KDE: 1854 LONDON CHOLERA OUTBREAK

Kernel Density Estimation (KDE), also known as a "heatmap," is a wonderful way to graphically convey epidemiological data for outbreaks of infectious disease. At a glance, one can discern likely points of origin, routes of transmission, and density by area. KDE maps are attractive and fairly easy to render in QGIS, but it can be exceedingly difficult to obtain spatial point data, which is necessary for creating the nodes used by the software to model density. For this KDE, the underlying raster image is John Snow's original 1854 map, with vector overlays of spatial point data showing water pumps and cholera deaths. The proportional mortality is most densely concentrated around the Broad Street pump (the source of infection as deduced by John Snow). For proper viewing, click HERE to enlarge.

Density radius: 30m
Decay rate: 0
Cell size X,Y: ~1,1
Global transparency: 20%
Pseudocolor

Snow's original map is available in a high resolution format here:
 http://upload.wikimedia.org/wikipedia/commons/2/27/Snow-cholera-map-1.jpg

Unfortunately I did not bookmark the site which offered the spatial point data for download, but if I can locate it again, I'll be sure to give appropriate credit here.

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H7N9 CHOROPLETH

After an extended hiatus, I've again taken to toying with QGIS. Below is a choropleth map that I made last week. It illustrates all reported cases of H7N9 in China, by province, as of 05/03/13. (Click to enlarge.)

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POX

I'm through about 25% of Deborah Hayden's book, POX: Genius, Madness, and the Mysteries of Syphilis. Thus far, the work is riveting. Competing theories on the biological evolution and epidemiology of syphilis are weaved throughout a cogent narrative, flavored with notable excerpts from historical records. Apart from the Great Mortality, I can't think of another disease which was so widely personified by poetic mythos and dark imagination as was syphilis. Consider this lurid description by 19th Century French poet Théophile Gautier:

"There is a splendid American pox here, as pure as at the time of Francis I. The entire French army has been laid up with it; boils are exploding in groins like shells, and purulent jets of clap vie with the fountains in the Piazza Navona . . . tibias are exfoliating in extoses like ancient columns of greenery in a Roman ruin . . . lieutenants walking in the streets look like leopards, they are so dotted and speckled with roseola, freckles, coffee-colored marks, warty excrescences, horny and cryptogamic verruccae and other secondary and tertiary manifestations which appear here after a fortnight." [1]

1. Hayden, Deborah. Pox: Genius, Madness, and the Mysteries of Syphilis. Basic Books, New York: 2003. Quoting Claude Quétel: History of Syphilis (1990).

EPIVENTURE

The Council of State and Territorial Epidemiologists website has posted a prototype educational module, developed with funding by the CDC, called "EpiVenture: Outbreak Investigation." This software lesson is very similar to proprietary training modules we use in the pharmacy, and it is a very effective tool. The course comprises a mixture of text outlines and terms, with multiple-choice tests and interactive case studies interspersed throughout. I found the prototype version of EpiVenture to be both informative and engaging. Hopefully the CDC/CSTE continue to develop and release new lesson modules for EpiVenture.

Try this self-instructional web course out for yourself:

http://www.cste.org/epiventure/index.html



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HAITI

Haiti, with all of its misfortune -- the atrocious sanitary conditions, profound socioeconomic disparity, and recent natural disasters -- serves as an ideal case study for epidemiologists. The U.N.'s ongoing role there provides an example of how organizational interaction can severely affect the health of a population, for better or worse.   

Global Failures on a Haitian Epidemic

Infectious Diseases of Haiti (E-Book)


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