[EpiData-list] re: ongoing outbreak

epidata-list at lists.umanitoba.ca epidata-list at lists.umanitoba.ca
Thu Jun 5 14:20:49 CDT 2008


I think this opportunity for open sharing of ideas and experiences is 
very good and unique

In general I discourage the use of boolean variables. In particular 
since these in many softwares can have only the values true (Y) or false 
(N), and not the value "no value".

With the introduction of value labels it is far more efficient to use 
integer variables, e.g. for the current outbreak:
qes file food items intaken :
v1 food item 1 (e.g. soup) #
v2 food item 2 (e.g. vanilla icecream) #
etc

Preparation of chk file is then easy.
1. add checks (#3 in entry)
2. define a value label (+) for v1:
       0 no
       1 yes
       9 missing
3. further define "9" as missing for v1:
    F9 (edit) and add
          missingvalue all 9
3. after defining that go to field 1 and press ctrl+c
4. go to v2 (and all other food items) and press ctrl+v
    now all fields have 0 and 1 defined and 9 as missing value.
5. enter your data

6 read data into analysis

define cases:
strategy 1:
define case #
case = 0
if (vomiting = 1) then case = 1
* remove those vomiting before 24 hours  or after 72 hours
if (vomiting=1) and (hourvomit < 24) then case = 0
if (vomiting=1) and (hourvomit > 72) then case = 0

* alternatively if we have a fixed date of exposure on 21st of may)
if (vomiting=1) and (datevomit < dmy(22,5,2008) then case = 0
if (vomiting=1) and (datevomit > dmy(24,5,2008) then case = 0

* all with diarrhoea are cases:
if (diarrhoea = 1) then case = 1

* date of symptoms:

define dateonset <dd/mm/yyyy>
If diadate < vomdate then onsetdate = diadate
If vomdate < diadate then onsetdate = vomdate
If vomdate =diadate then onsetdate = diadate
If vomdate =(.) then onsetdate = diadate
If diadate =(.) then onsetdate = vomdate

* now we are ready for the first simple analysis:
tab case v1 v2 v3 .... etc - all exposure variables..... /oa /t
epicurve  onsetdate  case
epicurve  onsetdate case /by=sex

The problems reported the latest days, such as:
using boolean  variables
changing from string to numerical etc. a

Can be handled by combining entry and analysis - as was shown on the 
list by others:
a. rewrite the qes file and some conversions are done by EpiData Entry 
when possible
b. take the file into analysis - generate the new numerical variables, e.g.
        gen i v1 = (upper(v1string) = "Y")
c. save the data (savedata newfile)
d. with entry create a qes file from the rec file (in Entry - menu tools)
e. change the format and labels in qes file and save the qes file
f. enter more data - entry will see that the qes file is new and adapt 
format of rec file.

But the best strategy is to have a standard qes file and rec file from 
the beginning and then adapt to the current outbreak.
Two examples of this is shown in the "field guide under way" in 
http://www.epidata.org/wiki/index.php/Field_Guide

Exciting to get more news on the ongoing analysis "down under" (seen 
from my perspective).

regards
Jens Lauritsen
EpiData Association


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