[EpiData-list] Outbreak analysis diary - Defining cases as a newvariable

epidata-list at lists.umanitoba.ca epidata-list at lists.umanitoba.ca
Sun Jun 8 22:58:23 CDT 2008


Hi Alistair

Thank you for that. I found a copy of your training manual for using Epidata/Epi Info for analysing outbreaks on the web and think it is excellent. 

Yes it is an interesting question about whether to change to Epidata Analysis for outbreak analysis. Like you I teach courses in using Epidata/Epiinfo and am interested in it from an ease of teaching/ease of use perspective as well as for my own use.  

For my own use I am pretty sure I will change to Epidata analysis. We just had another small outbreak come up at the same time as the one I have been writing to the list about and my colleague wanted the data analysed in a hurry. Data had been entered in a questionnaire that was based on our standard epidata master one, just as the large outbreak was. I copied the programme I had written and saved for the large outbreak in Epidata analysis - made a couple of small changes - and  was able to print out a symptoms profile, Epicurv graphs and two full attack rate tables - one with the outcome sick and one for the outcome of case (the case definition was created as part of the programme) for the 25 foods of interest less than 15 minutes. I thought that was pretty good. 

For my training courses though I am not so sure. A large group coming to these are field staff who are new and/or infrequent users of any outbreak analysis software. At the moment my instinct is that although Epidata Analysis does things more quickly and has some great features-  especially the attack rate tables which are brilliant -  I think Epi info is easier for these new or infrequent users to understand. 

I am thinking I may see if their is interest in me developing a one day course to introduce Epidata Analysis to people in public health units who are likely to take on a regular role analysing outbreaks, and stick with my current Epi info course for  the wider group who want a very basic knowledge - so that it an emergency they could get out the manual and follow the instructions if the main person is away. I am interested to see though that the Health Protection Agency in the UK is offering  both beginning and advanced  one day courses for in Epidata Entry/Epidata Analysis. I saw the course outlines on the web http://www.hpa.nhs.uk - click on training and events  -  but I would love to see if I could have a look at their training notes. Do you know anything about these courses?

In terms of a basic set of introduction notes I found the training notes (pdf file) provided by the International Union against Tuberculosis and Lung disease very helpful.  The link is http://www.tbrieder.org then go to Epidata

best wishes

Christine
>>> <epidata-list at lists.umanitoba.ca> 6/06/2008 7:41 p.m. >>>
Christine

These notes are really useful, thank you! Like you I have
'traditionally' used EpiData for questionnaire design and entry, and
then switched to Epi Info for Windows for the more user-friendly (to me
at least) data analysis. Hopefully your experiences will give a good
idea to others about the readiness of EpiData Analysis for use in this
type of situation. 

Thanks
Alastair

---------------------------------------
Alastair Tomlinson
Chartered EHP, Lecturer in Environmental Health
029 2020 1528
AGTomlinson at uwic.ac.uk 


-----Original Message-----
From: epidata-list at lists.umanitoba.ca 
[mailto:epidata-list at lists.umanitoba.ca] 
Sent: 05 June 2008 06:05
To: epidata-list at lists.umanitoba.ca 
Subject: [EpiData-list] Outbreak analysis diary - Defining cases as a
newvariable

Today we started doing the analysis of exposures for our outbreak. First
we need to create a new variable, as not everyone who is sick meets the
case definition for the outbreak.

Case definition
Our case definition is someone who has diarrhoea and/or vomiting 24-72
hours after the function.
I used the programme editor to define a new variable called Case I made
case a Boolean field so the relative risks would calculate correctly
(with  a Boolean field the Y appears first in a two by two table and
then the N and this is what you want to calculate relative risks
correctly). 

Diarrhoea and Vomit - the fields I needed to create the Case field were
also Booklean fields. For a long time I had a problem as I was trying
many combinations of If Diarrhoea = Yes or Y or "Y" in my code and it
was not working. Then my workmate suggested I try TRUE. I think this is
confusing as when you print a Frequency of a boolean Field it prints as
Y. Anyway here was the code that worked.

Define case <Y>
If Diarrhoea = TRUE or Vomit = TRUE then case = TRUE

This deals with the first part of the case definition - that they must
have diarrhoea or vomiting. The next part is that they are NOT a case if
the symptoms started on the same day.

The code I ended up using for this was IF onsetdate <=
date("24/05/2008") then case = FALSE. I had to put the date function as
well as the date itself or the code would not run. I don't know why that
is but any other combination I tried like "24/05/2008" or 24/05/2008 or
("24/05/2008") did not work.

Onsetdate
In the last post I asked if anyone had some code to create a single
onset date from two pieces of information - the vomitdate and the
diarrhoea date. My workmate helped me figure out something that worked
and this is it.

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 have a variables of case and onset date and I created an Epicurv
graph using them. It was great.
One more frustration. While we were working on the code we often used
browse to check our results. We wrote the browse command into the
programme editor but the results of the Browse do not appear in the
output so I had to do it over again each time in the output screen. I
tried list instead of Browse but this didn't work either. Any
suggestions for how you can build the output from a browse or line list
command into a programme will be welcome.

Next posting we will get on to analysing the exposures

thanks

Christine


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Christine Roseveare
Analyst
Regional Public Health
570 9194
027 495 9671





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any attachments is confidential and may be
legally privileged. If you have received this
message in error, please notify the sender
immediately and remove all copies of the message,
including any attachments.  Any views or
opinions expressed in this email (unless
otherwise stated) may not represent those of
Hutt Valley DHB. 
Thank you.
** Disclaimer added by HVDHB **



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