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Object Oriented
Data Analysis
MONOGRAPHS ON STATISTICS AND APPLIED
PROBABILITY
Reasonable efforts have been made to publish reliable data and information, but the author and
publisher cannot assume responsibility for the validity of all materials or the consequences of
their use. The authors and publishers have attempted to trace the copyright holders of all material
reproduced in this publication and apologize to copyright holders if permission to publish in this
form has not been obtained. If any copyright material has not been acknowledged please write and
let us know so we may rectify in any future reprint.
Except as permitted under U.S. Copyright Law, no part of this book may be reprinted, reproduced,
transmitted, or utilized in any form by any electronic, mechanical, or other means, now known or
hereafter invented, including photocopying, microfilming, and recording, or in any information
storage or retrieval system, without written permission from the publishers.
For permission to photocopy or use material electronically from this work, access www.
copyright.com or contact the Copyright Clearance Center, Inc. (CCC), 222 Rosewood Drive,
Danvers, MA 01923, 978-750-8400. For works that are not available on CCC please contact
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Trademark notice: Product or corporate names may be trademarks or registered trademarks and
are used only for identification and explanation without intent to infringe.
DOI: 10.1201/9781351189675
Typeset in Nimbus
by KnowledgeWorks Global Ltd.
Dedication
To our families for their ongoing strong support over the many years it took to
fully develop these ideas, and to the many colleagues who have played a vital role
in shaping this approach to data analysis.
v
Contents
Preface xi
1 What Is OODA? 1
1.1 Case Study: Curves as Data Objects 3
1.2 Case Study: Shapes as Data Objects 10
1.2.1 The Segmentation Challenge 10
1.2.2 General Shape Representations 12
1.2.3 Skeletal Shape Representations 13
1.2.4 Bayes Segmentation via Principal Geodesic Analysis 15
2 Breadth of OODA 19
2.1 Amplitude and Phase Data Objects 19
2.2 Tree-Structured Data Objects 23
2.3 Sounds as Data Objects 25
2.4 Images as Data Objects 28
vii
viii CONTENTS
5 OODA Preprocessing 71
5.1 Visualization of Marginal Distributions 71
5.1.1 Case Study: Spanish Mortality Data 72
5.1.2 Case Study: Drug Discovery Data 74
5.2 Standardization–Appropriate Linear Scaling 85
5.2.1 Example: Two Scale Curve Data 86
5.2.2 Overview of Standardization 89
5.3 Transformation–Appropriate Nonlinear Scaling 91
5.4 Registration–Appropriate Alignment 94
6 Data Visualization 97
6.1 Heat-Map Views of Data Matrices 97
6.2 Curve Views of Matrices and Modes of Variation 104
6.3 Data Centering and Combined Views 107
6.4 Scatterplot Matrix Views of Scores 116
6.5 Alternatives to PCA Directions 120
Bibliography 371
Index 416
Preface
xi
xii PREFACE
Acknowledgments
Many of the ideas and presentation style have been developed during the teaching
of a graduate course entitled Object Oriented Data Analysis and have been taught
roughly every other year at the University of North Carolina since 2005. There
were some important precursors, including a related course taught at Cornell Uni-
versity in 2002. Two such courses were offered at the Statistical and Mathemati-
cal Sciences Institute in 2010 and 2011 with lecturers (beyond the authors of this
book) including Hans-Georg Müller, James O. Ramsay, and Jane-Ling Wang. The
course was also taught at the National University of Singapore in 2015.
Several events have played a pivotal role in the development of Object Oriented
Data Analysis. One was the Statistical and Mathematical Sciences Institute pro-
gram on “Analysis of Object Data” during 2010–2011, with co-organizers Hans-
Georg Müller, James O. Ramsay and Jane-Ling Wang. Another pivotal workshop
was the November 2012 “Statistics of Time Warpings and Phase Variations” at the
Mathematical Biosciences Institute, with co-organizers James O. Ramsay, Laura
Sangalli and Anuj Srivastava.
General research in this area by the authors has been supported over the years
by a number of grants from the National Science Foundation, including DMS-
9971649, DMS-0308331, DMS-0606577, DMS-0854908 and IIS-1633074, and
the Engineering and Physical Sciences Research Council grants EP/K022547/1
and EP/T003928/1.
The material on sounds as data objects was kindly provided by Davide Pigoli.
The authors are especially grateful to Stephan F. Huckemann, John T. Kent, James
O. Ramsay, and Anuj Srivastava for providing formal reviews of early drafts that
fundamentally impacted the final version. Additional useful comments on various
drafts have been provided by Iain Carmichael, Benjamin Elztner, Thomas Keefe,
Carson Mosso, Vic Patrangenaru, Stephen M. Pizer, Davide Pigoli, and Piercesare
Secchi.
The authors are grateful to John Kimmel, for helpful advice at many points, and
for his patience over the long time it took for this book to come together.
CHAPTER 1
What Is OODA?
The fields of human endeavor currently known as statistics, data science, and data
analytics have been radically transformed over the recent past. These transforma-
tions have been driven simultaneously by a massive increase in computational
capabilities coupled with a rapidly growing scientific appetite for ever deeper un-
derstanding and insights. The notion of forming a data matrix provides a useful
paradigm for understanding important aspects of how these fields are evolving.
In particular, the currently popular context of Big Data has several quite different
facets, ranging from low dimension high sample size areas (the basis of classi-
cal mathematical statistical thought, which is perhaps typified by sample survey
and census data), through both high dimension and sample sizes (common for in-
ternet scale data sets of many types), and on to high dimension low sample size
contexts (frequently encountered in areas such as genetics, medical imaging and
other types of extremely rich but relatively expensive measurements). The press-
ing need to analyze data in this wide array of contexts has generated many exciting
new ideas and approaches.
Yet a deeper look into these developments suggests that the organization of data
into a matrix may itself be imposing limitations. In particular, there is a growing
realization that the challenges presented by Big Data are being eclipsed by the
perhaps far greater challenges of Complex Data, which are typically not easily
represented as an unconstrained matrix of numbers. Object Oriented Data Anal-
ysis (OODA) provides a useful general framework for the consideration of many
types of Complex Data. It is deliberately intended to be particularly useful in the
analysis of data in complicated situations, diverse examples of which are given in
the first two chapters. The phrase OODA in this context was coined by Wang and
Marron (2007). An overview of the area was given in Marron and Alonso (2014).
For more discussion of Big Data and its relation to statistics, see Carmichael and
Marron (2018) and many interesting viewpoints in the special issue edited by San-
galli (2018).
The OODA viewpoint is easily understood through taking data objects to be
the atoms of a statistical analysis, where atom is meant in the sense of elementary
particle, studied in several contexts of increasing complexity:
• In a first course in statistics atoms are numbers, and the goal is to develop
methods for understanding of variation in populations of numbers.
• A more advanced course, termed multivariate analysis in the statistical culture,
generalizes the atoms, i.e. the data objects from numbers to vectors and in-
volves a host of methods for managing uncertainty in that context. For example
DOI: 10.1201/9781351189675-1 1
2 WHAT IS OODA?
see Mardia et al. (1979), Muirhead (1982), and Koch (2014) (for a more up to
date treatment).
• At the time of this writing a fashionable area in statistics is Functional Data
Analysis (FDA), where the goal is to analyze the variation in a population of
curves. A good introduction to this vibrant research area, where functions are
the data objects, can be found in Ramsay and Silverman (2002, 2005). A case
study, illustrating many of the basic concepts of FDA which are useful for
understanding OODA is given in Section 1.1.
• OODA provides the next step in terms of complexity of atoms of a statistical
analysis to a wide array of more complicated objects. The important example
of shapes as data objects is considered in the case study of Section 1.2. A wide
variety of other examples, which highlight the breadth of OODA, appears in
Chapter 2.
Note that each of the above areas can be thought of as containing the preced-
ing ones as special cases. For example, multivariate analysis is the case of FDA
where the functions are discretely supported. Similarly multivariate analysis and
FDA are special cases of OODA. In later chapters it is useful to recall that OODA
includes these predecessors as special cases. This is because often simple multi-
variate examples are used for maximal clarity in the illustration of concepts and
methods, but the ideas are useful more generally for OODA.
A good question is: What is the value added to applied statistics and data sci-
ence from the concept of OODA and its attendant terminology? The terminology
is based on very substantial real-world experience with a wide variety of complex
data sets. A fact that rapidly becomes clear in the course of interdisciplinary re-
search is that there frequently are substantial hurdles in terminology. Especially at
the beginning of such endeavors, it can feel like collaborators are even speaking
different languages, so often serious effort needs to be devoted to the develop-
ment of a common set of definitions just to carry on a useful discussion. An added
complication is that for complex data contexts, it is frequently not obvious how to
even “get a handle on the data”. Usually there are many options available, which
are most effectively decided upon through careful discussion between domain sci-
entists and statisticians. In such discussions, the issue of what should be the data
objects? has proven to frequently lead to useful choices, thus resulting in an ef-
fective and insightful data analysis.
Real data examples demonstrating data object choices in a variety of contexts
are given in the following and Chapter 2. In particular, Section 1.1 introduces
curves as data objects. A more complex variant involves curves with interesting
variation in phase in place of, or in addition to, the usual FDA amplitude variation
discussed in Section 2.1. A mathematically deeper case is considered in Section
1.2 where shapes are the data objects which require special treatment as shapes
are most naturally viewed as points on a curved manifold. Section 2.2 considers
a perhaps even more challenging data set of tree-structured data objects. The data
objects in Section 2.3 are recordings of sounds, in particular human spoken words,
Other documents randomly have
different content
Do not try to make the forward cast on just the same plane as the
back cast for fear that the end of the line should snap like a whip-
lash, which if you were actually fishing would crack off your flies
pretty certainly. Therefore make the lift of the back cast with a slight
sweep (generally inward towards the body is the more natural), and
deliver the forward cast straight out towards its destination. But
always aim about your own height above the spot on the water you
mean to reach to insure the line falling lightly.
In all your practising remember that the key-note of good casting
is in getting a good, clean, high back cast, and in never sending the
line forward until it is quite straight out behind and above you in the
back cast. If you have with you some one to guide you as to when it
is straightened out it will be a great gain, particularly as the time
required for the straightening varies with the length of line that is
used.
Do not try to cast a long line until you have learned to cast a short
one well; and well means not only with a high back cast and straight
forward, but also accurately as to aim and delicately.
A good bait for large fish is a strip cut from the under side of a
small pickerel, perch, or sunfish, which is placed on the hook as
shown in Fig. 14.
Baits, and Where to Find Them
Many of the boys and girls who live near the sea-side are
interested in making and stocking aquariums, and many, no doubt,
have experienced the same difficulty which I did when I used to
stock aquariums myself.
I always found that the scoop-net which we use to catch the fish
with is good enough for certain kinds of minnows, but there are
others which are too lively or too shy to be caught in that way; so I
set to work to devise some plan for their capture. I claim no
originality for this trap—it is hundreds of years old; but as it
answered my purpose better than anything else, I used it. The way I
made it was as follows:
I took a piece of wire-netting about three feet square and bent it
so as to form a tube three feet long and about one foot in diameter
(Fig. 15). I then took two other strips of wire-netting, three feet long
at the top, one foot wide, and two feet at the bottom (Fig. 16); these
I bent into funnel shape. I sewed one funnel in about the middle of
my cylinder and another in one end, as shown in Fig. 15,
strengthening them in their position with strings from the small ends
to the sides of the cylinder. The other end of the cylinder I closed
with a piece of strong bagging so sewed on that there was a space
left at one side which could be untied when I wished to empty the
trap.
The manner of setting the trap is as simple as its manufacture. A
handful of clams or mussels, crushed so that the minnows can get at
the flesh, is thrown in between the first and second funnels. The fish,
little crabs, small eels, and the like, go in, and when they try to get
out they find it much easier to swim through the second funnel than
to find the small hole in the first. I have had several of these traps,
or “pots,” as the fishermen call them, in operation at one time, and
have caught as many as half a bushel of small fish in one night.
The trap can be made by making a frame of hoops and lath and
covering it with mosquito-netting, but it is not so desirable as the
fine wire, being more easily torn.
A Water-turtle Trap
An Eel-pot
All along the Atlantic coast eel-pots are made on the same general
plan, a bottle-shaped basket having a funnel fitted at the bottom and
provided with a hat that is held on by two straps of green oak.
Three forms are used on which to build up the basket-work. The
large form is usually ten inches in diameter and shaped down to
eight inches at the top or neck. This form is two feet long and has a
round stick driven in the small end. This in turn rests in a hole bored
in a solid piece of plank, so that it is held in an inverted position and
revolves in the hole. Green oak is used for the ribs and bands. This is
cut as straight and free from knots as possible, and is soaked in
water for weeks before it is split and slivered. Green oak will sliver in
an even and uniform manner if it is started right, and from the trunk
of an oak-tree six inches in diameter enough material can be had to
make several dozen eel-pots. The ribs are three-quarters of an inch
wide and about one-eighth of an inch thick, while the bands are a
trifle thinner and wider. A number of the ribs are tied around the
form as shown in Fig. 18, and beginning at the bottom the bands are
woven in and out around the form, turning it as the work progresses
so that the immediate parts are always in sight. Where the ends join
they are shaved down thin so that one laps over the other; then the
weaving continues until the top is reached. The ends of the ribs are
then shaved thin and bent back and slipped under some of the
straps. A thin ribbon of the oak is sewed over and over around the
edge to finish it. The top or small end of the basket is finished in a
similar manner.
The cone or funnel form is fifteen inches long, nine inches in
diameter at the large end, and tapers down to two inches at the
bottom as shown in Fig. 19. Ribs are tied to this form the same as in
the case of the large one, and the weaving begins at the bottom and
is carried to the top, where the ends of the ribs are shaved and
turned in as before described. The bottom or small end of the funnel
is the trap, and here the long, thin ends of the ribs are left, so that
the eel, when he goes through the funnel and into the pot, cannot
get back again.
The hat is woven the same as a basket by crossing the ribs and
adding a half-rib from the centre anywhere on the circle, so as to
make an uneven number of ribs; thus the weaving will not duplicate
after the first turn around the circle. This extra rib is shown at A in
Fig. 20. A hat form, shown in Fig. 21, is made of wood and mounted
on a block so that it will revolve the same as the other forms. When
a part of the hat is woven it is placed on the form and two small nails
driven through the ribs into the form to hold the weaving in place. It
is then shaped down over the rounded edges of the form and carried
one or two inches below the form so the lower edges of the ribs can
be shaved and bent easily. A long strap of the green oak is passed
under one of the ribs in the hat and caught under bands of the body
as shown in the drawing of a complete eel-pot. Fig. 22.
The funnel is sewed to the bottom edge of the body with thin
bands. As soon as the pots are finished they should be sunk in
shallow water to keep them wet and get them thoroughly water-
soaked.
Stakes or poles are to be driven or worked down into the bottom
of the bay and the eel-pots made fast to them with ropes. To bait an
eel-pot crack some hard-shell crabs or shrimp or put some pieces of
fresh, raw meat within the pot and drop it overboard. Run the pots
morning and night, and remove the eels by unstrapping the cap and
dumping them into a barrel which may be carried on the boat.
A Scap-net
A Hoop Drop-net
A hoop drop-net such as shown at Fig. 24 may easily be made
from three galvanized-wire rings and a mesh of tied string as
described for the scap-net. The hoops should be eighteen inches in
diameter and separated ten inches, thus making a net twenty inches
deep. A mesh is to be formed across the bottom, and at the top six
small ropes are tied and the ends brought together fifteen or twenty
inches above the top ring.
Place some crushed crab or any good bait in the bottom of the net
and slowly lower it until the rings rest on the bottom of the bay or
pond, but keep the small ropes clear from the net. Watch through
the water for visitors, and when the right subject is at the bait and
within the rings give a quick jerk and pull the net rapidly to the
surface. If fish are to be caught in this manner the hoops should be
larger and one more added to the net, making it thirty inches deep.
Fish are cunning and swift, and will often dart up and over the top
hoop faster than you can haul it up.
Chapter X
A Land-yacht
A few years ago the only kind of yacht known to the boys were those
that sailed in the water, but in this advanced time, when many
unheard-of things have been made possible, the land-yacht has
made its welcome appearance. Down on the Southern coasts,
particularly Florida and California, where the sand packs fine and
hard, the land-yacht is an important feature both for pleasure and
business, and if properly handled in a good breeze it will run from
ten to twenty miles an hour. No end of fun can be had with a
properly constructed boat, and the ingenious boy may employ old
baby-carriage or bicycle wheels for the running-gear.
A yacht of medium size can be made on the lines of Fig. 1 at a
comparatively small cost for the timbers and sail-cloth, spars and
hardware. The leg-of-mutton sail is used in preference to the square
sail, as it has the greatest area close to the ground and is less liable
to upset and much easier to handle.
To begin with, obtain some spruce joist clear-grained and free from
knots. They should be two-by-four inches and twelve feet long. Cut
one of them eight feet long and use it for the main cross-piece to
which the front wheels are attached. Form a V of two twelve-foot
joist, and fasten them to the cross-piece as shown in Fig. 2. About
ten inches of each piece should project beyond the cross-piece. The
timbers are bolted fast and at the rear end they are bevelled and
brought together, then bolted through from side to side as shown in
the plan (Fig. 2). Three feet back of the long cross-piece a shorter
timber is set in between the V-shaped frame as shown at A. At the
middle of this timber a hole one inch and a half square is cut and
into it a tenon on the butt-end of the bowsprit fits as shown in Fig. 3.
The bowsprit is seven feet long and is bolted fast to the long
cross-piece. Where the end fits into the timber A two angle-blocks
are nailed fast. Seat-planking is cut and screwed or nailed fast to the
V-shaped frame as shown in both Fig. 1 and Fig. 2. The boards
should be ten inches wide and cut to overhang the timbers an inch
or two at both ends.
If the wheels from an old baby-carriage are to be used the axle
should be cut in half with a hack-saw and each part clamped under
an end of the cross-timber with U-shaped clamps having the ends
threaded and provided with nuts and washers as shown at Fig. 4.
The rear or steering wheel is set in a fork that a blacksmith will make
from strap-iron, and a round piece of the same metal, having a
square-headed upper end, will do for the rudder-post as shown at
Fig. 5. A short axle threaded at both ends and provided with nuts will
hold the wheel in place, and when the post is passed up through a
hole made in the timbers a tiller can be slipped over the square
shoulder and bolted fast so that it will stay in place.
The tiller is of hard-wood two inches broad at the rear end, one
inch in thickness, and tapered so that it will be about an inch square
with the corners rounded where it is grasped by the hand. The
handle part of it should be bound with linen cord to improve the grip.
Give the deck wood-work and timbering a few coats of red, buff, or
light-green paint.
The mast-step is rigged over the forward cross-timber. Two upright
pieces of board twenty inches long and eight inches wide are
attached to the outside edges of the frame-joist with screws. On top
of these a cross-piece is made fast so that the step presents the
appearance of a bench. Two pieces of board six inches wide are
fastened from the corners down to the bowsprit and cross-timber to
brace the step as shown at Fig. 6. An iron brace is made fast to the
top of the step, behind the mast, and to the bowsprit, as may be
seen in the illustration.
A hole three inches in diameter is cut at the middle of the step-
board, and through this the mast is slipped. A half-inch round iron is
driven into the bottom of the mast after a hole has been bored with
a bit. It should be long enough to project out about two inches. This
steps into a hole bored in the top of the bowsprit, and with the three
wire stays that are caught at the top of the mast and into the eye-
bolts, shown by the arrow-heads in Fig. 2, the mast is held securely
in place.