% FATHOM: A Matlab Toolbox for Ecological & Oceanographic Data Analysis
% by Dave Jones<djones@rsmas.miami.edu>               
% http://www.rsmas.miami.edu/personal/djones
%
% f_AIC             - compute AIC (or BIC) for least-squares based methods
% f_anosim          - 1-way Analysis of Similarity (ANOSIM)
% f_anosim2         - 2-way crossed ANOSIM with no replication
% f_arrow           - Draw an arrow.
% f_bartlett        - Bartlett's test for Homogeneity of Variances
% f_bioenv          - correlation between distance matrix and all possible subsets of x
% 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_braycurtis      - calculate Bray-Curtis symmetric distance matrix
% f_brokenstick     - determine # of significant ordination dimensions via "Broken-Stick model"
% f_cap             - Canonical Analysis of Principal Coordinates using ANY distance matrix
% f_capVectors      - correlation vector plot for f_cap
% f_cda             - Canonical Discriminant Analysis
% f_center          - center data on column mean
% f_centroid        - returns coordinates of the centroid of X, optionally partitioned into groups
% f_corr            - Pearson's, Spearman's, or Kendall's correlation between 2 vectors
% f_cov             - returns covariance (= dispersion) matrix from X
% 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_distlm          - Nonparametric Multivariate Multiple Regression for ANY distance matrix
% f_eig             - eigenanalysis of a square matrix
% f_ekmanDepth      - depth of the Ekman layer
% f_euclid          - computes Euclidean distance matrix
% 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_firstOccur      - returns indices of the first occurrence of unique elements of input vector
% f_gregorian       - convert Julian date to Gregorian
% f_grpMean         - returns the mean of X (columnwise) separately for groups
% f_grpRel          - returns the relative proportion of X (column-wise) separately for groups
% f_halfchange      - scale nMDS configuration to half-change
% f_importSurferBln - import Surfer *.bln blanking file for M_Map
% f_importSurferGrd - import Surfer GRID (*.grd) file
% f_inv             - matrix inversion via "\" (left division)
% f_isDST           - determine if dates occur during Daylight Savings Time
% f_isOdd           - determine if integer is odd or even
% 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_labelplot       - create 2-d label plot
% f_latlong         - computes terrestrial distance matrix
% f_leapYear        - determine if a year is a leap year
% f_lenfreq         - length-frequency plot (adjusted for sampling effort)
% f_ll2utm          - convert longitude/latitude coordinates to UTM
% f_lowpass         - smooth columns of a matrix via a lowpass filter
% f_mantel          - standardized Mantel statistic for 2 symmetric distance matrices
% f_modelMatrix     - create model matrix for a Mantel Test
% f_mregress        - Multiple Linear Regression via Least Squares Estimation
% f_mst             - Minimum Spanning Tree from a symmetric distance matrix
% f_multicomb       - generate permutation distribution of grouping labels
% f_nmds            - run Steyvers's nonmetric Multidimensional Scaling program
% f_normal          - normalize values of X
% f_npManova        - nonparametric (permutation-based) MANOVA for ANY distance matrix
% f_npManovaPW      - a posteriori, multiple-comparison tests
% f_origin          - mark the origin of a graph with horizontal/vertical line(s)
% f_pca             - Principal Component Analysis of a data matrix
% f_pcoa            - Principal Coordinates Analysis (PCoA)
% f_pcoa2           - legacy version of Principal Coordinates Analysis
% f_pdf             - export current figure to Acrobat PDF file
% f_permtest        - two sample permutation test of means
% f_plotError       - add error bars to current figure
% f_plotUSGS        - plot USGS Coastwatch SST image with M_Map Toolbox
% f_poly            - create a matrix of polynomials of degree d
% f_procrustes      - Procrustes rotation of Y to X
% f_randRange       - returns n random integers ranging from min to max
% f_range           - return the min and max values of a vector
% f_ranging         - scale columns of x to range 0-1
% f_ranks           - ranks data in x (with averaging of ties)
% f_rda             - Redundancy Analysis
% f_rdaAIC          - stepwise selection of explanatory variables in RDA using AIC (or BIC)
% f_rdaDB           - prepare non-Euclidean distance matrix for db-RDA
% f_rdaPlot         - Ordination distance biplot for a Redundancy Anaysis
% f_rdaStepwise     - stepwise (forward) selection of explanatory variables in RDA
% f_readcwf         - import a Coastwatch Satellite SST file
% f_recode          - elements of vector as consecutive integers
% f_rewrap          - wraps vector into symmetric distance matrix (reverses f_unwrap)
% f_rgb             - utility program for selecting color of plot symbols
% f_shadeBox        - shade subsets of a time series plot
% f_shuffle         - randomly sorts vector, matrix, or symmetric distance matrix
% f_smooth          - smooth columns of a maxtix using a Moving Average filter
% f_stnd            - standardize values of a matrix, column-wise (= z-scores)
% f_struct2flat     - a structure into a flat table & optionally export
% f_subsetDisPW     - extract subsets of distance matrix based on all pairs of grouping factor
% f_svd             - singular value decomposition of a matrix
% f_symb            - utility program for selecting plot symbols
% f_trajectory      - get distance along a trajectory
% f_transform       - transform data by 7 methods
% f_unwrap          - unwrap lower tri-diagonal (w/o diag) of symmetric distance matrix into a column vector
% f_vecAngle        - counter-clockwise angle between 2 points
% f_vecDiagram      - plot Progressive Vector Diagram
% f_vecMagDir       - get magnitude & direction from u,v vector components
% f_vecPlot         - plot time series of velocity vectors
% f_vectorfit       - plot environmental ordination vectors via multiple linear regression
% 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_wascores        - weighted-averages scores of species for a site ordination
% f_windCman        - process & rotate CMAN (or NDBC) historical wind data
% f_windstress      - wind stress in dynes/cm^2
% f_xdiss           - calculate Extended Dissimilarities from a symmetric distance matrix
% m_2D_surf         - Draws a 2D surface on a map
% m_extContours     - extract contours from an M_Map map
% m_ginput          - get lon/lat coordinates from an M_Map figure
%
%
% ----- Third party utility functions:
%
% m_2D_surf        - Draws a 2D surface on a map