re: ongoing outbreak
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
Christine,
I echo my colleagues' thanks for your undertaking this diary of an outbreak. We have gone through these steps many times with our field epidemiologists. Most of my personal experience was with Epi6 and I have found that I can do everything I used to do and more with EpiData.
A tip for using the LIST command is that it follows the ECHO setting. I assume you are running programs and have
set echo=off
somewhere. If you put in your program
set echo=on list a b c d if x=y set echo=off
you should get what you want with only a minimum of extra text.
I posted to the listserve (November 2007) a solution to getting a table of frequencies of symptoms. This makes use of the CMD function, which may not be for the casual user, but is very powerful. You can try this. Add the following to the top of your Analysis program:
define sym ________________ global cmd asym count @sym /q if @sym="Y" // or whatever means yes type "@sym: @$count" end
And in your Analysis program, where you want the symptom table:
type "Frequency of symptoms" sym = "Vomit" asym sym = "Diarrhea" asym
There are ways to format this better, but this gives you the information.This can be done without using the CMD statement block, but this keeps the Analysis .pgm file simpler. If you want % of cases with each symptom, see my posting from last November.
Jamie
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