R you srs?

Who has heard of the open source statistical software package R? Anyone interested in statistics or who uses statistical software on a regular basis should know about R. Obviously, all of the six people who read this blog know about R, but I'm going to keep going with this for the people who accidentally stumble across this page looking for information on R. Or maybe for people who were searching for this who just happen to be familiar with statistical software packages but don't yet know R (an obviously miles-wide swath of the internet population).

As I mentioned in my previous post, I'm enrolled in an econ/development program at Evergreen right now, and along with that I have an individual learning contract with my professor studying econometrics using R. Econometrics is the mathematical application of economics. Mostly we're talking about regression models used to analyze things as mundane as marketing strategies for fast-food companies and as far reaching (and perhaps as abstract) as the value of a statistical life. Econometrics has enormous application potential, and trying to learn it or read studies or articles based on econometric research without a pretty solid foundation in statistics is, um, challenging.

R is a programming language, a topic I know essentially nothing about. What I do know is that R is based on S. So there you go. Any programmer folks who want to chime in on a richer history of R should definitely do so in the comments. It's actually pretty cool stuff, which I have read a bit about, but don't know enough of off the top of my head to say much more than I already have.

What's so great about R? Well, has anyone used Excel for any mathematical or statistical applications? It's pretty cool, right? First of all, Excel has a pretty easy to use interface. It's mostly a point and click tool. Also, for someone who is just learning stats and/or stats software, Excel seems to be moderately powerful. You can obviously store, arrange, and analyze all of your data in spreadsheets, and, using the data analysis, you can run ANOVA, basic regression models, and t-tests and F-tests and the like. Excel is good for these things. It's also good for keeping track of your budget, or doing a school presentation, or designing tables and graphs, etc etc. Excel is a broad tool with numerous applications whose mathematical and statistical applications are limited by the programmers who designed it.
R, by contrast, is limited only by the user. As I mentioned before, R is open source and was designed specifically for statistical analysis. What does open source mean? Any R user can design their own package in R to cater to their own particular needs. Theoretically, if there is a test you can't perform in R, you can design and program the test yourself and tell R to run it for you. With R, you are your own programmer. Not only that, but R has a huge community of users, many of whom are statisticians and programmers, who are often available to offer assistance in the use of R. The strengths of R can also be a barrier to using it. With R, it's garbage in, garbage out. There is a steep learning curve, and it is very intimidating to those of us who do not come from a world of programming.
A vital point which makes R perhaps the best bang for the buck: it is totally free to use. Go here to download it right now. Excel isn't too expensive, relative to programs like SPSS, SAS, and STATA which can cost hundreds of dollars (but which are all more powerful than Excel).

So anyhow, I'm learning both R and econometrics right now, but what I'd really love is to know of anyone who uses R in epidemiology applications. I've begun to delve into the academic world of epidemiology in reading Epidemiology: An Introduction, but I'd love to hear from epi students about the kinds of statistical methods used in epidemiology. It would also be brilliant to hear from some epi students who know/use R. Also, what other statistical software are folks using in the world of epidemiology? Does anyone have experience with multiple software packages and have a preference?
I'd love to hear thoughts and opinions on this.

Shaking off the Cobwebs and an Econ Hangover

My last post started with a statement along the lines of "It's been awhile since my last post." Well, it's been even longer since that one. Here's my excuse-o-rama:

1.) I was unable to get into any public health related programs at Evergreen. Well, more accurately, there weren't any for me (I'll explain why after a few hundred words about econ/development). Instead, I've been in a economic development program. This was NOT my ideal choice, but there are some obvious parallels and overlaps between the goals of public health and economic development.
My takeaway from the program thus far?

   a) Economics is a phenomenally frustrating subject. Too many assumptions are accepted as fact and there are too little opportunities to test assumptions before they become accepted theories in the field. Thus, far-reaching policies are designed based on those assumptions. This isn't an econ blog, so I'll provide quick example with no evidence to support my claim: the Washington Consensus and the Bretton Woods Institutions that championed free-trade starting in the late 70s and early 80s. What a horrifying failure. I encourage anyone interested in seeing why the world has been thrust into such atrocious poverty to do a little research into those two things.

   b) Development economics is a phenomenally frustrating subject. There are a lot of people working to solve the world's poverty issues who are doing great work, trying to make the world a better place for everyone. Unfortunately, development is another area rife with unchecked and untested assumptions. The book Poor Economics is a discussion on performing randomized controlled trials (RCT) to test ideas in small settings before creating systemic policy changes. This is an idea of which I generally approve coming from the public health mind frame, but in the world of development, there are massive ethical snags (for which the authors seem to have no thought). Performing RCTs on a vulnerable population to observe whether or not giving mosquito nets away for free (rather than selling them for market price or at a subsidized price) is the best way to get the highest number of nets out into an area where malaria is prevalent seems... sketchy to me. There is no informed consent for the subjects of the trial. There is little interaction with the people themselves to ask what they might think would work best for their personal situation. Treating people as little more than test subjects rubs me the wrong way.
On the other hand, I think the RCT approach is better than making assumptions and implementing them with no data to suggest possible outcomes ahead of time. RCTs could be done better, and could very well provide small scale interventions for people suffering some of the worst effects of gut-wrenching poverty. I do recommend the Poor Economics book.

   c) Reading textbooks by economists is phenomenally frustrating. To illustrate, I'll cherry pick a suggested policy prescription from one of the development textbooks the class is reading this quarter:

"[I]ndiscriminate educational expansion will lead to further migration and unemployment. [There are] important policy implications for curtailing public investment in higher education."

... Right. So one solution for the problem of mass migration in say, India, from rural to urban areas is to curtail education. The thought here is that educated people are more likely to migrate into the cities but there are too few jobs, so people wind up crowding into filthy, crowded shantytowns. Because (in part) there is too much indiscriminate investment into education. I'll just let you think about that one, fair reader. (This came from the book Economic Development by Michael P. Todaro and Stephen C. Smith, FYI. The section quoted came from a description of the "Todaro migration model" as described in the textbook. I have so many complaints and critiques of this book I could write an entire counter-book against it. But I'm not a PhD, so what do I know?)


   d) There are some great people doing brilliant work in development. Paul Farmer has one of the best books I've ever read on the subject, Pathologies of Power. Any looking into Paul Farmer's history will reveal my bias toward him; he's a physician and a medical anthropologist whose work in development is based on what he calls "O for the P," option for the poor. He insists that any policy that doesn't benefit the worst off people is missing the point at best, or more likely useless. I'll write more on Farmer in the future. For now, along with Pathologies of Power, I recommend Mountains Beyond Mountains by Tracy Kidder for a bit of a biography of Farmer and his organization Partners in Health.
Another man who has changed the way development is viewed is Amartya Sen, Nobel prize winner, philosopher, economist, and someone who reminded economists and policy makers that Adam Smith's original intent was to solve the problems of poverty rather than increase revenue (in not so many words). Sen was a co-creator of the Human Development Index, which measures economic development not just in terms of income per capita, but also in measures of agency, access, health, and education. Go figure.


(Now continuing with my excuses...)

2.) I haven't actually taken any epidemiology courses. As much as I love Evergreen, I wish the college's pedagogical design allowed for some advancement in certain subject areas. For anyone unfamiliar with Evergreen, the college offers no majors or degree tracks (other than in the sciences, which are intensive and incredibly competitive, and three graduate programs). Unfortunately, this means I essentially exhausted my public health study options last year, hence my enrollment in this development/econ course.
I've been reading an epidemiology textbook (y'know, for fun, in all my spare time) and hope to move more into this world after I graduate, and I hope to provide posts more germane to epidemiology on here soon.


3.) My family is growing. Baby number three is on the way, and should be here in fewer than two weeks (fewer than two days, my wife hopes). Here's to baby girl!


4.) I'm lazy.


5.) I've been busy. Lay off me.

Alright, that's what's going on right now. Thanks for reading the novel. I get carried away sometimes. But guess what? I have more to say. Check back for (hopefully) more frequent updates that actually pertain to epidemiology.

When all you have is a hammer...

It's been a while, folks. It's summer. Need I say more?

Let me get right to it. Why the sky high health care costs? Why the climbing insurance costs? What the French, toast?
Obviously, books upon books can be written on this subject (and have been). There are an enormous number of reasons for the insanely high costs (that continually climb) of health care in this country. Clearly, a profit-based health care system is leaving many out in the cold.

But what I want to focus on here is our medical delivery system. The fascinating history of medicine in this country has fenced us into a system that encourages complex, expensive procedures for every ailment, injury, or malady. The more of these procedures that can be completed on a patient, the better (i.e., the more that can be charged to insurance companies, leading to higher premiums, leading to higher co-pays, more cost-sharing... but I'm getting ahead of myself).
Patients that only need a prescription for antibiotics or have a minor complaint or simply need a check up are in no way making the money these docs need. Well, can we really blame the docs for wanting the more complex cases? Look at the crushing debt they've acquired! But really, we can begin to understand how the disillusionment with our physicians (and thus the insanely high incidence of malpractice suits) originated. Family practice and primary care can be interpreted as a patient mill,  the goal being to get people in and out as quickly possible, to see the highest number of patients in order to maximize income. I'm really generalizing here, but these generalizations are broadly supported by fact and can be easily confirmed with quick internet or academic searches. A great place to look is Paul Starr's book, "The Social Transformation of American Medicine."

The origins of Medicare are partly to blame for this complexity phenomenon. Medicare was designed to compensate more complex procedures in a manner seen as more fair. Lobbying by medical stakeholders (the AMA, insurance companies) allowed for more medical and surgical specialties. These specialties, of course, come at a premium. The costs to patients rose, insurance companies became more prominent, and further lobbying allowed them to make more profits from premiums. Insurance companies, for their part, mostly follow the same methodology as Medicare for procedure compensation.
Again, considering that enormous debt, any medical student would certainly want to enter a specialty that paid more. And that's exactly what has happened. Our system is top heavy, like an inverted triangle. Our country enjoys an (over)abundance of specialists who make up the largest part of the triangle; cardiologists, perinatologists, oncologists, and on and on. The more specialists we have, the more specialized procedures are given (necessary or not), and so health costs climb. As befits the triangular imagery, our primary care physicians are far fewer in number, occupying the downward pointing tip of the triangle.

Now let's be realistic; in a country of over 300 million, most people's health needs are not met by specialists. Don't get me wrong, when I keel over during a cardiac event, you can rest assured that I want the best cardiac physicians in the world to save me, and here in the U.S., I have that. But, interestingly, we know that heart disease is the number one killer in the nation, so a growing number of people do need the skills of specialists.
But the question must be asked; if we had more primary care physicians to help us monitor the little things (blood pressure, cholesterol, diet, etc), would we need so many specialists? A quick illustration: England's care provision is the reverse of ours. It looks like a point side up triangle, with a vast majority of physicians in the primary care fields, and fewer in secondary and specialty fields. Their National Health System is cheaper than ours and provides better outcomes for patients (not the least of which are a longer life expectancy and a lower infant mortality rate). Of course, healthcare is far too complex an issue to break down into this one category as the smoking gun for all our cost problems, but the issue is relevant and bears further study, and certainly some reflection for the public.

Of course, the discussion of health care and its various issues encompasses every facet of our lives. It is as basic as personal responsibility and as complex as Obamacare. It is as intimate as the patient/provider relationship and as far-reaching as global economics. It is as fundamental as public education and as esoteric as the most complex scientific studies. Each facet lies adjacent to the next, and an adjustment to one invariably changes the shape of each of the others.

The Smoking Gun

Alright, here's the abstract:
-Epidemiology and heart disease
-Heart disease -- more about what you do or where you do it?
-Fundamental causes
-Contextualizing risk factors
-"Stress is the new tobacco."
-A big bunch of links to several academic webpages and articles.

So I've discussed a bit about epidemiology and my interest in the social determinants of health (SDH). Traditionally, epidemiology focuses on individual behaviors as causal factors for non-infectious disease risk (non-infectious diseases such as diabetes, heart disease, cancer, etc. A case can be made that SDH plays a role in incidence of infectious diseases as well. I'll touch on that another time).

I'll use not only the most deadly non-infectious disease, but the number one killer in the U.S. as an example: heart disease.
Epidemiology focuses on population level risk factors for heart disease. As such, perhaps we should take a step back and contextualize individual behaviors within the broader picture of where and how people live. What factors have an effect on behaviors? Can there be earlier interventions for better preventive measures? What I'm talking about here is what puts people at "risk of risk," as Jo Phelan and Bruce Marmot called it.

What is the fundamental cause of heart disease? Bio-medically speaking, we can talk about artery blockages that reduce blood flow to the heart, starving tissues of oxygenated blood and eventually causing a cardiac event (heart attack or stroke). But what causes the blockages? Physicians consider many factors: Does the patient have a healthy diet? Is the patient obese? Does the patient take time to exercise daily? Does the patient smoke? What is the racial identity of the patient (this can make a difference, I'll explain further in a moment)? There are several measurements taken into account by physicians, and often times a regimen including better diet and exercise, smoking cessation, and medication are prescribed.

I'll contextualize these factors, and address each one individually. Studies have shown that those in poverty are less likely to have a healthy diet, a factor which is directly related to obesity. Those in poverty are less likely to exercise, and this often isn't a choice. In fact, there is evidence to support the idea that regardless of income level, living in a "poor area" has a negative impact on your health. Furthermore, we know that those living in poverty are far more likely to smoke, increasing risk of heart disease. Read more on the links between poverty and tobacco use here. Multiple studies have shown that there is a major link between poverty and race, and people who identify as African Americans and non-white Hispanic suffer the most. The links between race, poverty, and disease have been discussed and researched again and again and again. A simple perusing of the available research quickly demonstrates a clear link between socioeconomic status and heart disease. The ability to treat and recover from heart attacks is also directly related to socioeconomic status. The stresses involved in dealing with our complex medical and insurance system has cost lives and hope in the battle toward recovery, and that stress is increased for those of low socioeconomic status.

Then what about stress? There's a lot of talk out there about how stress is the "new tobacco." Stress responses were originally present in our bodies as a way to protect ourselves from danger. The old "fight or flight" response. The opposite of this is the perhaps less known "rest and digest." So the difference in our modern world is the lack of life-threatening saber tooth tiger attacks and the over-filled bag of deadlines and schedules. Fight or flight is supposed to be temporary, to subside once we've flown or fought. A sustained state of fight or flight cuts down our body's ability to rest and digest, to repair itself, to do the upkeep necessary to stay healthy. What that means is that sustained levels of stress cause cortisol buildup in the body, interfering with the rest and digest state, causing damage to our internal organs and processes. Modern day stress is a major contributor to heart disease. It's killing us.

So let me make my point in no uncertain terms: There is an undeniable link between health and socioeconomic status. Inequality is deepening, and the poor of our country are suffering and dying at increasing relative rates, while our medical technology and life-saving measures keep getting better. It is unethical and unacceptable. We see here that simple behaviors or biomedical measurements are important, but they aren't the smoking gun. To get a true understanding of health in our country, we must fully understand the effects of socioeconomic status.

I love school... Where do I go from here?

School has been an amazing experience so far. I love the Evergreen State College. As I'm about to finish my junior year, it's time to really start thinking about grad schools.
I'm looking to get an MPH in epidemiology. I want to have an additional concentration on social causations of health outcomes and public policy implications -- things of this sort. I'd love to work in a state department of health or social services. Non-profit work, such as with Kaiser would be incredible as well.
Eventually, I'd like to pursue a PhD in epidemiology and teach at a collegiate level. I'd like an opportunity to lobby at some point too, assuming I'm not working for a public agency.

So where do I go from here? Here's my short list.

UW School of Public Health is highly rated. Check out their epidemiology dept here. This program is the closest to where I live. The next closest is Portland.

Drexel University in Philadelphia has a school of public health that is gaining traction on the ratings list. Their site is incredibly informative, and there are several programs that really interest me. There seems to be a major focus on policy and social health issues.

George Washington University in D.C. has some pretty intensive programs. Also, it's in D.C. Location is a major factor here, as so many powerful organizations are located or do so much work here at the federal seat of the country.

So that's what I'm looking at. I'd LOVE to hear from folks who have experience with any of these schools! Further suggestions are welcome too, of course.

Have a great weekend everyone!

The Social Determinants of Health

Pre-read summary:
-What are social determinants of health, and why should I care, you fascist?
-Another mention of Dr. Mukherjee.
-Not that kind of social network.
-Stressed out mommies make stressed out babies.
-This article by Dr. Bezruchka.
-More reasons for libertarians to think I'm a commie.
-Social context.

Now THIS is a big topic.

So earlier I mentioned this concept of the social determinants of health and made the contention that the social context of the world we live in plays a larger role in our health than other individual factors, such as availability and quality of health care or the number of cardiologists in your area. But what exactly does this mean? What in the hell are "social determinants of health?"

To help answer that question, let's look at Siddartha Mukherjee's (MD, by the way, so pay attention) question in his book:

"Epidemiologists typically measure the risk factors for chronic, noninfectious illnesses by studying the behavior of individuals. But recently, they have asked a very different question: what if the real locus of risk lies not in the behaviors of individual actors, but in social networks?"

This isn't about Facebook. What Dr. Mukherjee was referring to here was the idea that behaviors (positive and negative) are reinforced through social norms. That is, the group you hang out with has a large influence on your behavior. The example he goes onto refer to in the book is social networks of smokers and the proliferation of lung cancer within these circles.

Social groups play a large role in rates and incidences of noninfectious diseases. But it goes beyond the groups an individual associates with. Policy measures having to do with social inequality also play a big role. For instance, there is a growing body of evidence that suggests that environmental factors during first 1000 days of life can have life-long effects on a child. Psychosocial stress certainly has a negative impact in utero. Political measures that disallow or make difficult the ability for parents to care for their newborns just may have an irreversible impact on that child's life.

 Let's see what Dr. Bezruchka has to say about this:

"The United States does not provide paid maternity leave nor paid prenatal leave, which may be important factors in affecting health outcomes."

Now, he didn't just pull that statement out of the ether. This quote comes from his article "The Hurrider I Go, the Behinder I Get." That one statement has seven citations to support it. This particular article describes (in great detail) how universal medical care and personal behavior are not limited in their ability to determine health outcomes when compared to social inequality and lack of health outcome orientation in political infrastructure.

Another argument addressed in Dr. Bezruchka's article is one I've only rarely heard, but bears scrutiny. Doesn't the fact that people of so many different ethnic and racial backgrounds skew the health outcome numbers for this country? Are unhealthy immigrants bringing our numbers down? It doesn't look like it. Can you believe that first generation Hispanic immigrants have lower infant mortality and longer life expectancy numbers than non-Hispanic whites in the U.S.? It's true. (Interestingly, studies of second-generation immigrants demonstrate a substantial lowering in those numbers).

So. Health outcomes are bigger than what medicine you take, which doctor you see, and how many gallons of soda you imbibe on a daily basis. To be sure, each of these things is important. But in order to the full picture of how important these things are, we need to contextualize them within the bigger framework of the social setting in which we all live. This contextualizing is what makes clear the importance of the social determinants of our health.

Why epidemiology?

Quick summary:
Epi-whatever
I have a talent for making cool things boring.
Epidemiology has scientific power.
Siddhartha Mukherjee wrote a brilliant book about cancer. Read it.
WashYourHandsingTon
Libertarians might hate epidemiology.

So just what is epidemiology anyway?

Most people I've told about my wanting to go into epidemiology react in one of three ways. Most frequently people say "What the hell is epi-whatever?" I've been surprised by the number of people who take a stab at what epidemiologists do. "So that's like... some kind of skin doctor?" The least common reaction is "Epi is so cool." Well, okay.

Epidemiology is about tracking disease incidences over time and space. The idea is to quantify data having to do with when, where, and how diseases spread in the hopes of developing measures to slow, stop, and prevent diseases from occurring. There's research and data gathering. There's a lot of statistical analysis involved. I have a talent for making things sound boring.

The power of epidemiology is what fascinates me. The ability to use quantitative data to devise methods and policies to slow infections or incidences of disease or death is incredible. Epidemiology is a fantastic mix of mathematics, biology, and social sciences that can and has allowed for enormous strides in reducing the impact of some of the world's deadliest diseases. The reason for this is the epidemiological emphasis on prevention.

It should be known that prevention of disease has had a far greater global impact on human survival than has treatment. Siddhartha Mukherjee describes well the impact of preventive medicine in his brilliant book The Emperor of All Maladies:

"If one plotted the decline in deaths from tuberculosis, for instance, the decline predated the arrival of new antibiotics by several decades. Far more potently than any miracle medicine, relatively uncelebrated shifts in civic arrangements -- better nutrition, housing, and sanitation, improved sewage systems and ventilation -- had driven down TB mortality in Europe and America."

Think, too, of seat belt and helmet laws, food labeling (for trans fats and the like), vaccines for all children, and shifts in public policy to encourage balanced diets and regular exercise. Remember those ads in our state (Washington), "Wash-your-hands-ington!" Brought to you by the state Dept of Health... based on epidemiologic knowledge. Of course hygiene is basically common knowledge now, but we have epidemiology to thank for that knowledge in a broad sense. Epidemiological studies play an important role in public policy, and as the cornerstone of public health, have shaped many aspects of our modern lives, both overtly and covertly.

So you can see that the power of epidemiology lies not only in the analytical and scientific heft of the study, but in advocacy and social health issues as well. There are some who undoubtedly shift uncomfortably in their seats reading about this, feeling that no institution or field should hold such sway. The ethical and moral sway of public health policy is yet another captivating aspect of the field for me. I wonder what Drew Carey thinks of epidemiology?

Good luck and good health, everyone.