Jason Bryer

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LaTeX and Sweave

1 December, 2009 (18:56) | Software | By: Jason

LaTeX is a typesetting language that is known for its beautiful mathematical formulas. It is similar to HTML in that you write your document in plain text and process (or compile) it to create a postscript or PDF file. You will need to download a LaTeX processor for your platform. On Windows, TeXnicCenter (http://www.texniccenter.org/) is very good and on Mac TeXShop (http://www.uoregon.edu/~koch/texshop/) is very good. Both these applications provide a text editor in addition to the LaTeX processors. Here are a list of excellent resources for learning LaTeX (note that many of these are in psarelated/LaTeX folder on Dropbox):

Sweave allows for the embedding of R code directly in your LaTeX documents. The best resource is the Sweave User Manual (http://www.stat.uni-muenchen.de/~leisch/Sweave/Sweave-manual.pdf). In short, simply place the following in your LaTeX file:

<<myrcode1>>=
2 + 2
@

There is a Sweave function in R. Issuing the Sweave(file.choose()) command will first prompt for the file (by convention use Rnw file extension), execute all the R code and generate a tex file. This file can then be run through your typical LaTeX processor or editor. Once you go through the Sweave manual, I recommend printing page 13 which lists all the options that can be issued to Sweave.

To create presentations, the Beamer class is what is generally used. The LaTeX beamer class homepage has several exmaples (http://latex-beamer.sourceforge.net/). The Beamer manual is included on Dropbox or when you download the classes (I do believe Beamer is built into both TeXnicCenter and TeXShop).

Laslty, I have included a few of my own files on Dropbox for a recent paper and presentation I’ve done. I used Sweave for the paper (see Bryer.LocatingStudents.Paper.Rnw). I also included the generated LaTeX file (Bryer.LocatingStudents.Paper.tex) as well as the final PDF version. For the presenation, I used Beamer but since I was working from the paper, I simply cut and paste sections from the generated tex file to Bryer.LocationStudents.Presentation.tex. Note the first two lines of this file:

%\documentclass[handout]{beamer}
\documentclass{beamer}

The percent character is a comment line in LaTeX so in order to create the handout version I simply commented out the second line instead of the first. Both versions are included on Dropbox for your review.

Backing Up

28 September, 2009 (10:19) | Uncategorized | By: Jason

Over the past few months it has become very clear that many of my family and friends are not adequately prepared for a computer failure. Part of being prepared is having a good backup system and then sticking to it. However, though backup seems like a seemingly simple concept, the complexities involved become quickly apparent. Perhaps the most problematic is the sticking to it. That is, it is good to have a backup plan but if you don’t keep up on your backups, then why bother making a plan? There is a simple adage to keep in mind whenever you create or save some data (i.e. photo, video, document, etc.): If the file is not in two places, it does not exist! I will briefly explain some of the tools I have either used or know about that can assist in creating and following through on a backup plan.

Your first layer of backup

Probably the most common reason you will need to use your backup is due to a hard drive failure. Therefore, it is probably a good idea to have a complete system backup so that you can quickly recover after replacing the failed drive. For Mac users, I recommend using Time Machine with an external hard drive.This will create incremental backups whenever the drive is attached. If you have more then one computer in the house, then it is probably worth investing in a Time Capsule. This will allow backups to occur over wifi. The hard drive in my wife’s laptop died  a year ago which spurred a much needed upgrade anyways. When we brought the new laptop home, the Mac setup wizard asked if we would like to restore from a backup, we said yes, it found the Time Capsule on the network and about an hour later, she had a new laptop that looked and behaved just like the one that died (albeit a lot faster).

Sorry Windows users, but I’m not sure if there is a similar system. Once upon a time when I owned Windows computers I would use Norton Ghost, however I cannot attest to its usefulness now. If someone knows a better tool, let me know (Mac users: Carbon Copy Cloner is also very good and works somewhat like Norton Ghost).

Alternatively, you can always manually backup your files using the Finder on Mac or Explorer on Windows. I generally don’t recommend this as then you are now relying on remembering to perform a backup then it just happening automatically.

For your home backup, I think that Western Digital My Books are very good for the price. They are external USB drives that will work with Time Machine or any other backup software. However, if you are serious about keeping your data safe (read: FAMILY PHOTOS), then I would recommend a Drobo. Admittedly quite a bit more expensive, but these external hard drive enclosures hold up to four hard drives. I recommend starting with two 1 TB hard drives (you need at least two drives to start). What a Drobo does is spread your data over multiple drives so that if one fails, your data is still safe. If a drive were to fail, a light on the front of the Drobo turns red, you replace that drive with a new one, and all is good. Moreover, the Drobo can grow with you as you acquire more data. If you start with two 1TB drives, you will actually have 1TB usable (since the other 1TB is used for protection). Once you begin to fill that 1TB, simply add a third drive, say another 1TB drive, and instantly you have 2TB of storage. Moreover, say you have four 1TB drives (resulting in 3TB of usable storage) and you have reached it’s capacity, you can then remove one drive and replace it with a larger drive (2TB are soon to be available) therefore increasing the capacity of the Drobo.

Your really important files

I am currently working on a dissertation. As you can imagine, I’m very concerned about the safety of these files as I work on them. One of my favorite services now is Dropbox. After installing a small utility on your Mac or Windows computer, you pick a directory that will sync with the Dropbox service. What then happens is anytime a file changes in that directory (or subdirectories), that file is copied to the Dropbox service (assuming you are connected to the internet). Moreover, Dropbox will keep a copy of all revisions for the last 30 days. Additionally, Dropbox has a sharing feature so that you can share a directory with any number of other users. After setting up the share, any changes you make are sent automatically to other users. This has proven to be an  invaluable tool for collaborating with colleagues on various projects. This service is free for up to 2GB of storage, $50/year for 25GB, and $100/year for $50GB.

Offsite Backup

In general, I think that two copies in not enough. More specifically, I will keep two copies in my home (i.e. my computer and one backup) and one somewhere else. For a while I was carrying a hard drive to work once a month. This way, if the worst happened (e.g. house burnt down) I would only loose about a months worth of data. However, there are two very good and relatively cheap alternatives available that allow you to backup unlimited data online. Backblaze ($5/month or $50/year) and Carbonine ($55/year) are both available for both Mac and Windows. The only disadvantage of these services is that the initial backup may take quite some time to complete. For example, I’m currently using Backblaze (a Google search for ‘backblaze coupon code’ will find you a 10% coupon) and it took about a week for my laptop to backup. I’m currently backing up all my photos (over 500GB worth!) and it has been working for about a month now. However, once the initial backup completes, it is relatively quick for updates and/or new files to be backed up.

Reframing the Health Care Debate

9 September, 2009 (06:06) | Uncategorized | By: Jason

Over the past few weeks as the debate over a national health care option has moved from the halls of Congress to the water cooler I have found myself engaging in several discussions with those opposed to a national health care option. There are several problems with how this debate is going. First, in typical republican style, those who oppose national health care have attempted to boil the debate down to simple talking points and rhetoric. Any attempt to point out that such a complex topic as this is inherently nuanced and requires complex analysis is dismissed outright since in my opinion many Americans don’t seem to have the attention span to fully understand the topic. This is exemplified in a recent interview of Republican Party Chairman Michael Steele by Steve Inskeep on NPR[i]. Inskeep’s assertion that Steele’s position is nuanced is forcefully rejected. If we can get beyond the talking points and rhetoric and treat this debate with the careful thought it deserves, I believe that the weak foundation of those opposed to national health care will crumble. This essay attempts to provide a logical foundation and reason for my support of a national health care option. The first portion of the essay will define four key philosophies that help provide a context for the debate. I will then describe how I think this debate should be reframed. Finally, I will provide direct rebuttals to some of the more common criticisms of the health care option.

A Foundation for Debate

There are four opposing philosophies that are at play in this debate: individualism, collectivism, capitalism, and democracy. Understandings of these opposing forces provide valuable insight into the differing points-of-view on this debate.

Individualism and Collectivism

Individualism is a philosophical or moral stance whereby independence and self-reliance are emphasized. Collectivism on the other hand is the philosophical or moral stance that emphasizes human interdependence and the importance of a collective. In most international studies that look at the individualism/collectivism spectrum, the United States nearly always ranks as the most individualistic nation, and usually by substantial margins. Though the Constitution provides a foundation for both philosophies (e.g. “We the people” supports collectivism; the Bill of Rights supports individualism), clearly over the last decade value of the individual has taken precedence. This extreme tendency towards individualism is perplexing as in many instances moving toward a more balanced society would benefit more individuals. Take Joe the Plumber’s view from the last election. He opposed Obama’s economic views because he felt it would infringe on his individual rights, and assuming his business would put him in the top 2% of the wealthiest Americans, he is correct. However, in reality Obama’s proposed economic policies would benefit him more than McCain’s would have. This is now the case with health care. Unless you are one of the lucky one to two percent of Americans, public health care will most likely benefit you. This is exemplified by the fact that nearly 60% of bankruptcies (75% of which had insurance) filed in the United States are the result of medical bills[ii]. So even if you are fortunate enough not to be one of the nearly 42 million uninsured Americans, consider that you are one medical emergency away from bankruptcy.

It is also important to point out the hypocrisy of religious leaders, particularly Christians, who argue for a moral government but ignore the preaching of Jesus of whom they hold as a model. Based on my understanding of his life, I believe Jesus would be in favor of national health care. His charity at the individual level does not imply individualism. In fact, most of his decisions were done with intent of helping the collective, that is, wasn’t he sent to Earth to save humanity?

There are countless examples of how the collective will often benefit the individual. Malcolm Gladwell argues that the success of individuals can largely be attributed to their environment or community. That is, raw talent, whether genetic or not, is not enough to be successful. It is raw talent along with opportunities provided by the community that allow one to be truly successful. However, it is Howard Zinn who provides a very damning critique of individualism:

It is an irony that these rugged individuals so loved individualism that they ganged up together to enslave black people, steal land from Mexico, and carry out an ethnic cleansing of the continent. At other times they ganged up to abuse and mistreat, among others within their borders, Chinese people and Japanese people and Jews and Catholics, before ganging up to abuse peoples of Central and South America and so on around the world. A nation of individuals saying, “I am an individual. Don’t blame me for the collective crimes of this country.”[iii]

Capitalism and Democracy

For nearly two centuries, capitalism and democracy have coexisted with minimal issues. However, the delicate balance between capitalism and democracy has been tipped in favor of capitalism, especially since corporations have been granted the rights of personhood. The Supreme Court will hear soon hear additional arguments in Citizens United v. The Federal Election Commission that brings into question the constitutionality of the McCain-Feingold bill. At the heart of the matter is the question of whether corporations have the same unfettered First Amendment right to free speech. The McCain-Feingold bill attempts to limit corporate speech during times of elections since corporations have an unfair advantage given their tremendous financial resources. This is merely the most recent example of how corporations are increasing their dominance over our democratic system. The systematic deregulation of the economic system over the last half-century has brought into question the viability of coexistence of capitalism and democracy.

It is my opinion that capitalism must be suspended for fundamental services/rights of society, two of which are health care and education. In these areas we must acknowledge that the collectivist approach will lead to a more harmonious society where all individuals benefit. We value our education system as providing a means for social mobility. However, as decades of educational research reveal, social economic status is still the biggest predictor of academic success. This is exacerbated by our system of funding schools by property taxes thereby creating a natural inequitable system. When profit motives come in play as they currently are with an increase of for-profit charter schools, the problem is only worsened as exemplified by the failure of charter schools in post-Katrina New Orleans[iv].

One of the problems is the disparate value placed on goods by consumers and share holders. Take Apple for example. It is in Apple’s best interest to create and increase the value of their products as to increase consumer demand. Therefore working to better their consumer’s experience not only benefits consumers, it benefits their shareholders as well. However, the correlation between consumer and shareholder interest falls apart for health care and education because the consumers of the service are not necessarily or usually the payers of these services. For education, it is tax money in the form of property taxes that are redirected to the for-profit companies. The same holds true for health care, except it is generally directed through the employer. Employers often have a choice of health care providers, but rarely do the individuals. Understand it is the service providers’ legal obligation to act in the best interest of their shareholders. In these cases where the consumer is not the payer, it is not the case that the consumer and shareholder interest coincide. This results in a system where the most efficient way for an insurance company to increase shareholder value is to simply reduce the number claims they pay. Or eliminate those individuals who are too costly.

Reframing the Debate

Though I argue that national health care is ultimately a nuanced argument, where proponents of national health care have failed is in articulating their entry point to discussion. That is, the question of health care for all is a moral decision. More specifically, the question must be asked: Is it moral for anyone to make money on someone else’s care? By no means am I arguing that doctors and health care professionals not make any money. I agree that having high paid doctors attracts the most qualified individuals to such an important profession. However, the profit I am opposed to is the money that is directed to Wall Street and investors. In effect, these people are valuing profit over a person’s health. Bill Moyers put it best: “we should be treating health as a condition, not a commodity”[v].

Direct Rebuttals to Opposing Arguments

I have provided the basic framework from where I decided that national health care is a fundamental right of all individuals. In this section I will provide direct answers to some of the more common arguments I have encountered against national health care.

I don’t want the government deciding what care I can get.

In no way has the proposed health care bill suggested that the government will control the health care individuals receive. In fact, under the government plan control of one’s healthcare will be better controlled by the individual and their doctor. Reuters has recently reported that on average, 21% of claims filed in California were denied[vi]. As explained above, insurance companies are motivated to reduce costs to increase profitability, including denying claims whenever possible.

With respect to “death panels,” this idea coined by Sarah Palin but initiated by Betsy McCaughey has been duly debunked. It stems from language in the proposed bill that indicate that doctors could partially be rated based upon their creating an end-of-life plan with patients and the extent to which they followed those plans. For example, if a patient indicates that they want every possible attempt to be made to be kept alive, a doctor who does not follow this end-of-life plan could potentially be rated poorly. Conversely, doctors who do not honor a patient’s do-not-resuscitate will also be negatively rated. These provisions are an attempt to ensure individuals and their families are prepared for end-of-life treatment and to hold doctors accountable for honoring their patient’s wishes. Might I suggest watching John Stewart rather entertaining debate with Betsy McCaughey[vii]?

The Social Security program is going bankrupt, how can the government do better with health care?

At the time the Social Security Act was signed in 1935, the life expectancy was 60, but for a child born in 2005 they can expect to live to 78[viii]. Moreover, the retirement age has only increased 2 years from 65 to 67 resulting in an increase of number of Americans over 65 from 6.7 million to 34.9 million[ix]. Clearly the Social Security Act needs to be amended to account for a changing society, it the program itself and of itself not a failure.

We already have the best health care in the world.

This is simply a fallacy. Spend a few minutes at the World Health Organization (WHO)[x] and you will quickly see that the United States ranks fairly poorly on many quality of life metrics. The WHO last provided an overall ranking of health systems in 2000 where the United States ranked 37th; the US ranks 42 in life expectancy; and 29th in infant mortality. And to make matters worse, we spend more per capita than any other nation on health care.

The Government is already too big.

This is a particularly comical argument coming from the party that gave us The Patriot Act and the largest deficit in history. The former arguably stripped more civil liberties than any other law passed. The starting of two wars, irresponsible tax cuts during a time of war, among other arcane policies despite evidence to the contrary undermine this argument (e.g. abstinence only sex-education programs despite evidence of their lack of effectiveness). The republican’s idea of small government includes corporations ability to create unlimited access to profit while at the same time dictating what is moral, despite the irony that those most strongly preaching for a “moral” America are those caught engaging in immoral acts themselves.


[i]http://www.npr.org/templates/story/story.php?storyId=112281170
[ii]http://www.cnn.com/2009/HEALTH/06/05/bankruptcy.medical.bills/
[iii]Zinn, Howard (2005). A People’s History of the United States: 1492-present. Harper Perennial Modern Classics.
[iv]There are many resources available on this topic, but The Shock Doctrine (2007) by Naomi Klein provides an excellent analysis of the impact of pure Milton Freidman economics.
[v]http://www.pbs.org/moyers/journal/09042009/watch3.html
[vi]http://www.reuters.com/article/pressRelease/idUS202570+02-Sep-2009+PRN20090902
[vii]http://www.thedailyshow.com/full-episodes/246932/thu-august-20-2009-betsy-mccaughey
[viii]http://www.sciencedaily.com/releases/2007/09/070912141110.htm
[ix]http://www.ssa.gov/history/lifeexpect.html
[x]http://www.who.int/whosis/en/

Protected: Robert Moses Keynote

8 April, 2008 (08:44) | Education, Mathematics | By: Jason

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Junk Food Mathematics

11 December, 2007 (11:13) | Education, Mathematics | By: Jason

As an undergraduate one of the rites of passage for seniors was taking Bruce Johnston’s Junk Food Theology course. The idea arose out of the observation that during the 20th century in America there was on one hand a decline in attendance at weekly religious services but on the other, an increase in those who believe in some version of God. How could such an event occur was the question raised by Prof. Johnston in the first class. His theory is that societies religious and spiritual needs are being met and supported by popular culture. More specifically, by movies. Seeing a movie such as Star Wars, and the subsequent near cult (or dare I say religious) following it’s not hard to see the parallels to more traditional religious stories.

If one were to accept this theoretical framework then it stands to reason that popular culture significantly influences individual beliefs, and core beliefs at that. In what other ways is popular culture influencing our beliefs?

In a recent study I conducted regarding math anxiety, one of the results was that 66% of pre-service teachers identified as having math anxiety. Moreover, according to the Trends in International Mathematics and Science Study (TIMSS, 2003) the United States ranked 14th in mathematics ability in eight grade. I was also stuck by how readily participants admitted, and even bolstered, about their dislike and lack of ability in mathematics. It would appear that it is socially acceptable to be poor in mathematics.

Now thinking about Johnston’s course I began to wonder if perhaps popular culture is in some way supporting this culture of math ambiguity. True to Johnston’s form, I began thinking about how mathematicians are portrayed in movies. Here are some recent movies containing a mathematician:

  • Proof, 2005
  • A Beautiful Mind, 2001
  • Pi, 1998
  • Good Will Hunting, 1997
  • Contact, 1997 (admittedly I know Jodi Foster played an astronomer, but I couldn’t resist referencing Carl Sagan and is consistent to my point)
  • Jurassic Park, 1993

The characteristic common to the mathematicians portrayed in each of this movies is that they are at minimum eccentric, or at worst crazy. We can’t underestimate the influence popular culture has over one’s beliefs. I’ll admit, I find each of these movies very entertaining. But I also approach them from a very different point of view given my mathematics background. But for many this is probably their only exposure to mathematicians outside of their high school teachers. However, according to my results, 44% have already experienced at least one significant negative math experience before even entering high school. Research suggests that parents and teachers are a significant correlate to children who develop math anxiety (Norwood, 1994; Tobias, 1995; Williams, 1988; Greenwood, 1984; Handler, 1990). Clearly there is a chicken and egg problem, but at this juncture answering this question is academic. We must begin to attempt to counter the culture of math ambiguity.

That is not to say this hasn’t already begun. The CBS show Numb3rs is portraying mathematics in a much more positive light. One of the shows advisers and faculty member at Williams College, Edward Burger, has written an excellent book Chaos, Coincidences, and all that Math Jazz that attempts to present relatively complex mathematical concepts in a form that anyone can understand. John Allen Paulos with his books regarding innumeracy provide insight into the consequences of poor mathematical understanding. And if you fin yourself grappling with math anxiety, Sheila Tobias’ book Overcoming Math Anxiety is a must read.

With the continued technological advances and statistical studies (both political and otherwise) it is critical that everyone have some basic level of mathematical literacy. Though I wouldn’t suggest that great storier as those in the movies mentioned above not be told, we need to get to a point where they have an unfortunate consequence of perpetuating a culture of math ambiguity, or what Paulos would call, innumeracy.

Trevor Owens, Technology Evangelist for Zotero

3 December, 2007 (11:31) | Education, Software | By: Jason

The latest issue of Innovate Journal of Online Education has an interview with Trevor Owens, a technology evangelist for George Mason University’s Center for History and New Media. Of interest is the planned 2.0 version due out in 2008 that will include server side functionality.

Innovate: Next-Generation Bibliographic Manager : An Interview with Trevor Owens:

James Morrison’s interview with Trevor Owens explores Zotero, a free, open-source bibliographic tool that works as a Firefox plug-in. Previous bibliographic software, such as EndNote or Refworks, worked either online or offline to collect references and citations. Zotero leverages the power of the browser to allow users to work either online or offline and integrates citations with other research materials in a way that promises to reshape the way research is done. Zotero 2.0, due out in early 2008, will expand the potential of Zotero by providing server-side functions that allow for the sharing of bibliographies and accompanying annotations.

Bibliographic Software

29 November, 2007 (09:36) | Education, Software | By: Jason

As a graduate student I’ve amassed a large number of research articles and books. The question is, how do you keep all of this information organized as to be able to find information later? The answer is: bibliography software. There are many options available for both Windows and Mac but the two clear leaders are Zotero and Endnote. For a while now I’ve been using both; Zotero to collect reference and Endnote to manage citations.

Zotero, which is a Firefox plugin, makes the process of adding references to you library incredibly easy. When viewing a page (e.g. from EBSCO or Amazon.com) you simply click an icon in the address bar and magically all of the data is imported into you personal library. You can even attach (or take a snapshot) of web pages and/or PDF files when available. Once a reference is in your library you can attach tags (think keywords), notes, or any other file (e.g. PDF, Word document, csv, etc). With all your references collected into a single repository it becomes very easy to find that article from a few years ago.

But collecting and organizing your references is only the beginning. Zotero and Endnote both include a Microsoft Word plugin (Zotero also has a plugin for OpenOffice) that will assist in adding citations from your library (Endnote calls this Cite While You Write, or CWYW). When you reach a point where you need to insert a citation, you click a button on the provided toolbar. This will then take you to your library where you can search and find the desired reference(s). Click insert and your citation is placed at the cursor. Both programs provide a wide variety of styles including APA, Chicago, and MLA not to mention many different journal specific formats.

When using citations you’re inevitably going to need a references page. Endnote will do this automatically once you insert your first citation. Zotero will also automatically manage your reference page but you first have to insert it where you would like (it’s just one click on Zotero toolbar).

My workflow until now has involved collecting references with Zotero, exporting my library in RIS format (using RIS instead of Endnote, which Zotero supports, will preserve notes), and then importing the exported library to Endnote. This is because the beta version of Zotero did not format citations exactly write. However, with the official 1.0 version of Zotero out, it’s Word plugin is just as good as Endnote’s. At this point I would recommend that everyone get started with Zotero (it is free after all!) especially given that you can easily move your library from Zotero to Endnote later if necessary. That said, many universities and institutions have invested in Endnote. Plus Endnote allows for separate libraries which, when collaborating with colleagues, can be useful when sharing. Zotero provides one library but does have collections within the library. Which every your choice, Zotero is the clear winner for collecting your references.

For completion sake, I’ve included the list of all the bibliographic software, along with their prices (as of this writing), that may worth looking into. Some of these have been designed for specific disciplines so it may be worth looking into if you have specific needs that Zotero or Endnote does not satisify.

Name Platform Regular Price Student Price
Biblio Windows $49  
Bibliographix Windows 98 Euro 49 Euro
Biblioscape Windows $139 $99
Bookends Mac $99 $69
Citation Windows $99  
Endnote X1 Windows/Mac $250 $110
Library Master Windows $249 $125
PowerRef Windows $129 $69
Scholar’s Aide 4 AE Windows $149 $99
SquareNote Windows $49  
Zotero Windows/Mac/Linux FREE FREE

Hello world!

14 November, 2007 (07:19) | Uncategorized | By: Jason

Well, I’ve finally got around to updating my website. Instead of using a desktop application I’ve moved into the modern web and migrated to Wordpress! I’ve been using for my son’s blog but really like how well it handles static pages as well. Though not as powerful as full content management system such as Drupal, Wordpress is pretty great.

Though I’ve tried blogging in the past, I seem not update very often. However, I’m going to attempt to use this format to keep some of my information organized, particularly as I find stuff on the web related to my studies in Educational Psychology. You may want to also check out my photography blog.