NDBC) historical wind data % f_windstress - wind stress in dynes/cm^2 % f_writeTxt - write character array to a text file % f_wtMean - weighted mean % f_xMatrix - design matrix of contrast codes for ANOVA linear models % f_xdiss - calculate Extended Dissimilarities from a symmetric distance matrix % f_xmlExtract - extract node, name, attribute, or tag from XML tree % finder - open present working directory in a MacOS X's 'FINDER' window % m_2D_surf - draw a 2D surface on an M_Map map % m_bubble - M_Map compatible version of f_bubble % m_extContours - extract contours from an M_Map map % m_ginput - get lon/lat coordinates from an M_Map figure % m_scaleBar - create horizontal scale bar for M_Map plots % m_subset - create a subset of an M_Map usercoast file % saver - save workspace to file tagged in 'fname' variable to current directory