Archive for the 'Writing and Literature' category

Hannibal, Napoleon, and Joseph Charles Minard

 | February 22, 2010 5:49 pm

Charles Minard - Railroad Routes

No study of the history of scientific communication can be complete without mention of Joseph Charles Minard, a 19th Century French civil engineer and cartographer.

At the end of his life, Minard created two very famous examples of statistical charts, called flow maps, that every scientist, engineer and student should be familair with.  The first showed Hannibal’s crossing of the Alps (218 BC, Second Punic War), and the second describes Napoleon’s disastrous invasion of Russia (1812-1813).

Both examples are beautiful works of art and masterful examples of evidence.  But they are also more than that, they tell cohesive and interesting stories.  In this post, I thought it might be interesting to take a closer look at the history of Hannibal and Napoleon, and highlight the ways which Minard’s charts help us to explain their eventual outcome.

(Note: High resolution, PDF versions of the two maps are available for download.  These versions have been translated from the original French.  To download, either click on the images, or here for the Hannibal invasion of Northern Italy, and here for the French Invasion of Russia.)

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Working With Words, Numbers and Images: A Reading List

 | February 14, 2010 2:10 pm

There are three tools that a professional, scientific or technical writer needs to make use of: words, numbers and images.  In many cases, such as an effective illustration or chart, all three will be used.

The following books introduce principles and examples of how to use these tools to their fullest extent.  Some of the titles are historical and others are academic.  In every case, though, they highlight strategies that can be used to more effectively communicate ideas.  Additionally, each one is also an interesting and fantastic read.

Math and the Mona Lisa Math and the Mona Lisa by Bulent Atalay. For more than 500 years, the name of Leonardo Da Vinci has been synonymous with brilliance.  His careful observation of nature, collection and analysis of evidence, and use of mathematics to explain his observations represented a radical shift that foreshadowed the modern scientific method.In this book, Bulent Atalay explains why Leonardo was a remarkable artist, engineer and scientist.  He looks at the hidden patterns, geometric concepts and impeccable perspective in order to probe the mind that dreamt of helicopters, unsinkable ships and underwater exploration.
Leonardo's Notebooks Leonardo’s Notebooks, edited by H. Anna Suh.  To understand a man, you must read him in his own words.  This volume provides an opportunity to sample Da Vinci’s writings on anatomy, botany, architecture, sculpture and the physical sciences.  The key illustrations from his notebooks have also been reproduced.
Galielo at Work: His Scientific Biography by Stillman Drake.  Like Leonardo, Galileo was a scientific titan.  As Stephen Hawking aptly summarized, “Galileo, perhaps more than any other single person, was responsible for the birth of modern science.”But why?  What was it about his innovative combination of experiment and mathematics that was so important.  How did he analyze data?  How did he present it to others?This book attempts to answer those questions.  It lays aside the philosophical implications of Galileo’s rift with the Catholic church and instead looks at how Galileo focused his mind on physical quantities and the mathematical relationships between them.
The Visual Display of Quantitative Information The Visual Display of Quantitative Information by Edward Tufte.  Communicating complex ideas is difficult.  One of the most important tools in that struggle are charts, graphs and illustrations.  Unfortunately, however, these important figures often receive less attention than other aspects of a manuscript.In this book, Tufte provides inspiring examples of graphics that are beautiful to behold and illuminating to ponder.  He also includes shockingly bad examples and explains why they are so dangerous.
Visual Explanations by Edward Tufte Visual Explanations by Edward Tufte.  In his earlier work, Tufte showed how important it is for numbers to be communicated clearly and without distracting  ornamentation.  In this volume, he turns his attention to a slightly different series of questions: What is the best way to show cause and effect?  Or to demonstrate evolutionary change?But the most important question he asks is far more universal: How can an information display be be used to reveal the truth?  To answer this, he analyzes a cholera epidemic in 19th century London and explains how poor communication contributed to the explosion of the Challenger space shuttle.
Beautiful Evidence by Edward Tufte Beautiful Evidence by Edward Tufte.  Like in his previous books, Tufte again tackles the question of how to best reveal truth through the graphical display of information.  But where earlier books focused on principles, Beautiful Evidence is about how seeing turns into showing.  To explore that theme, this book is filled with hundreds of spectacular examples and thoughtful commentary on what makes them unique.
Now You See It by Stephen Few Now You See It by Stephen Few.  The human mind is amazingly adept at seeing and understanding patterns.  An informed eye can distinguish between authentic and forgery and arrive at startlingly accurate calculations with minimal effort.  But even though we are capable of recognizing the hidden influences in the world around us, we can also be mislead and exploited far too easily.  We become awash in a sea of data of our own making.This book attempts to explain how the mind interprets and sees information.  As the author explains in the introduction, “[This book] provides tools to dive into the ocean of information, net the best of it, bring it back to shore and sort it out.”  In essence, it’s a book about seeing and distinguishing patterns on a conscious level.
Visual Thinking Visual Thinking by Rudolf Arnheim.  It’s long been known that “seeing is believing.”  This book explains why seeing is also synonymous with thinking.
Maps and Civilization Maps and Civilization: Cartography in Culture and Society by Norman J.W. Thrower.  The history of exploration and discovery is also the history of cartography.  As mankind sailed out of sight of shore, he needed to learn techniques for representing his position and understanding the natural forces that he might encounter.  This book tells the history of mapmaking and how advances in cartography impacted civilization.
The Elements of Graphing Data The Elements of Graphing Data by William S. Cleveland.  In this book by William Cleveland, he presents the nuts and bolts (the how-to) of graphing data.  Then he goes on to explore the science in which his principles are based..
Visualizing Data Visualizing Data by William S. Cleveland.  Whereas The Elements of Graphing Data is primarily  focused on the principles of quality display and exploration of many types of common statistical charts, Visualizing Data takes the next logical step.  It introduces a number of new chart types and techniques for creating insightful and clear graphics.
Fiasco: American Military Adventure in Iraq by Thomas E. Ricks Fiasco: The American Military Adventure in Iraq, 2003 to 2005 by Thomas E. Ricks.  Serious endeavors require careful forethought and nuanced planning; and few enterprises are more serious than the business of war.  This controversial book looks at the missteps and mistakes of the American military as it justified, planned and executed the 2003 Iraq War.It contains haunting examples of how information can be distorted and obfuscated by both well-meaning individuals and those with insidious hidden agendas.  It also explains how the adoption of American corporate culture and leadership by PowerPoint lead to serious miscommunication and early failure.
Challenger Launch Decision The Challenger Launch Decision: Risky Technology, Culture and Deviance at NASA by Diane Vaughan.  The Challenger explosion on January 28, 1986 changed the course of manned space flight forever.  But how did it happen?  What factors lead to it?  Might it have been prevented?In The Challenger Launch Decision, Diane Vaughan attempts to answer those questions.  In the process, she reveals that the Challenger explosion wasn’t the result of intentional wrongdoing but rather a slow-creeping definition of “normal” and comfort with the status quo.

Image Gallery: The Notebooks of Leonardo Da Vinci

 | February 5, 2010 12:31 am

DaVinci - HandsWhen I graduated from college and had to choose between a career in industry or academics, I found it to be an easy decision: I stayed in academics.  I like to have my head in the clouds and enjoy the intellectual lifestyle.  (I actually consider the label of “absentminded” to be a compliment.)

It should come as no surprise, then, that one of the most enjoyable aspects of writing a book has been the opportunity to research my subject.  My reading list has included books on analytic design, illustration, anatomy, typesetting, scientific communication, web technologies, LaTeX, the history of science, statistics and informational graphics. And as I worked my way through it, I took some extremely interesting side trips.  One of the most intriguing, however, was an extended tangent through the notebooks of Leonardo Da Vinci.

Da Vinci died in the year 1519, nearly five hundred years ago.  Yet, the modern world remains fascinated by him.  His name adorns the side of best selling books and conspiracy fiction; and his drawings have become cultural icons.  As an example of his popularity:

In October of 2009, Martin Kemp, a professor of art and history at the University of Oxford, found a portrait of an Italian girl.  Up until Kemp took an interest, it was widely accepted that portrait had been painted sometime in the nineteenth century by an unknown artist.   After a great deal of investigation and the use of a multispectral camera, however, Kemp discovered something startling.  The painting had actually been done by Leonardo and nearly overnight, it went from a value of 19,000  British pounds to over 100 million.

I’m no different than the masses.  Leonardo fascinates me.  He had a very distinctive way of seeing the world and an engaging style.  Maybe that’s why it’s so easy to lose yourself in the details of his work.  Given my interest, a thorough study of Leonardo’s notebooks seemed only natural.

What I didn’t foresee, however, is that I would start to digitally collect his sketches; and in the past several months, I’ve put together a rather eclectic mix from across the internets.  Earlier today, I realized that the images might be of interest to others as well; thus, I’ve created a special online gallery for them.  It can be found under “Art and Photography” –> “The DaVinci Notebooks”  To get there more quickly, you could also just click here.


About This Book Thing

 | January 28, 2010 5:22 pm

daVinci-SkullIn the past few weeks, I’ve had several observant readers ask about one of my “secret” projects.  They’ve wondered what I’m up to and why it’s detracting from other endeavors.  After answering another query this morning, I decided that it’s probably time to speak openly about it.  So, here’s my public confession: I’m writing a book.

It’s about scientific and professional writing and open source.  Moreover, it will be interesting, intriguing and revolutionary.  (Yes, I have an inflated sense of ego.)

Before really diving into the details, I’d like to give a bit of personal background.  This might help you understand why I’m passionate about the subject.


Ten years ago, had someone told me that I would end up a scientist and engineer, I would have laughed at them.  At the time, I had just started at University and I was fully set on a career in either illustration, design or architecture.  I was much too “visual” and “right-brained” to surround myself by geeks, freaks and nerds.  It didn’t help that I spent a huge amount of time grooming myself to be an “artist”.

During high school, I had been cursed with moderate talent and highly indulgent instructors.  They praised my artwork.  They called it interesting and innovative.  They encouraged me to refine my technique and to major in visual arts.  So, I did.

But as time went on, I realized that I wasn’t very happy.  I realized that I had other interests.  I enjoyed art, I did well in it; but art classes weren’t my favorites.  That honor, as it turned out, was reserved for mathematics and science.

There was also another problem, I found that I lacked the discipline required to systematically create an individual style and build a portfolio.  I wanted create art for myself, not for other people; and that is a fatal flaw in an illustrator (the type of work that most interested me). Illustration, by definition, is work that has been requested for a particular use.  I was more interested in my own whims than those of potential clients.  Thus, not long after recognizing my problem, I decided to go a different direction and changed my major to engineering.

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Typeset Your Curriculum Vitae – Part 3: Automatically Generate a List of Publications

 | December 2, 2009 11:19 am

Publications are the currency of ideas.  Through them the experts, thinkers and dreamers of this world can share their thoughts and insights.  A good publication is not only influential, but it’s even capable of shifting the course of a whole society, as Martin Luther King demonstrated with his “Letter from a Birmingham Jail”.

Since publications are so important to the dissemination of knowledge, there is a rather high expectation that an academic author should publish prolifically.  The mantra “Publish or Perish” is not just a clever quip, but a very serious way of life.

It is ironic, then, that the most prolific of academic writers can suffer from a surprising problem: it can be very difficult to keep track of all of their work.  Yet, an up to date CV is very important.  After all, publishing your work in influential journals is an important first step toward establishing tenure!

Members of a research team or those who collaborate outside of their institution experience this same problem, only more so.  Such a person may work on many projects at once, but only have direct responsibility for one or two of them.  This places the researcher in the unenviable position of trying to track the work of others.  This situation becomes even more complicated if the collaborator refuses to play by the rules of common decency.

It would be nice, for example, if the primary author of a publication would notify the co-authors of its progress, or when it has been submitted.  But … that doesn’t always happen.  Academic researchers are busy people and soliciting feedback from all of your collaborators can be difficult … and there is a tendency for difficult things to go undone.  Thus, if you don’t follow what your team mates are working on, it is quite possible that an abstract might have gotten submitted while your back was turned.

To stay on top of the “delightful chaos”, you need to have some kind of system.  Personally, I keep my list of projects and publications in three places. The first (and perhaps most important) is the hand-written list in my experimental notebook. Any time I hear about a new project, it gets added to this list. I keep track of what I’ve contributed, what papers or abstracts have been created from the data, and what their status is. When I know that an abstract or paper has been accepted, I then create an entry for the item in my bibliography manager. Once in the bibliography manager, I can cite the reference in other documents such as proposals or related papers.

About once a year, I go through the tedious process of updating my CV. This typically involves manually sorting through both my project list and my reference database and account for new items or reconcile differences. Every time I do this, it's painful; and because I’ve historically formatted the reference list by hand, it's not uncommon for a typo to sneak its way in or for an author to accidentally get left off of a citation. These mistakes are never intentional, but they do happen.

When I find such an error in the reference database, I fix it. But since I often import these references from websites, the errors tend to be few and far between. Moreover, my reference database is something that I use every day; as a result, it gets a lot of scrutiny. My CV, on the other hand, gets updated much less frequently and errors tend to persist longer.

For a very long time, I've wanted to automate the process. Instead of keeping three separate lists – active projects, reference database, and CV – I’d prefer to keep only one (or two). But I've never found a really satisfactory way of doing so.  Or at least I hadn’t found a system until quite recently.

In my last review of different ways to typeset a CV, I came across an interesting article by Dario Taraborelli.  In it, he described how to create a CV based on the standard “article” document class.  It was well designed, elegant, simple and attractive.  From his work, I created the xetexCV document class.  Additional research turned up an add-on module that makes it convenient to automatically generate a list of publications.  So, for the first time  in a great while, I have finally found a way to automatically generate a publications list in a simple and automated manner.  In this article, I will demonstrate how that is done.

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Typeset Your Curriculum Vitae – Part 2: Extending and Customizing an Existing Document Class

 | November 30, 2009 2:54 pm

Many first-time users of LaTeX often mistakenly look at the language as a a type of glorified word processing software – albeit a particularly complicated one.  While such an analogy may be apt in helping new users become acclimatized to the language, it suffers from a rather nasty problem: LaTeX isn’t a word processor.

If anything, LaTeX shares more in common with a programming languages than any type of application.  In fact, the document processing system is really nothing more than a bunch of re-usable pieces of programming called macros.  Everything is a macro.  That includes the commands that every user is familiar with: \title{}, \section{}, \subsection{}; in addition to the internal formatting commands that allows LaTeX to function.  (Most of the macros were originally created or packaged by Leslie Lamport as a way of making TeX – the typesetting system created by Donald Knuth – easier to work with.)

This has some rather practical consequence; because everything in LaTeX is a macro, it is far more extensible than a word processor could ever hope to be.  If you require a feature that doesn’t yet exist, it typically isn’t all that difficult to add it.  And when your extension is packaged inside a style or class, you can use those customizations in anything that you want to write.

But though creating macros isn’t particularly complicated, it is a different beast than just using the stock macros for writing.  This is not surprising, the craft of design is inherently different than the craft of writing.  There are different conventions to follow and different topics to obsess about.  In the first article of this series, I introduced the xetexCV document class, which is one example of where I decided to don the designer hat.

But before you get too far down the road of customizing and extending, there are a some important things that you need to know.  These include the general conventions used when working with document classes, their internal anatomy, an understanding of how macros are created, and how to handle formatting and layout challenges.  In this article, I will look at these issues more in detail, particularly as they pertain to xetexCV.  In the process of reviewing these topics, I will also explain some of my design choices.

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Typeset Your Curriculum Vitae – Part 1: The xetexCV Document Class

 | November 25, 2009 12:02 am

Very few documents are more personal than a curriculum vitae (CV).  A CV lists a person’s educational history, who they’ve worked for and what they’ve accomplished.  Moreover, a CV is frequently used to judge a person’s inherent worth and value (or at least exploitability).  A quality curiculum vitae matters, a lot.

For that reason, a CV not only needs to include all the pertinent information of a person’s life, but it also needs to look good. An attractive CV with good spacing and contrast leaves a positive impression and makes it easier to find information.  When laid out correctly, a reviewer might just find themselves scouring past accomplishments for interesting tidbits: “I didn’t realize that this applicant organized a lecture series with Patch Adams and other notables, that’s interesting!”

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Customizing LyX: Character Styles and the LyX Local Layout

 | November 14, 2009 5:00 pm

Imagine for a minute that you’re writing a book or technical manual.  Let’s say it’s a book on technology, maybe the open source tools used for scientific writing (to randomly pick an example).  As you write this book, you realize that you need some way to cue the reader into different parts of the text.

For instance, you might want all definitions to appear in bolded text so that a reader pick out key terms quickly.  Or you might want code examples to appear in a different font than the regular text, again, so they’re easy to find.  What’s the best way to do this?

Sure, you could just bold the definitions, or manually change the font for the code examples.  But that’s painful!  Changing typeface and size every time that you have a section of code will eventually result in a lot of lost time.  Moreover, you might make a mistake, which destroys your consistency and makes your writing look unprofessional.  There must be a better way!

Thankfully, there is.  It’s through the consistent use of styles.

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Patronage in the Digital Age

 | November 10, 2009 2:20 pm

As wonderful as the internet may be, it causes a lot of problems.  For starters, it is putting newspapers out of business.  It’s also radically changing how artists, writers and musicians make their living.  And in case you weren’t paying attention, it’s starting to look like a crisis.

Different groups have responded to the impending collapse of publishing in different ways.  Some writers sell sponsorships for their books and then offer an acknowledgement when it is printed.  Many musicians have adopted the self-publishing and distribution tools long available to authors, leading to experiments like Amazon’s CreateSpace.  And there are those who have gone the route of directly asking for contributions and donations to support their work; the digital equivalent of a performer passing the hat, you might say.

The problem is that some of these experiments are running head-long into good old American sensibility and propriety.  There are even people saying that some of the new content generation schemes are inappropriate; including that old bastion of American common sense, Ms. Manners.  Manners has even gone so far as to say that for a novelist to ask for a contribution is the same as begging, or panhandling.

She says it like it’s a bad thing.  The simple truth is that artists, musicians and storytellers have long been beggars.  The content industry of the 20 industry is a tremendously new invention, and as I noted above, it’s running into another time tested American value: frugality and a love of private property.

In fact, there seems to be this attitude that, “After I’ve purchased the novel or CD, I own the work and ideas.  I’ve invested in its creation.”   This little nugget rears it’s head most commonly when discussing music.  Even the great Steve Jobs has been known to say, “People don’t want to rent music, they want to own it.”

Except … that’s bullshit.  An interesting idea, or a well written book, or a beautiful piece of music isn’t like paying for a hamburger.  You aren’t reimbursing someone for providing you a good or service.  And I’m frankly shocked that anyone would think that Beethoven’s 9th Symphony or Antonio Vivaldi’s “Four Seasons” is only worth the price that paid on iTunes.  The true worth is far greater than the price of admission.  Would you seriously think yourself exploited for buying a second recording, or for paying to hear it at a concert?

Of course, that’s when people can be bothered to pay for content at all.  An exacerbating factor is that many people expect ideas to be free or very inexpensive.  How many times have you heard a variant of this argument, “I would buy more music (or books) if it wasn’t so expensive!  Nine dollars for an album is just out of my budget!”  Ironically, these same people don’t blanch at dropping hundreds or thousands of dollars for an iPod or iPhone.

While bad, this attitude can further devolve into something much more poisonous: “The artist owes me for reading, viewing or listening to their work.  My piracy is helpful!  After all, I am promoting them and making them famous!”  But being famous doesn’t pay the bills.  There have been many authors, artists or musicians who lived in squalor while enjoying enormous fame and prestige.

A music or literature pirate might even justify their position by saying, “I’m sticking it to the music industry (or publishing industry), they’re a bunch of greedy pigs!”  And the pirate might have a point, if he weren’t doing far more damage to the creator of the content than to its distributor.  Big businesses like record labels and big publishing houses don’t respond to that attitude by lowering prices or dealing fairly with their customers.  Rather, they become more draconian in how that content is disseminated.  Ever wonder why Digital Rights Management (DRM) and related technologies were born?  It might just have something to do with the American sense of entitlement.

Clearly, something needs to change.  Artists and musicians can continue to experiment with different pricing and distributions schemes, but I remain rather unconvinced that it will have a lasting effect.  What we really need is a return to the patronage system of old, with a few major modifications.  Certainly, artists should continue to sell recordings, books and other tangible goods.  But the public should also undergo a shift in our attitudes and ideas about what the arts are and how we support them.  That might mean that we transform our understanding of what a “donation” is.

When buying a book or donating to a writer, it’s foolish to think that you are somehow providing a fair compensation for the ideas and entertainment that you receive.  Instead, it is much healthier to view your contribution as a support so that the artist can continue to create future content.  This notion actually fits in pretty well with the concept of Fair Trade.

We also need to understand that the price we pay for a book or CD isn’t about the value of the materials.  Textbooks aren’t expensive because they are printed on beautiful paper with artwork and in color; they’re expensive because researching and writing their content is hard.  For example, the “Contributors and Reviewers” page for Gray’s Anatomy (the anatomical guide, not the television show) lists sixty different authors and content reviewers, though only the editor and chief is credited on the cover.

Except, how do you actually bring about the needed shift in attitudes and culture?

That’s an excellent question, and I’m not sure that I can offer any insight.  The Europeans have tried to shape public perception through generous subsidies.  But direct governmental support of news agencies and publishers is controversial for good reason.  As a cure, it might even be worse than the illness.  If you’ve got any ideas, let’s hear ‘em!

Statistics With R – Part 1: An Old Dog Learns New Computing Tricks

 | November 8, 2009 10:21 pm

When doing math or numerical analysis, the knowledge of the technique is far too often tied to the tool performing the calculation.  Consider an engineer whose understanding of the Fast Fourier transformation is inseparably tied to the fft function in Matlab.  Of course this hypothetical engineer understands what the results mean (more or less) but may not be able to duplicate his analysis if Matlab were taken away.

In most cases, it is likely that no deeper understanding will be required.  But what happens if the computer makes a mistake?  Or the program becomes unavailable?  Both situations are entirely possible.  Computer algorithms aren’t perfect and occasionally arrive at results make little sense; and hardware has been known to fail.

When the engineer understands how the computer arrived at the answer, however, he can recognize, understand, and ultimately correct those cases where the results are unexpected.  This is an important reality check that can prevent costly disasters later down the line.  Or, if the hardware is unavailable, he can use an alternative tool or software package to duplicate the analysis.

But while such a situation can arise with any type of numerical software, it’s most likely to happen to users of a statistical package.  I find this extremely ironic since a proper understanding of statistics is essential to live in the modern world.  (Much more so than an understanding of the Fast Fourier transform, at any rate.)  The rules of probability, the normal curve, correlation, and multivariate statistics can have a direct impact on how we live our lives.  They are used in making important decisions in finance, medicine, science and government.  A misunderstanding of stats and the methods of science (from which statistics is inseparable), underlies the most divisive issues of our day: abortion, stem cell research, and global warming.

Moreover, neither side has a monopoly on ignorance or misunderstanding.  People fail to distinguish between correlation and causality, or insist in using the word “average” as a slur.  Nearly as bad are those that – like the hypothetical engineer described above – only understand statistics within the narrow context of their stats package.  Casual statisticians are nearly as dangerous as the wholly uninformed.

The Statistical Package for the Social Sciences (SPSS), is one of the biggest perpetrators of this crisis.  Which is hugely ironic, because I happen to love SPSS.  SPSS is probably the first statistical package that has placed advanced statistical methods within the grasp of the novice user.  I’ve been a happy user for nearly a decade (ever since I was introduced to the program in high school).  But there is no doubt that I’ve come to understand statistics within the context of SPSS and its GUI.

Please don’t misunderstand me, I have a pretty good grasp of basic statistics.  I can sling probability with the best of them and take relish in describing when to use the Fischer Exact test instead of a Chi-Square; but advanced statistics are a completely different matter.  Advanced stats scare me.  I can certainly use these more complicated methods.  I’ve analyzed and written about multi-variate models and even ventured into Analysis of Variance (ANOVA).  But I have to rely on SPSS and the aid of my institution’s biostatistician to help me recognize when there is a problem.

Which is why, in a time of tight budgets, losing the institution’s SPSS license has been a crushing blow to my productivity.  (Whoever made that decision should be hauled out and shot!)  Because I don’t have my statistics software any more, there are certain aspects of my job that are much more difficult to do.  And unfortunately, there is only logical conclusion to draw: I’ve become a victim of the statistical ease of SPSS.

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