[EpiData-list] Re: Outbreak analysis diary - attack rate table
epidata-list at lists.umanitoba.ca
epidata-list at lists.umanitoba.ca
Sun Jun 8 18:00:50 CDT 2008
thanks very much Jens, Hans and Jamie for the suggestions and Alistair for the encouragement.
Hans thanks I tried your suggestion for the browse and it worked well. The other suggestions will take a bit longer to work through. I will report back when I do but this post I want to report on the analysis and also the success of creating and combining two data entry files.
Attack rate table of exposures
As has been said several times on this list but is worth saying again, the 'outbreak analysis' function in Epidata that creates a single attack rate table showing attack rates, relative risks, CIS and pvalues of all exposures of interest against the outcome of 'case' is a wonderful feature. The command is TAB CASE .....all exposures of interest/OA
The steps I took were:
1. Click on Browse Data from the menu bar
2. Tick my outcome of interest (Case) and all my exposures of interest (foods etc)
3. Click on Paste (this copies all the selected variables into the section at the bottom of the output screen)
4. I then copied this line into the programme editor, took out the browse at the start and added/OA at the end
TAB CASE ANYFOOD COURTL1 COURTL2 JUNGLEPLAY JTOILET BTOILET KIOSK M1NUGGETS M2CHEERIOS M3CHIPS M4SAUCE M5PIZZA M6JUICE M7JELLYICE M8YOGURT M9CHOCCRAC M10CAKE M11LOLLIES M12TEA M13COFFEE M14SAV M15SAND M16HOTDOG M18FISHBIT M19FISHFIL M20FRUITSA M21DANISH M22BURGER/OA
Note: Adding EX after OA gives the pvalue
I then selected run programme - this creates the attack rate table in the output screen, and also in the default output file.
I really like the outbreak analysis feature but on my wish list would be
1. for 'outbreak analysis' to be an option in one of the menus somewhere. I only knew about this feature through someone mentioning it on the list and I had to search through the docuentation to find it. Maybe this was what the 'attack rate plus RR' option was but I could not seem to select this - it stayed greyed out.
2. If a select' has been used for this to show above the attack rate table. I ran the outbreak analysis above again but this time selecting only people who had attended the centre on a certain date. The command I used was Select Day25 = TRUE
I know the select has worked because N has gone down from 251 to 66, but there is no indicaiton on the output file or the information under the attack rate table that a 'select' is in place.
Thank you all again for your feedback on these postings. I will do one maybe two more - covering the process of sending the data output to a report and a final summary of the main steps and final programme I used.
Having more than one data entry file
We ended up with 250 questionnaires so decided we would try using several data entry operators to enter the data
Regional Public Health
027 495 9671
>>> <epidata-list at lists.umanitoba.ca> 6/06/2008 8:56 a.m. >>>
Just a quick comment on BROWSE.
Did you use the command:
set display databrowser=on
before issuing the BROWSE field1 field2 command? The default is that
the browser is off. Note that this works fine with the public release
version, but if you experiment withe (marvelous) test version build
134, there seems to be some hickup that occasionally blocks the program,
but I believe to have noted that it works if the command is in the
beginning of the program before reading the file (not yet certain).
In any case, I appreciate your telling us your experiences, they are
useful for many. Apologies for not taking the time to answer to more of
your queries, but I am currently a bit taken with traveling between
epidata-list at lists.umanitoba.ca wrote:
> 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 =es 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 =RUE 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 <=ate("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.
> 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 =iadate
> If vomdate < diadate then onsetdate =omdate
> If vomdate =adate 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
Hans L Rieder, MD, MPH
Tel: +41 31 829 4577
Mob: +41 79 321 9122
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