U.S. county mortality paper

The U.S. county mortality paper, a study analyzing 21 cause groups of death in every U.S. county from 1980 through 2014, was published in JAMA on December 13th along with a trove of other useful resources on county health including updated county profiles, an updated US Health Map data tool, a new US Data GHDx page, a new animated GIF, and two videos produced by JAMA.

Congratulations to IHME study authors Laura Dwyer-Lindgren, Amelia Bertozzi-Villa, Rebecca Stubbs, Chloe Morozoff, Michael Kutz, Chantal Huynh, Ryan Barber, Katya Shackleford, Abraham Flaxman, Mohsen Naghavi, Ali Mokdad, and Christopher Murray.

Additional congrats to the Global Engagement Team (GET) members and alumni involved in the dissemination of these important findings: Dean Owen, Kevin O’Rourke, Kate Muller, Bill Heisel, Dawn Shepard, Sofia Cababa Wood, Katie Leach-Kemon, Adrienne Chew, Pauline Kim, Rachel Fortunati, and Kayla Albrecht.

Stories by CNN, HealthDay, NBC, and Reuters were picked up by hundreds of local news stations and papers across the nation, totaling nearly 500 media mentions since 8:00am Tuesday. Here are a few of the top news stories covering the paper; many include their own graphics using IHME county mortality data:
• Janet Adamy with the Wall Street Journal wrote What kills Americans varies widely by region. ““It’s much more complicated than saying ‘Everything’s bad in Mississippi and Alabama, and everything’s good in places with high life expectancy,’” said Christopher J. L. Murray, director of the Institute for Health Metrics and Evaluation at the University of Washington and an author of the study.”
• Olga Khazan with the Atlantic wrote Why are so many Americans dying young? “’A place like Colorado, there’s an incredibly low death rate for heart disease, one of the lowest in the world, and low rate for diabetes,’ Murray said. ‘If you look at places like West Virginia, things are getting worse, and it’s not just opioids.’”
• Jacqueline Howard with CNN wrote What’s the most common cause of death in your county? “’We know that unequal access and quality of care create health disparities in the US for many causes of death, while other causes are linked to risk factors or policies. The results of this study prompt future research to further identify what drives health disparities in our country,’ said Dr. Christopher Murray, a professor and director of the Institute for Health Metrics and Evaluation at the University of Washington, who was a co-author of the new study.”
• Anna Maria Barry-Jester with FiveThirtyEight wrote How Americans die may depend on where they live. “Lead author Laura Dwyer-Lindgren, a researcher at the Institute for Health Metrics and Evaluation at the University of Washington, says she hopes the data can be useful to local health workers and the public. ‘If you go to any state health coordinator, they probably know what was recorded on the death certificates. But it can be really difficult to interpret them,’ she said. She hopes that collapsing the various causes of death down to 21, rather than looking at everything that can kill a person, will make it easier to target regional problems.”
• Maggie Fox with NBC News wrote Where you live determines what kills you. “’Heart disease is particularly high in the southeast of the United States,’ said Murray, who has pioneered many different ways to crunch health statistics. Experts know lifestyle — poor diet, a lack of exercise and less access to good medical care — are mostly to blame.”
• Andrew Seaman with Reuters wrote U.S. death rates vary drastically by county. “’Within any individual county, knowing how big of a problem a condition is’ can help counties know which conditions need attention, resources and policies, said the study’s lead author Laura Dwyer-Lindgren, of the Institute for Health Metrics and Evaluation at the University of Washington in Seattle.”
• Dennis Thompson with HealthDay wrote Where you live may determine how you die, which was picked up by U.S. News and World Report. “Armed with this sort of information, county and city health departments can focus their efforts on the specific problems affecting their communities, said lead researcher Ali Mokdad. He is a professor with the department of global health at the University of Washington, in Seattle.”
• Julia Belluz and Sarah Frostenson wrote These maps show how Americans are dying younger. It’s not just the opioid epidemic. “Different geographic regions are experiencing extreme variations in despair-related outcomes like suicides, drug overdoses, and heart disease, said Abraham Flaxman of the University of Washington, one of the authors of the new JAMA paper. ‘If you look at geographic patterns, you can say it’s despair that’s leading people to drink and do drugs. But then why wouldn’t that apply to leading people to overeat and become obese and diabetic? These trends are happening in different places.’”
• Agata Blaszczak-Boxe with Live Science wrote Leading causes of death in US vary greatly by region. “The reasons why higher death rates vary across geographic areas are not completely clear, but the authors suggested some ideas. For example, the higher death rates from cardiovascular diseases might have something to do with higher rates of obesity in these areas, said study co-author Christopher J. L. Murray.
• Carolyn Gregoire with the Huffington Post wrote This GIF sums up the impact of addiction and mental illness on America. “In a cluster of counties in Kentucky, West Virginia and Ohio, researchers uncovered striking death toll increases of 1,000 percent or more. Topping the list were Clermont County, Ohio (the site of one of the worst heroin epidemics in the state), which saw a 2,206 percent spike, and opioid-stricken Boone County, West Virginia, with a 2,030 percent increase.”
• (UK) Mia De Graff with the Daily Mail wrote What is the typical cause of death in YOUR county? Incredible maps show leading killers in each region of America. “Where you live determines how you die. That is the conclusion of a new study that lays bare the most common causes of death county-by-county across the United States, and how it has changed since 1980.”
• (UK) Celine Gounder with the Guardian wrote How long will you live? That depends on your zip code. “In an analysis of 80 million deaths in the United States between 1980 and 2014, a study published on Tuesday finds dramatic differences not only in life expectancy, but also in cause of death from county to county. ‘We’re not narrowing the gap. The gap is widening,’ said Christopher JL Murray, one of the authors of the study.”

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py.test recipes for slowness

Useful material on how to deal with slow tests in py.test, a bit buried in the docs:

From http://doc.pytest.org/en/latest/usage.html, to get a list of the slowest 10 test durations:

pytest --durations=10

From http://doc.pytest.org/en/latest/example/simple.html, to skip slow tests unless they are requested:

# content of conftest.py

import pytest
def pytest_addoption(parser):
    parser.addoption("--runslow", action="store_true",
        help="run slow tests")

# content of test_module.py
import pytest


slow = pytest.mark.skipif(
    not pytest.config.getoption("--runslow"),
    reason="need --runslow option to run"
)


def test_func_fast():
    pass


@slow
def test_func_slow():
    pass

Very convenient to know.

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CCA for diverticulitis

A short paper from my work on predicting who will get elective surgery for diverticulitis is on arXiv: https://arxiv.org/abs/1612.00516 [tag: my-research]

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Einstein’s Obituary for Emmy Noether

A children’s book on women in STEM led me to this gem:

[get nytimes screenshot, possibly tell story about using privilege, and the sooner the better[

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A problem with measuring mortality

Preparing for the release of our paper of leading causes of death in US counties led me to review the origins of a quote often attribute to Stalin: http://quoteinvestigator.com/2010/05/21/death-statistic/

Lots to unpack there. The important thing for me is remember that there are individual human tragedies behind the 80 million data points in our study. Respect.

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Advice from Abett

Abett is my former colleague Mike Hanlon’s new startup, and its advice app is now publicly available.

I remember fondly the days I spent working with Mike, who has a wealth of stories from has time as employee #7 at Amazon. He was in the cruicble as AMZN formed, stormed, and normed, and I got a lot of insight into what IHME’s fast growth could look like from his battle tales.

He has lofty goals for Abett as well, to use “big data”, in this case meaning user trace data, to help _people_ instead of advertisers. I’m 100% for that.

From http://www.abett.com/:

There is no advertising on our service, and never will be. We don’t care which products you buy, or if you buy any at all. We want you to make the right decision for you. Advertising would bias that objectivity, and thus we don’t accept it.

For more: http://www.abett.com/blog/2016/10/31/hello-world/

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Non-associativity of floating point addition and why testing scientific Python is hard

I’m lecturing Python II for a Software Carpentry Bootcamp in Jan, and I thought I’d find a little example of a funny fact I’ve heard: IEEE floating point addition does not obey the associative law.

I must be spending too much time with doctors, because I didn’t try to make an example myself and started by looking it up in Google. The first example I found put it cleanly: http://www.walkingrandomly.com/?p=5380

>>> x=(0.1+0.2)+0.3
>>> y=0.1+(0.2+0.3)
>>> x==y
False
>>> print('%.17f' %x)
0.60000000000000009
>>> print('%.17f' %y)
0.59999999999999998

This shows the rumor is true: addition is not associative. It does not seem like a big deal, though, since I usually round my numbers to one or two significant digits, and I know how to test with `np.allclose`.

The second example I found makes the problem clearer, though: http://cass-mt.pnnl.gov/docs/pubs/pnnleffects_of_floating-pointpaper.pdf

x = (17 + 1e32) - 1e32
y = 17 + (1e32 - 1e32)

Can’t `np.allclose` that, unless you know what “close” means…

Additional reading: http://www.macaulay.ac.uk/fearlus/floating-point/

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Long tables, cold coffee, and late nights

Sherry Turkle: https://www.uni.edu/provost/sites/default/files/u29/how_to_teach_in_an_age_of_distraction_-_the_chronicle_of_higher_education.pdf

Reminds me of the math cafes of Poland pre-WWII that I read about. That sounded so fun to me when I was a student.

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2016 Stephen Stewart Gloyd Endowed lecture: Sanjay Basu

Dr. Sanjay Basu gave the 2016 Stephen Stewart Gloyd Endowed lecturer on May 19, 2016. He spoke on the challenges and importance of measuring the health impact of government programs and policies. The Stephen Stewart Gloyd Endowed Lecture was established in 1982 to recognize Dr. Park Willis Gloyd. The lectureship was renamed by the family to recognize Park’s son, Stephen Gloyd, who is the Associate Chair for Education and Curriculum for the UW Department of Global Health, and a professor in Health Services at the School of Public Health.

Sanjay Basu, MD, PhD, is an Assistant Professor of Medicine at Stanford University. He is a primary care physician and an epidemiologist, focusing on the study of how population health is influenced by social and economic programs. Dr. Basu received his education from MIT, Oxford, and Yale, and serves on advisory panels for the United Nations, World Health Organization, the American Heart Association, and the Global Burden of Disease Project. In 2013, he was named one of the “top 100 global thinkers” by Foreign Policy Magazine, and in 2015 he won the New Innovator Award from the Director of the National Institutes of Health. Dr. Basu is the co-author of “The Body Economic: Why Austerity Kills,” which discusses recessions, budget battles, and the politics of life and death.

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Learning in Surgeons

New paper: Assessing surgeon behavior change after anastomotic leak in colorectal surgery
Authors
Vlad V Simianu, Anirban Basu, Rafael Alfonso-Cristancho, Richard C Thirlby, Abraham D Flaxman, David R Flum
Publication date
2016/10/31
Journal
Journal of Surgical Research
http://www.sciencedirect.com/science/article/pii/S0022480416301962

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