% Exploratory Data Analysis (EDA) Toolbox
% 
% Contents
% Version 1.0, November 2004
% Contributed files may contain copyrights of their own.
% This toolbox is meant to accompany the book: Exploratory Data Analysis
% with MATLAB, Wendy and Angel Martinez, CRC Press, 2004.
% 
% LICENSE:
% The EDA Toolbox comes with ABSOLUTELY NO WARRANTY; for details
% see license.txt. This is free software and is provided under the GNU license.
% You are welcome to redistribute it under certain conditions;
% see License.txt and http://www.gnu.org/copyleft/gpl.html
%
% DISCLAIMER:
% This software and documentation are distributed in the hope that they will be useful, 
% but they are distributed without any warranty and without even the implied warranty of 
% correctness or fitness for a particular purpose. 
% 
% The federal government, in particular the Department of the Navy and the Department of Defense, 
% disclaims all responsibility for this software and any outcome from its use. In addition, 
% this software and documentation does not reflect the views of and is not endorsed by the federal 
% government nor the Department of the Navy.
% 
% The code has been tested with care, but is not guaranteed to be free of defects and is not guaranteed 
% for any particular purpose. Bug reports and suggestions for improvements are always welcome at
% wendymar@myexcel.com.
%
% HELP files:
% Can be accessed via Contents.html.
%
% CLUSTERING
% adjrand	        Adjusted Rand index to compare groupings.
% agmclust	        Model-based agglomerative clustering.
% genmix	        GUI to generate random variables from finite mixture.
% mbcfinmix	        Model-based finite mixture estimation - EM.
% mbclust	        Model-based clustering.
% mixclass	        Classification using mixture model.
% mojenaplot        'Mojena Rule' plot for estimating the number of clsuters
% plotbic	        Plot the BIC values from model-based clustering.
% randind	        Rand index to compare groupings.
% reclus	        ReClus plot to visualize cluster output.
% rectplot	        Rectangle plot to visualize hierarchical clustering.
% treemap	        Treemap display for hierarchical clustering.
% 
% DATA TOURS
% csppstrtrem	    Remove structure in PPEDA.
% intour	        Interpolation tour of the data.
% kdimtour	        k-dimensional grand tour.
% permtourandrews     Permutation tour using Andrews’ curves.
% permtourparallel    Permutation tour using parallel coordinate plots.
% ppeda	            Projection pursuit EDA.
% pseudotour	    Pseudo grand tour.
% torustour	        Asimov grand tour
% 
% DIMENSIONALITY REDUCTION
% gtm_pmd	        Calculates posterior mode projection (GTM Toolbox).
% gtm_pmn	        Calculates posterior mean projection (GTM Toolbox).
% gtm_stp2	        Generates components of a GTM (GTM Toolbox).
% gtm_trn	        Train the GTM using EM (GTM Toolbox).
% GTM Toolbox       The entire GTM Toolbox is included.
% hlle	            Hessian eigenmaps.
% idpettis	        Intrinsic dimensionality estimate.
% isomap	        ISOMAP nonlinear dimensionality reduction.
% lle	            Locally linear embedding.
% nmmds	            Nonmetric multidimensional scaling.
% som_autolabel	    Automatic labeling (SOM Toolbox).
% som_data_struct	Create a data structure (SOM Toolbox).
% som_make	        Create, initialize and train SOM (SOM Toolbox).
% som_normalize	    Normalize data (SOM Toolbox).
% som_set	        Set up SOM structures (SOM Toolbox).
% som_show	        Basic SOM visualization (SOM Toolbox).
% som_show_add	    Shows hits, labels and trajectories (SOM Toolbox).
% SOM Toolbox       The entire SOM Toolbox is included.
% 
% DISTRIBUTION SHAPES
% bagmat.exe	    Executable file to get arrays needed for bagplot.
% bagplot	        M-file to construct actual bagplot.
% boxp	            Boxplot - regular.
% boxprct	        Box-percentile plot.
% polarloess	    Bivariate smoothing using loess.
% quantileseda	    Sample quantiles.
% quartiles	        Sample quartiles using Tukey’s fourths.
% 
% GUIs
% brushscatter      Scatterplot brushing and linking.
% genmix		    Executable file to get arrays needed for bagplot.
% isomapeda      	Explore results of ISOMAP.
% scattergui	    Scatterplot with interactive labeling.
% 
% SMOOTHING
% loess	            1-D loess scatterplot smoothing.
% loess2 	        2-D loess smoothing from Data Visualization Toolbox.
% loessenv	        Loess upper and lower envelopes.
% loessr	        Robust loess scatterplot smoothing.
% polarloess	    Bivariate smoothing using loess.
% 
% VISUALIZATION
% brushscatter	    Scatterplot brushing and linking.
% coplot	        Coplot from Data Visualization Toolbox.
% csandrews	        Andrews' curves plot.
% csparallel	    Parallel coordinates plot.
% dotchart	        Dot chart plot.
% hexplot	        Hexagonal binning for scatterplot.
% mojenaplot        'Mojena Rule' plot for estimating the number of clsuters
% multiwayplot	    Multiway dot charts.
% plotbic	        Plot the BIC values from model-based clustering.
% plotmatrixandr	Plot matrix of Andrews' curves.
% plotmatrixpara	Plot matrix of parallel coordinates.
% reclus	        ReClus plot to visualize cluster output.
% rectplot	        Rectangle plot to visualize hierarchical clustering.
% scattergui	    Scatterplot with interactive labeling.
% treemap	        Treemap display for hierarchical clustering.
% 
% DATA SETS
% abrasion        Rubber experiments
% animal          Brain weights and body weights of animals
% bank            Genuine and forged money
% calibrat        Radioactivity counts to hormone level
% cereal          Assessment of eight brands of cereal
% environmental   Environmental variables: ozone, solar radiation, temperature, wind speed
% ethanol         Compression ratio, equivalence ratio, NO_x for a single-cylinder engine
% forearm         Length in inches of the forearm of adult males
% example*        Various data sets for the example in the boook
% galaxy          Velocities of the spiral galaxy
% geyser          Waiting times in minutes between eruptions of the Old Faithful geyser
% hamster         Organ weights for hamsters with congenital heart failure
% iradbpm         Interpoint distance matrix (IRad) for the BPM data set
% iris            Fisher's iris data. Species are in different arrays.
% L1bpm           Interpoint distance matrix (L1) for the BPM data set
% leukemia        Gene expression level of patients with leukemia
% livestock       Livestock counts from a 1987 census of farm animals
% lsiex           Term-document matrix used in Example 2.3, illustrating LSI
% lungA           Gene expression data for lung cancer
% lungB           Gene expression data for lung cancer    
% matchbpm        Interpoint distance matrix (match coefficient) for the BPM data set
% ochiaibpm       Interpoint distance matrix (Ochiai similarity measure) for the BPM data set
% oronsay         Particle size measurements for sand
% ozone           Daily maximum ozone concentrations at ground level on 132 days in 1974
% playfair        Populations of 22 cities and diameters used for display by William Playfair
% pollen          Artificial data set created for 1986 Joint Statistical Meetings
% posse           Data sets from Christian Posse, used for projection pursuit EDA
% salmon          Size of spawning stock of salmon along the Skeena River
% scurve          Data from an S-curve manifold
% singer          Height in inches of singers
% skulls          Measurements of 40 skulls. 18 are female and 22 are male
% software        Data on software inspections
% spam            Attributes of email, some of which are spam
% sparrow         Measurements on sparrows. The first 21 survived, and the rest died.
% swissroll       Data from the Swiss roll manifold
% votfraud        Democratic and Republican pluralities of voting machines and absentee votes
% yeast           Gene expression data for yeast cells - two cell cycles and five phases
% 
% CONTENTS IN ALPHABETICAL ORDER:
% adjrand	        Adjusted Rand index to compare groupings.
% agmclust	        Model-based agglomerative clustering.
% bagmat.exe	    Executable file to get arrays needed for bagplot.
% bagplot	        M-file to construct actual bagplot.
% boxp	            Boxplot - regular.
% boxprct	        Box-percentile plot.
% brushscatter	    Scatterplot brushing and linking.
% coplot	        Coplot from Data Visualization Toolbox.
% csandrews	        Andrews' curves plot.
% csparallel	    Parallel coordinates plot.
% csppstrtrem	    Remove structure in PPEDA.
% dotchart	        Dot chart plot.
% genmix	        GUI to generate random variables from finite mixture.
% gtm_pmd	        Calculates posterior mode projection (GTM Toolbox).
% gtm_pmn	        Calculates posterior mean projection (GTM Toolbox).
% gtm_stp2	        Generates components of a GTM (GTM Toolbox).
% gtm_trn	        Train the GTM using EM (GTM Toolbox).
% GTM Toolbox       The entire GTM Toolbox is included.
% hexplot	        Hexagonal binning for scatterplot.
% hlle	            Hessian eigenmaps.
% idpettis	        Intrinsic dimensionality estimate.
% intour	        Interpolation tour of the data.
% isomap	        ISOMAP nonlinear dimensionality reduction.
% isomapeda         Explore results of ISOMAP.
% kdimtour	        k-dimensional grand tour.
% lle	            Locally linear embedding.
% loess	            1-D loess scatterplot smoothing.
% loess2 	        2-D loess smoothing from Data Visualization Toolbox.
% loessenv	        Loess upper and lower envelopes.
% loessr	        Robust loess scatterplot smoothing.
% mbcfinmix	        Model-based finite mixture estimation - EM.
% mbclust	        Model-based clustering.
% mixclass	        Classification using mixture model.
% mojenaplot        'Mojena Rule' plot for estimating the number of clusters
% multiwayplot	    Multiway dot charts.
% nmmds	            Nonmetric multidimensional scaling.
% permtourandrews     Permutation tour using Andrews’ curves.
% permtourparallel    Permutation tour using parallel coordinate plots.
% plotbic	        Plot the BIC values from model-based clustering.
% plotmatrixandr	Plot matrix of Andrews’ curves.
% plotmatrixpara	Plot matrix of parallel coordinates.
% polarloess	    Bivariate smoothing using loess.
% ppeda	            Projection pursuit EDA.
% pseudotour	    Pseudo grand tour.
% quantileseda	    Sample quantiles.
% quartiles	        Sample quartiles using Tukey’s fourths.
% randind	        Rand index to compare groupings.
% reclus	        ReClus plot to visualize cluster output.
% rectplot	        Rectangle plot to visualize hierarchical clustering.
% scattergui	    Scatterplot with interactive labeling.
% som_autolabel	    Automatic labeling (SOM Toolbox).
% som_data_struct	Create a data structure (SOM Toolbox).
% som_make	        Create, initialize and train SOM (SOM Toolbox).
% som_normalize	    Normalize data (SOM Toolbox).
% som_set	        Set up SOM structures (SOM Toolbox).
% som_show	        Basic SOM visualization (SOM Toolbox).
% som_show_add	    Shows hits, labels and trajectories (SOM Toolbox).
% SOMToolbox        The entire SOM Toolbox is included.
% torustour	        Asimov grand tour
% treemap	        Treemap display for hierarchical clustering.


