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Exploratory Data Analysis (EDA) Toolbox

Contents
Version 1.0, November 2004

The EDA Toolbox comes with absolutely no warranty and is distributed under the GNU license. For details see the license.txt file. This is free
software, and you are welcome to redistribute it under certain conditions (see the license.txt file and the GNU license)

It is intended that this toolbox accompany the book Exploratory Data Analysis with MATLAB, Wendy and Angel Martinez, CRC Press, 2004.
However, you do not need the book to use this toolbox.

We have several upgrades in mind (GUIs, functions), so please keep checking the download websites for new versions.

Acknowledgments

Disclaimer

Platform

Installation

Contents by category

Contents in alphabetical order

Data Sets

Documentation

GTM Toolbox

SOM Toolbox

Acknowledgments:
We would like to acknowledge code that has been contributed by other authors (under the GNU license):

GTM Toolbox
SOM Toolbox
ISOMAP
LLE
HLLE
Data Visualization Toolbox
Model-Based Clustering Toolbox

Other references are available on the above websites and on the individual function help pages. We are also grateful for helpful suggestions
regarding MATLAB coding from Tom Lane, The MathWorks, Inc.

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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.

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Platform:
This code has been developed for the Windows system, using MATLAB 6.5 and 7.0. The M-file functions should work on any platform, but the
installation steps would be different. Consult your system files or The MathWorks website for more information.

Note that for full functionality, the user should have the MATLAB Statistics Toolbox, Version 4 or higher.

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Installation:

The following installation instructions are for Windows versions of MATLAB. This toolbox can also be used with Unix and Linux operating
systems, with suitable changes to the directory structure for toolboxes and paths.

1. First download the required files and save it in a temporary directory.

2. Make a new directory under your current MATLAB toolbox installation. In most cases, this would be: C:\MATLAB7\toolbox\edatool
3. Double click on the.zip file and extract files to the above directory. Note that you could also create this new directory in the unzipping
process.
4. The MATLAB search path must be updated for you to use the toolbox files from any directory. The search path is kept in the pathdef.m file.
By default, it is stored in the following directory: C:\MATLAB7\toolbox\local
5. Before starting MATLAB, open the file pathdef.m using any text editor. One way to do this is to double-click on the file from Windows
Explorer. This will open the file in the MATLAB text editor. Add the new directory matlabroot, '\toolbox\edatool;',... to the path.
6. Close and save the file. Start MATLAB. Type helpwin at the command line to bring up the Help Browser. Click on edatool for a list of the
available functions in the EDA Toolbox.

Alternative way to set the path:

a. Start MATLAB.
b. Start the Set Path dialog box from the File menu in the MATLAB Command Window.
c. Add the new directory for the EDA Toolbox to the path. Hit the Save button to permanently save your changes to the pathdef.m
file.
d. Close MATLAB and restart it to see the changes in the Help files.

Changing the MATLAB environment for the EDA Toolbox:

1. To provide access to the toolbox via the START button, see the instructions on The MathWorks online documentation.
2. To add the Help files in the Help Browser, see the instructions on The MathWorks online documentation.

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Contents by Category
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 clusters
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).
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).

DISTRIBUTION SHAPES
bagmat.exe Executable file to get arrays needed for bagplot.
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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 clusters
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.
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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

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votfraud Democratic and Republican pluralities of voting machines and absentee votes
yeast Gene expression data for yeast cells - two cell cycles and five phases
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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).
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).
torustour Asimov grand tour
treemap Treemap display for hierarchical clustering.
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