heading 1 - home | department of physicsweb2.physics.miami.edu/~agleason/comp_other/disser… ·...

ACKNOWLEDGEMENTS

Insert acknowledgements here.

iii

TABLE OF CONTENTS

LIST OF FIGURES.........................................................................................................vii

LIST OF TABLES.............................................................................................................x

Chapter 1: Introduction.................................................................................................11.1 What can be mapped with single-beam acoustic seabed classification in

the coral reef environment?..................Error! Bookmark not defined.1.2 What applications can utilize single-beam acoustic seabed classification

in the coral reef environment?..............Error! Bookmark not defined.1.3 Outline ..................................................................Error! Bookmark not defined.

Chapter 2: Introduction to the QTC acoustic seabed classification system.....Error! Bookmark not defined.

Chapter 3: Consistency of single-beam acoustic seabed classification among multiple coral reef survey sites..............Error! Bookmark not defined.

3.1 Background.........................................................................................................43.2 Previous Work.......................................................Error! Bookmark not defined.3.3 Methods..................................................................Error! Bookmark not defined.

3.3.1 Acoustic surveys.........................................Error! Bookmark not defined.3.3.2 Acoustic classification.................................Error! Bookmark not defined.3.3.3 Identification of acoustic classes.................Error! Bookmark not defined.3.3.4 Accuracy assessment...................................Error! Bookmark not defined.

3.4 Results ..................................................................Error! Bookmark not defined.3.5 Analysis: where were the errors?........................Error! Bookmark not defined.

3.5.1 Lee Stocking Island.....................................Error! Bookmark not defined.3.5.2 Andros Island Area......................................Error! Bookmark not defined.3.5.3 Carysfort Reef and Fowey Rocks................Error! Bookmark not defined.

3.6 Discussion...............................................................Error! Bookmark not defined.3.7 Conclusions............................................................Error! Bookmark not defined.

Chapter 4: Reproducibility of single-beam acoustic seabed classification under variable survey conditions.....................Error! Bookmark not defined.

4.1 Background............................................................Error! Bookmark not defined.4.2 Previous work........................................................Error! Bookmark not defined.4.3 Methods..................................................................Error! Bookmark not defined.

4.3.1 Survey site and data acquisition..................Error! Bookmark not defined.4.3.2 Vessel attitude and grazing angle computation.........Error! Bookmark not defined.4.3.3 Acoustic data processing.............................Error! Bookmark not defined.4.3.4 Classification reproducibility......................Error! Bookmark not defined.

iv

4.3.5 Echo, FFV, and Q-value correlation with survey parameters.............Error! Bookmark not defined.

4.4 Results ..................................................................Error! Bookmark not defined.4.4.1 Environmental conditions, vessel attitude and grazing angle.............Error! Bookmark not defined.4.4.2 Classification reproducibility......................Error! Bookmark not defined.4.4.3 Echo, FFV, and Q-value correlation with survey parameters.............Error! Bookmark not defined.

4.5 Attempts to improve reproducibility...................Error! Bookmark not defined.4.5.1 Cluster into fewer classes............................Error! Bookmark not defined.

4.5.1.1 Merge baseline classes four through six into a single class.........Error! Bookmark not defined.4.5.1.2 ACE-2...................................................Error! Bookmark not defined.

4.5.2 Keep only near-nadir echoes.......................Error! Bookmark not defined.4.5.2.1 Within 5 degrees of vertical (echoes stacked by 5). .Error! Bookmark not defined.4.5.2.2 Pitch within 2 degrees of vertical (echoes stacked by 5).............Error! Bookmark not defined.4.5.2.3 Within 5 degrees of vertical (echoes stacked by 1). .Error! Bookmark not defined.4.5.2.4 Pitch only within 2 degrees of vertical (echoes stacked by 1).....Error! Bookmark not defined.4.5.2.5 Incidence angle less than 5 degrees (echoes stacked by 1)..........Error! Bookmark not defined.

4.5.3 Stability of principal components...............Error! Bookmark not defined.4.5.3.1 Robust PCA..........................................Error! Bookmark not defined.4.5.3.2 Consistent PCA.....................................Error! Bookmark not defined.4.5.3.3 Dataset Size..........................................Error! Bookmark not defined.

4.5.4 Features least subject to ping-to-ping variability......Error! Bookmark not defined.

4.6 Summary and Conclusions...................................Error! Bookmark not defined.

Chapter 5: Acoustic signatures of the seafloor: tools for predicting grouper habitat......................................................Error! Bookmark not defined.

5.1 Background............................................................Error! Bookmark not defined.5.2 Methods..................................................................Error! Bookmark not defined.

5.2.1 Acoustic Survey..........................................Error! Bookmark not defined.5.2.1.1 Data Collection and Seabed Classification........Error! Bookmark not defined.5.2.1.2 Acoustic Variability Index....................Error! Bookmark not defined.

5.2.2 Diver Survey...............................................Error! Bookmark not defined.5.2.3 Comparison of Acoustic and Diver Surveys.............Error! Bookmark not defined.

5.2.3.1 Acoustic Classification Accuracy Assessment...Error! Bookmark not defined.

v

5.2.3.2 Grouper Abundance vs. Acoustic Classification and Variability Error! Bookmark not defined.

5.3 Results ..................................................................Error! Bookmark not defined.5.3.1 Acoustic Survey..........................................Error! Bookmark not defined.5.3.2 Diver Survey...............................................Error! Bookmark not defined.5.3.3 Acoustic Classification Accuracy Assessment.........Error! Bookmark not defined.5.3.4 Grouper Abundance vs. Acoustic Classification and Variability.......Error! Bookmark not defined.


Chapter 6: Geomorphology of grouper and snapper spawning aggregation sites in the upper Florida Keys, USA. . .Error! Bookmark not defined.

6.1 Background............................................................Error! Bookmark not defined.6.2 Methods..................................................................Error! Bookmark not defined.

6.2.1 Acquisition and acoustic classification.......Error! Bookmark not defined.6.2.2 Identification of acoustic classes.................Error! Bookmark not defined.6.2.3 Diver-based assessment of classification at Carysfort Reef...............Error! Bookmark not defined.6.2.4 Locations of FSAs relative to seabed features..........Error! Bookmark not defined.6.2.5 Geomorphologic “signatures” of FSAs.......Error! Bookmark not defined.

6.3 Results ..................................................................Error! Bookmark not defined.6.3.1 Acquisition and acoustic classification.......Error! Bookmark not defined.6.3.2 Identification of acoustic classes.................Error! Bookmark not defined.6.3.3 Diver-based assessment of classification at Carysfort Reef...............Error! Bookmark not defined.6.3.4 Locations of FSAs relative to seabed features..........Error! Bookmark not defined.6.3.5 Geomorphologic “signatures” of FSAs.......Error! Bookmark not defined.


Chapter 7: Conclusions..................................................................................................6

References ................................................................................................................7

vi

LIST OF FIGURES

Figure 2.1: Flowchart of QTCV processing....................Error! Bookmark not defined.Figure 3.1: Map showing locations of Lee Stocking Island (LSI), Carysfort Reef

(CF), Fowey Rocks (FR), and Andros Island (AI) study sites........Error! Bookmark not defined.

Figure 3.2: Underwater photographs of pole-mounted transducer, video camera housing, and sample frames grabbed from underwater video.........Error! Bookmark not defined.

Figure 3.3: Sediment grain size distributions for samples from the survey areas..Error! Bookmark not defined.

Figure 3.4: LSI acoustic classification and video classification plotted on top of a true-color IKONOS image of the LSI study area..Error! Bookmark not defined.

Figure 3.5: Andros acoustic classification and video classification plotted on top of a true-color IKONOS image of the study area.........Error! Bookmark not defined.

Figure 3.6: Fowey rocks acoustic classes and diver estimated substrate...............Error! Bookmark not defined.

Figure 3.7: Within-frame accuracy for the LSI dataset...Error! Bookmark not defined.Figure 3.8: Depth-frequency histogram for sediment-dominated video frames in the

LSI dataset...............................................Error! Bookmark not defined.Figure 3.9: Classified acoustic tracks, video frames, and dive sites in the Adderly Cut

portion of LSI study area.........................Error! Bookmark not defined.Figure 3.10: Selected underwater photographs from the Adderly Cut portion of the LSI

study area.................................................Error! Bookmark not defined.Figure 3.11: Within-frame overall accuracy histogram for the Andros dataset.....Error!

Bookmark not defined.Figure 3.12: Oblique underwater photographs of four seabed types in the Andros Island

survey area...............................................Error! Bookmark not defined.Figure 3.13: Within-frame overall accuracy histograms for the Carysfort and Fowey

Rocks datasets..........................................Error! Bookmark not defined.Figure 3.14: Plot of overall accuracy as a function of the number of acoustic classes.

.................................................................Error! Bookmark not defined.Figure 3.15: Example of the utility of rock / sediment seabed classification in

interpreting bathymetry to predict fish habitat......Error! Bookmark not defined.

Figure 3.16: Cross shelf profile of part of the Navassa Island insular shelf...........Error! Bookmark not defined.

Figure 4.1: Fowey Rocks survey site and depth profiles..............Error! Bookmark not defined.

Figure 4.2: Wind speed and water temperature for the periods of the six surveys. Error! Bookmark not defined.

vii

Figure 4.3: Boxplots of daily mean and maximum within-stack attitude measurements..........................................Error! Bookmark not defined.

Figure 4.4: Transducer attitude data from May 28, 2007.............Error! Bookmark not defined.

Figure 4.5: Q-space of each of the six daily datasets clustered independently......Error! Bookmark not defined.

Figure 4.6: All 18 replicates of both the northern and southern transects..............Error! Bookmark not defined.

Figure 4.7: Independently classified replicate track lines lines, Q-space, and pitch measurements along the northern transect on May 2, 2007............Error! Bookmark not defined.

Figure 4.8: Classified track lines, Q-space, and pitch measurements along the transect for independent clustering of each pass along the northern transect on two days...................................................Error! Bookmark not defined.

Figure 4.9: Renumbering of daily classes.......................Error! Bookmark not defined.Figure 4.10: Plots illustrating the locations of four stations from which echoes,

FFVs, Q-values, and survey parameters were extracted.................Error! Bookmark not defined.

Figure 4.11: Plot of multidimensional angle between echo envelopes versus the distance between echoes for all pairwise comparisons at all four test stations.....................................................Error! Bookmark not defined.

Figure 4.12: Plot of multidimensional angle between echo envelopes versus the minimum grazing angle at the times of center echo of each stack..Error! Bookmark not defined.

Figure 4.13: Plot of the magnitude of the difference between echoes versus the minimum grazing angle at the times of center echo of each stack..Error! Bookmark not defined.

Figure 4.14: Plot of the magnitude of the difference between FFVs versus the minimum grazing angle at the times of center echo of each stack..Error! Bookmark not defined.

Figure 4.15: Plots of daily Q-space (left) and renumbering of daily classes (right) for datasets classified by ACE with just two clusters. Error! Bookmark not defined.

Figure 4.16: Plot of Q-space for each day and renumbering of daily ACE classes after filtering out all stacks with maximum transducer pointing vector greater than 5 degrees off vertical...........Error! Bookmark not defined.

Figure 4.17: Plot of Q-space for each day and renumbering of daily ACE classes after filtering out all stacks with max pitch greater than 2 degrees off vertical.....................................................Error! Bookmark not defined.

Figure 4.18: Plot of Q-space for each day and renumbering of daily ACE classes after filtering out all unstacked echoes with max transducer pointing greater than 5 degrees off vertical........................Error! Bookmark not defined.

viii

Figure 4.19: Plot of Q-space for each day and renumbering of daily ACE classes after filtering out all unstacked echoes with pitch greater than 2 degrees.....................................................Error! Bookmark not defined.

Figure 4.20: Plot of Q-space for each day and renumbering of daily ACE classes after filtering out all unstacked echoes with incidence angle greater than 5 degrees.....................................................Error! Bookmark not defined.

Figure 4.21: Plot illustrating the concept of robust PCA..............Error! Bookmark not defined.

Figure 4.22: Plots illustrating the concept of robust PCA with more points..........Error! Bookmark not defined.

Figure 4.23: Echogram created from the BORIS dataset.............Error! Bookmark not defined.

Figure 4.24: BORIS dataset FFVs, FFV coefficient of variation, and loadings of the first principal component computed from the FFVs....Error! Bookmark not defined.

Figure 4.25: Q-space for the BORIS dataset using seven different subsets of features input to the PCA......................................Error! Bookmark not defined.

Figure 4.26: FFVs of the May 1, 2007 Fowey rocks dataset........Error! Bookmark not defined.

Figure 5.1: Acoustic survey track lines superimposed on an IKONOS satellite image of Carysfort Reef and surroundings............Error! Bookmark not defined.

Figure 5.2: Overview of acoustic processing..................Error! Bookmark not defined.Figure 5.3: Illustration of the computation of acoustic variability......Error! Bookmark

not defined.Figure 5.4: The three main acoustic classes and diver-estimated substrate at Carysfort

Reef..........................................................Error! Bookmark not defined.Figure 5.5: Grouper abundance at each dive site relative to acoustic classification and

acoustic variability...................................Error! Bookmark not defined.Figure 5.6: Acoustic classification and acoustic variability computed from the echoes

closest to each dive site and grouped by the presence / absence of groupers...................................................Error! Bookmark not defined.

Figure 5.7: Depth, acoustic class, and acoustic variability along transect A-A’, shown in Figure 5.5.................................................Error! Bookmark not defined.

Figure 6.1: Map of the study area...................................Error! Bookmark not defined.Figure 6.2: Mean echoes for the six acoustic classes at Davis Reef.. .Error! Bookmark

not defined.Figure 6.3: Acoustic classification and satellite image for the Davis Reef survey

area...........................................................Error! Bookmark not defined.Figure 6.4: Visualization of processed acoustic data surrounding the Carysfort Reef

survey area...............................................Error! Bookmark not defined.

ix

Figure 6.5: Visualization of processed acoustic data surrounding the Watson’s Reef survey area...............................................Error! Bookmark not defined.

Figure 6.6: Visualization of processed acoustic data surrounding the Davis Reef survey area...........................................................Error! Bookmark not defined.

Figure 6.7: Visualization of processed acoustic data surrounding the Ocean Reef survey area...........................................................Error! Bookmark not defined.

x

LIST OF TABLES

Table 1.1: Technologies for surveying coral reef environments at different scales..................................................................Error! Bookmark not defined.

Table 1.2: Summary of systems, frequencies, sediment mineralogy, and seabed classes used in previous single-beam ASC studies...........Error! Bookmark not defined.

Table 3.1: Seabed classes reported by previous efforts to map coral reef environments with single-beam acoustic seabed classification systems...............Error! Bookmark not defined.

Table 3.2: Characteristics and settings of the QTCV system used in this study....Error! Bookmark not defined.

Table 3.3: Values of tunable parameters used when processing each survey with the IMPACT software...................................Error! Bookmark not defined.

Table 3.4: Acoustic class labels and sizes (by percent of total echoes) in each survey area and aggregation of classes at fine descriptive resolution to coarse descriptive resolution...............................Error! Bookmark not defined.

Table 3.5: Error matrices for acoustic hard bottom / sediment classification at multiple sites............................................Error! Bookmark not defined.

Table 3.6: Diver descriptions of Adderly Cut dives from July 2002.. Error! Bookmark not defined.

Table 3.7: Probe depths and rugosity for dive sites in Adderly Cut.. .Error! Bookmark not defined.

Table 3.8: Error matrix for the LSI survey excluding hard bottom sites covered with a thin sediment veneer.............................Error! Bookmark not defined.

Table 3.9: Error matrix for the Andros survey excluding hard bottom sites covered with a thin sediment veneer.....................Error! Bookmark not defined.

Table 4.1: Optimum number of clusters identified by ACE for each daily dataset clustered separately..................................Error! Bookmark not defined.

Table 4.2: Optimum number of clusters identified by ACE for each transect when clustered separately..................................Error! Bookmark not defined.

Table 4.3: Overall accuracy and Kappa coefficient between pairs of daily classified datasets.....................................................Error! Bookmark not defined.

Table 4.4: Percent AMI for the reclassed ACE-best and the original ACE-best dataset......................................................Error! Bookmark not defined.

Table 4.5: Summary of visual assessment of correlation between envelopes, FFVs, or Q-space and survey variables..............Error! Bookmark not defined.

Table 4.6: Overall accuracy and Kappa coefficient between pairs of daily classified datasets reclassed to 6 classes but then with classes 4-6 merged to a single class...............................................Error! Bookmark not defined.

Table 4.7: Percent AMI for daily classified datasets reclassed to 6 classes but then with classes 4-6 merged to a single class.Error! Bookmark not defined.

xi

Table 4.8: Overall accuracy and Kappa coefficient between pairs of daily datasets classified by ACE with just two clusters. Error! Bookmark not defined.

Table 4.9: Percent AMI for pairs of daily datasets classified by ACE with just two clusters.....................................................Error! Bookmark not defined.

Table 4.10: Summary of off-nadir experiments..............Error! Bookmark not defined.Table 4.11: Overall accuracy and Kappa coefficient between pairs of datasets clustered

by day after filtering out all stacks with maximum transducer pointing vector greater than 5 degrees off vertical..............Error! Bookmark not defined.

Table 4.12: Percent AMI between pairs of datasets clustered by day after filtering out all stacks with maximum transducer pointing vector greater than 5 degrees off vertical..................................Error! Bookmark not defined.

Table 4.13: Overall accuracy and Kappa coefficient between pairs of datasets clustered by day after filtering out all stacks with maximum pitch greater than 2 degrees off vertical..................................Error! Bookmark not defined.

Table 4.14: Percent AMI between pairs of datasets clustered by day after filtering out all stacks with maximum pitch greater than 2 degrees off vertical.Error! Bookmark not defined.

Table 4.15: Overall accuracy and Kappa coefficient between pairs of datasets clustered by day after filtering out all unstacked echoes with maximum transducer pointing vector greater than 5 degrees off vertical.Error! Bookmark not defined.

Table 4.16: Percent AMI between pairs of datasets clustered by day after filtering out all unstacked echoes with maximum transducer pointing vector greater than 5 degrees off vertical........................Error! Bookmark not defined.

Table 4.17: Overall accuracy and Kappa coefficient between pairs of datasets clustered by day after filtering out all unstacked echoes with pitch greater than 2 degrees.....................................................Error! Bookmark not defined.

Table 4.18: Percent AMI between pairs of datasets clustered by day after filtering out all unstacked echoes with pitch greater than 2 degrees...................Error! Bookmark not defined.

Table 4.19: Overall accuracy and Kappa coefficient between pairs of datasets clustered by day after filtering out all unstacked echoes with incidence angle greater than 5 degrees..............................Error! Bookmark not defined.

Table 4.20: Percent AMI between pairs of datasets clustered by day after filtering out all unstacked echoes with incidence angle greater than 5 degrees..Error! Bookmark not defined.

Table 4.21: Overall accuracy and Kappa coefficient between daily classified datasets created from a single PCA using the median eigenvector of all six days..........................................................Error! Bookmark not defined.

Table 4.22: Percent AMI for daily classified datasets created from a single PCA using the median eigenvector of all six days.....Error! Bookmark not defined.

xii

Table 4.23: Optimum number of classes as determined by ACE as a function of dataset size for the entire merged Fowey rocks dataset.. . .Error! Bookmark not defined.

Table 4.24: Optimum number of classes as determined by ACE as a function of dataset size for the Watson’s Reef dataset...........Error! Bookmark not defined.

Table 4.25: Subsets of features and their colors as shown in Figure 4.24C, and Figure 4.25..........................................................Error! Bookmark not defined.

Table 4.26: Overall accuracy and Kappa coefficient between daily classified datasets using the ACE clustering after computing Q space with only features 1-15..........................................................Error! Bookmark not defined.

Table 4.27: Percent AMI for the datasets using ACE clustering after computing Q space with only features 1-15..............Error! Bookmark not defined.

Table 4.28: Summary of experiments and range of the majority of OA, Kappa, and AMI values in each..................................Error! Bookmark not defined.


Table 6.1: Survey areas and the spawning aggregations in each area.Error! Bookmark not defined.


Table 6.3: Values used for tunable parameters in IMPACT software for processing QTCV echoes...........................................Error! Bookmark not defined.

Table 6.4: Clustering results for the four survey areas.. Error! Bookmark not defined.Table 6.5: Agreement between proposed FSA site model criteria and observations of

the sites surveyed.....................................Error! Bookmark not defined.

xiii

Chapter 1: IntroductionThe purpose of this document is to present a few Microsoft Word tricks for

formatting long documents in a simple way. The overall format (margins, fonts etc..) was

taken from my Ph.D. dissertation, therefore it might be suitable as a starting point or

“template” of sorts for preparing a thesis or dissertation for the University of Miami. You

must check the electronic dissertations web site1 before doing this, however, as the format

can vary from year to year. This file worked for spring semester 2009.

1 http://etd.library.miami.edu/grad/formatting.html

1

Chapter 2: MS Word StylesStyles are critical for organizing a long document. If you don’t know about styles

do some background reading in the Word help or do some web searches for tutorials.

Here, I’ll assume a basic familiarity with styles and just describe the ones I used.

Normal style: I left as the default, but made sure the font was one of the

acceptable ones. (I used times new roman 12, which was the old default, but in Office

2008 for mac it has been changed…)

Chapter headings and subheadings are in the “Heading *” style, where * is 1, 2,

3… This makes section numbering automatic, which is one key reason to use styles (see

discussion in Chapter 4:, below).

For short documents, writing the text in normal style is OK, but for the

dissertation I used three additional styles:

Normal_var_space is what I used for the text. First, I coped normal style, added

left first line indent = 0.5” and made it double space. The advantage of using a different

style for the main text is apparent when you use either indents or double spacing; if you

change either of these for “normal” then the headings will change too, which is not what I

wanted. Using “Normal_var_space” also gave me the flexibility to change the line

spacing. The final dissertation is required as double spaced, but personally I hate double

spaced text for writing because it takes so much paper to print drafts and you have to

scroll farther on the screen to move up and down. Using “normal_var_space” I wrote

with the style set to single spacing for all my drafts and then just for the final formatting I

switched it to double spaced. If you try this strategy using the “normal” style then you

have to go back and change the line spacing of everything that is based on normal (like

the headings).

2

3

“Normal_var_space_no_indent” was defined as “normal_var_space” without the

indented first line. This style is useful when you need to split a paragraph by putting a

figure in the middle. Say for example like this map of the RSMAS campus (Fig. ). When

you need to put an image in the middle of a paragraph for formatting reasons you do not

want the text immediately following the figure to start indented because it is still part of

the old paragraph.

When you define the “Normal_var_space_no_indent” style, just use

“Normal_var_space” as the style for next paragraph and you will get the indentation back

on the next paragraph.

4

You will want a style for figure captions and table legends. The word built-in

style “caption” probably works fine for this, as would just using “normal,” but I defined a

new style called “normal no space,” which is just a copy of the normal style, to use for

figure captions.

Finally, you will want a style for the references, since they have to be formatted

with different spacing than the rest of the text. I modified the built-in “Bibliography”

style to match the dissertation specifications. That is nice because if you work with

EndNote, it automatically applies the Bibliography style when you format the references.

Chapter 3: Page numbering with section and page breaks

The dissertation format guidelines are very strict about page numbering. There are

two tricky parts. First, the first page of a section has to have the page number centered at

the bottom of the page and the remaining pages in that section have to have the page

number near the upper right corner of the page. Second, the front matter has to be

numbered with roman numerals all at the bottom of the page. The way to deal with both

of these is by using section and page breaks in the right places (see the Insert | break

menu).

The basic strategy is to put one section break between the front matter and the

introduction and then another section break before the beginning of each chapter. To cope

with the first requirement, have your page numbers in the front section start with page 3

and use roman numbers (you can look in word help how to do this or you can just use this

word file as a template). Have your page numbers in section 2 (first chapter, i.e. the

introduction) start over with 1, and use Arabic numbers.

The way to deal with the second problem is to use a “different first page” within

each section. If you are formatting your own document, once you type more than a page

you’ll see that the second page of each section has the page number in the same place, for

example bottom-centered, as the previous page. To change this you can select use

different first page and set the numbers appropriately. That has been done in this

document so you can see how it looks. When I was setting up this word file what I did

was just paste a bunch of text and extra returns in for each chapter until I got it to wrap

over onto two pages, then I could set the numbers right, delete the garbage and actually

concentrate on just writing without having to reset the page numbers for each chapter.

5

6

Actually I did this with all the chapters at once. If you don’t want to set it up from scratch

you can use this document as a starting point.

Finally, you’ll note that this document starts with page iii. There are a title page

and signature page etc... that have to go before page iii. These can be downloaded as a

template from the grad school and I would recommend not trying to combine them into

this file as one document. Just do those pages as a second independent file and you will

be much better off.

Chapter 4: Legends, captions, numbering and cross-referencing for the tables of contents

4.1 Section numberingSome people like to use section numbers (i.e. Chapter 4, 4.1, 4.1.1 etc..) others

don’t. I forget whether they are required by the grad school or not (probably not). But if

you want to use them, you will be very glad you used the heading styles to create the

titles for each section. Adding basic numbers is very easy, just go to “Format | bullets and

numbering” then select outline numbered and chose the style you like.

Most people, however, will need to make their headings a bit more complicated

than the default outline numbered schemes. The most common problem is that you want

numbers like Chapter 1,2,3 and so on for the chapters, but then no numbers for sections

like References and Appendix. In this case you have to customize the numbering scheme.

Under “Format | bullets and numbering” then select outline numbered there is a button

called “customize.” There you can add the text “Chapter:” before the number at the

heading 1 level. Don’t add it for the other levels and you get the numbering scheme as

used here. When you get to a section that you do not want numbered, say “References”,

then type that in and initially you will get “Chapter X: References”, where X is whatever

the next number is. You cannot just delete the “Chapter X:” part. You have to go back to

“Format | bullets and numbering” then select outline numbered then select “none” and the

numbering will go away for that section.

4.2 Cross-referencing section headingsWord has a pretty decent (if somewhat unintuitive) cross-referencing facility

built-in. An example would be: “To learn about page numbering see Chapter 3:” If you

put your cursor over Chapter in that sentence you will see the entire thing is shadowed.

7

8

That is because it is a cross reference. Now, if you change the chapter orders the correct

number is automatically updated in this link. This can be a very big time saver, maybe

not with chapters themselves, but with sub-section numbers. To insert cross references

just use the “Insert | Cross-reference” menu item. There are a few options for how the

reference is formatted. Play with it a bit to get the hang of it.

One problem is that with the numbering scheme I have outlined here, if you just

want to insert the numbers (like the example above), you will get the colon at the end of

Chapter when cross-referencing the top level headings. Probably this is not what you

want, but there is no easy way around it using the built in cross-referencing scheme. The

solution I used was for level 1 references just type it in (e.g. Chapter 3) and don’t use the

word utility at all. This worked for me because I knew what my chapters were going to be

and in what order before I started writing the final master document. Therefore, even

though the sub-sections moved around a lot as I added and deleted them, the actual

chapter headings did not. The only alternative to this is to use the much more complicated

numbering scheme described in Section 4.4. I felt that the complicated numbering was

worth it for the figures but not for the chapter headings.

4.3 Basic captions (the way Word wants you to do it)Word has a simple built-in cross-referencing scheme for captions. It is easy to

use, but has virtually no flexibility. I found it maddening, and figured out a much more

flexible, but much more complicated, way to do the numbering. I’ll describe my method

below, but want to illustrate the shortcomings of the word method so you can decide

which to use.

9

I wanted my figures to start with “Figure C.N:” in bold, where C is the chapter

number and N is the figure number within the chapter, and then to have the rest of the

caption in regular text. One way to do this is just manually format everything (Fig. 4.0).

Figure 4.0: Another map of the RSMAS campus. Note that this caption uses the “normal_no_space” style and is manually formatted.

There are two problems with manual formatting. First, if you insert, delete, or

move a figure you need to change all the other figure numbers after it and all the cross-

references to it. What a nightmare. The second problem is that you can’t use Word’s table

of contents feature for the table of figures and table of tables, which are both required.

Therefore you will have to type those in by hand, which is doable, but more work than

necessary especially when you have to figure out what page each figure is on. No thanks.

Word has a figure numbering scheme. So I could use the “Insert | caption” menu

item with the figure label option (Figure 4.2). This is pretty nice you can use captions

inserted this way in cross-references, as I did in the previous sentence, and for generating

a table of figures. Cool! The problem is that your formatting options are limited. If you

want the “Figure C.N:” in the actual caption to be bold then the cross-reference will also

be bold. Also, if you use the “Figure” prefix in the caption then your cross-references will

10

always use the full word spelled out. It is not possible to use an abbreviation (Fig. C.N).

Finally, if you use the “insert | index and tables | table of figures” command it will

generate a nice table for you, with the correct page numbers, but the entire figure caption

will be placed in the table of figures. That can get ugly if you have a long caption

explaining the symbols in the figure or whatever. In this case, I would want the table of

figures to include only “Figure 4.1: A map of the RSMAS campus” and the page

number. Using the default scheme I could not find a way to do this.

Figure 4.2: A map of the RSMAS campus. Note that the numbering for this caption was generated with the “Insert | Caption” command followed by manually changing the “Figure C.N:” part bold.

4.4 Nice looking captions (the way I did it)Text for chapter 3.

Chapter 5: ConclusionsInsert conclusions here (your job not mine).

11

ReferencesI used EndNote to manage my references, which is why if you click on one of the

entries below the whole list is shaded as a field (a byproduct of how EndNote formats

bibliographies). I am just leaving the whole list in here so you can see how the formatting

looks and how different reference types are supposed to be formatted for the dissertation.

Actually, I think they are not so picky about what style you use as long as it is consistent.

Also note, if you click in here you will see these paragraphs are formatted as

“Bibliography” style. If you go to modify that style you can see how it was defined.

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