Sunday, 21 June 2015

Matching MERS case identification numbers from two differing sources...

Update #1 27JUNE2015
Update #2 28JUNE2015
Sometimes people work from different playbooks.
Figure 1. MERS in South Korea. Most cases now plotted
on graph using their dates of illness onset.
An outbreak in decline. This is up-to-date - 3 new cases
from 21JUN2015 added (column at right hand side -
onset dates unknown)
Click on graph to enlarge

In this instance, the data from the World Health Organization's (WHO) new list of Middle East respiratory syndrome (MERS) cases - with extra detail - uses a case identification key that's out of synchrony with that produced by the South Korean (SK) Health Authority which can be found in each of its posts announcing new MERS cases and deaths. 

Attempting to link the two lists has mostly been an exercise in pedantry, but sometimes it is useful to know which case one is talking about when discussing an outbreak or cluster of disease....'Hey Bill, what didja think of that 70 year old MERS case who drove the ambulance carrying that infected 75 year old MERS case and then those others got MERS as well..?' doesn't really roll off the tongue does it?



Embedded image permalink
Figure 2. What the graph above looked like before
we had dates of illness onset. Many cases
were 'moved' to earlier time points because
report dates always follow onset of illness dates
and they can follow by varying periods of time -
sometimes a day, sometimes a week or more.
Two file formats are in the folder I've linked to below. This is my first attempt - yes, it is a work in progress - to match up the new WHO case list from the 19th June which includes the highly prized date of illness onset (DOOs) for most cases - with that of the South Korean (SK) Health Authority. They do differ. Quite a bit. And in several ways. For example, the numbering scheme is off by one or more, SK69 seems to be missing from the WHO list, there is a question mark hanging over SK152 & SK156 and the WHO data seem to have a number of different ages from the SK data- mostly differing by one year (presumably someone is rounding up or down). 

If I've stuffed anything up or if you can solve my problem cases - please pass that info along and I'll update the files on this page. Hopefully the next WHO version will have addressed all of this anyway (it didn't but perhaps a future one will).

These are publicly available and you can download them for your own interest.


There is a download arrow at the top of the Google Drive page.

  1. Google Drive folder with MERS data files
    https://drive.google.com/open?id=0B5sEcTjB5Ailfm1PcU1oNDF6M2hiaDduUDgzQUdxNlZxeHBkU0FHeVBRRFJkbHIxTmdjX3c&authuser=0
Updates...
  1. With the help of FluTrackers updated line list to cross check against, the first half of my list has been updated - some bugs fixed. 
  2. After about 5 hours - on and off - FluTrackers helped me sort out a few errors and the latest version of my list has been uploaded into the the folder linked above. Some typos corrected.