- EpiData-list - University of Manitoba Mailing Lists

Re: EpiData-list Digest, Vol 56, Issue 5
by epidata-list＠lists.umanitoba.ca 10 Jun '08

10 Jun '08

Thank Chrystine, To solve this issue, one way (of course may not be the best) is to append datasets (providing ID are different) using EpiData Entry/Analysis which ever is convenient for you). Not sure if merge is an appropriate way for such combination of datasets. If the two datasets have some common features such as unique key values for example ID, then merge may be required to deal with it. Alternatively try append, the two file or more files should be combined to produce one. Perhaps the memory needs to be cleared prior to READ other files, then append/merge them to be READ in one file. First of all "cls" to clear the screen out then "read". Save replace, save your new dataset (golden rule). Best wishes Tieble 2008/6/10 <epidata-list-request(a)lists.umanitoba.ca>: > Send EpiData-list mailing list submissions to > epidata-list(a)lists.umanitoba.ca > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.umanitoba.ca/mailman/listinfo/epidata-list > or, via email, send a message with subject or body 'help' to > epidata-list-request(a)lists.umanitoba.ca > > You can reach the person managing the list at > epidata-list-owner(a)lists.umanitoba.ca > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of EpiData-list digest..." > > > EpiData-list mailing list > ___________________________________ > > Today's Topics: > > 1. Re: Re: Outbreak analysis diary - multiple data sets > (epidata-list(a)lists.umanitoba.ca) > 2. EpiData Analysis notes (epidata-list(a)lists.umanitoba.ca) > 3. RE: If..then (epidata-list(a)lists.umanitoba.ca) > 4. Re: Re: Outbreak analysis diary - multiple data sets > (epidata-list(a)lists.umanitoba.ca) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 10 Jun 2008 12:04:34 +1200 > From: epidata-list(a)lists.umanitoba.ca > Subject: Re: [EpiData-list] Re: Outbreak analysis diary - multiple > data sets > To: <epidata-list(a)lists.umanitoba.ca> > Message-ID: <484E6DD2020000CA00016D7A(a)GW.hvh.co.nz> > Content-Type: text/plain; charset=US-ASCII > > Hi Jamie > > Sorry I sent the message without finishing my section on multiple data > sets. > > Working with Multiple data sets in Epidata Analysis > > What I was going to say was our first attempt at working with several > copies of an outbreak dataset had been sucessful. This was a timing thing - > we wanted to get the data in more quickly. We had already entered 150 > records when we decided to use another data entry person, but that was Ok > the process still worked. > > Our steps were > 1. Created a file and entered records (outbreak1) > 2. Used Tools copy structure to create a new file (outbreak 2) > 3. Entered records in both outbreak 1 and outbreak 2 > 4. Used Data in/out then Append/merge option B to create a new file > outbreak_final, that was outbreak1 and outbreak 2 combined. > > What was good about this was that it was easy, and I also really liked the > option to copy the check file we had set up for the first file to use with > the new file when you copied the structure. > The only thing I didn't like so much was we ended up with a duplicate ID > which we wouldn't get with an autoID (which we usually use for our ID field) > but I used a number field rather than AutoID this time as I thought it > would be a problem with the merge to have auto ID. > > Using Multiple data sets in Epidata Analysis - READ and multiple data sets > Could you explain a bit more about how to do this. When I try and READ more > than one data set it says "no data will be lost close first". Then - what > does the SAVEDATA do - create a new file like MERGE does? Which do you > recommend to combine data - Merging in Epidata entry or in Analysis. > > Using Epidata analysis in a field epidemilogy course > I'm very interested in how you use Epidata Analysis in your field > epidemiology course . Would I be able to find out a bit more about this from > you - perhaps off the list to avoid taking up too much time on this topic? > As I am involved in teaching courses using epidata/epi info to support field > epi I am very interested in what you cover in your courses but realise > others may not have the same interest > > Many thanks > > Christine > > > For multiple data sets (we do this every year in our Field Epidemiology > Course), you can use Merge in EpiData Entry or just READ multiple data > sets on one line in Analysis and then SAVEDATA. > > Jamie > > Christine wrote: > > 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 > > > Christine Roseveare > Analyst > Regional Public Health > 570 9194 > 027 495 9671 > > > > > > > -- > The information contained in this email and > 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 ** > > > > ------------------------------ > > Message: 2 > Date: Tue, 10 Jun 2008 09:39:25 +0100 > From: epidata-list(a)lists.umanitoba.ca > Subject: [EpiData-list] EpiData Analysis notes > To: <epidata-list(a)lists.umanitoba.ca> > Message-ID: > <AD682418821AA34BAB0650CECBC8B92D074D02(a)colhpaexc001.HPA.org.uk> > Content-Type: text/plain; charset="us-ascii" > > Dear Christine > > We do have notes (although different trainers have different notes to > reflect their own style). If you wish we can discuss further off-list > (e-mail neville.verlander(a)hpa.org.uk). > > Regards, > > Neville > > ------------------------------------------------------------------------ > ------------------------------------------------------------------------ > ------------------------------------------------------------------------ > ----------------------------- > Neville Verlander > Statistics Unit > Statistics, Modelling and Bioinformatics Department > Health Protection Agency Centre for Infections > 61 Colindale Avenue > London > NW9 5EQ > > Tel: (direct) (+44) (0)208 3277426 > Fax: (+44) (0)208 200 7868 > > > > > ----------------------------------------- > ************************************************************************** > The information contained in the EMail and any attachments is > confidential and intended solely and for the attention and use of > the named addressee(s). It may not be disclosed to any other person > without the express authority of the HPA, or the intended > recipient, or both. If you are not the intended recipient, you must > not disclose, copy, distribute or retain this message or any part > of it. This footnote also confirms that this EMail has been swept > for computer viruses, but please re-sweep any attachments before > opening or saving. HTTP://www.HPA.org.uk > ************************************************************************** > > ------------------------------ > > Message: 3 > Date: Tue, 10 Jun 2008 10:58:20 +0200 > From: epidata-list(a)lists.umanitoba.ca > Subject: RE: [EpiData-list] If..then > To: <epidata-list(a)lists.umanitoba.ca> > Message-ID: <ED5A894B497B0040A17FD2AE66D789B07517B1(a)xch-2.ivs.local> > Content-Type: text/plain; charset="iso-8859-1" > > Should be written as follows (only 1 argument per line) > > -----Message d'origine----- > De : epidata-list(a)lists.umanitoba.ca [mailto: > epidata-list(a)lists.umanitoba.ca] > Envoyé : mercredi 28 mai 2008 17:48 > À : epidata-list(a)lists.umanitoba.ca > Objet : [EpiData-list] If..then > > Hi, > might be easy question, i am trying to write condition under check file to > write value of 9 in 2 places if one cell equal to NA (code below), it does > not work (and no error message), any tips? > > AFTER ENTRY > IF v64=NA THEN > V65=9 > V66=9 > goto V67 > ENDIF > > > Thank you in advance > best regards > ziad > > > > ------------------------------ > > Message: 4 > Date: Tue, 10 Jun 2008 07:37:20 -0400 > From: epidata-list(a)lists.umanitoba.ca > Subject: Re: [EpiData-list] Re: Outbreak analysis diary - multiple > data sets > To: epidata-list(a)lists.umanitoba.ca > Message-ID: <484E6770.8070508(a)sympatico.ca> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > 1. Merge vs. Read and Append in Analysis > > Apologies - the correct syntax to read multiple files in Analysis is: > > read file1 > append /file=file2 > > you can keep adding files. > > SAVEDATA will save a new .rec file. This is especially useful if you > have temporary variables that are used to manipulate the data. You can > do this: > > VAR DROP temp1 temp2 temp3 > SAVEDATA finaldata.rec > > Merging with Entry provides a bit of documentation of what was done and > can be automated with EPIC (but thats another level of data management). > > 2. Merge and IDNUM. I normally avoid IDNUM as it is often useful to > record ID numbers before you get to enter the data. However, you can use > IDNUM and merge data successfully, if you assign each data entry person > a unique range of IDs. In EpiData Entry, you can set an option for the > first ID to use when entering the first record of a file. It is under > File, Options and the Advanced tab. So one person could go with the > default (1) and another could change this to 1001 before entering any data. > > Another approach, where IDNUM was used and both sets of data start with > 1 (although this is really not good data mangement practice, you might > do this by including another code that indicates who entered the data). > In this case, use Analysis to merge the data as above. Analysis doesn't > care about unique ID numbers. > > 3. Field Epidemiology course and EpiData - we do a small field survey or > observational study each year. We can send more info. Contact us via the > e-mail address found at http://www.phac-aspc.gc.ca/cfep (Put my name in > the subject line). > > Jamie > > > ------------------------------ > > ________________________________________ > EpiData-list(a)lists.umanitoba.ca > http://lists.umanitoba.ca/mailman/listinfo/epidata-list > > > End of EpiData-list Digest, Vol 56, Issue 5 > ******************************************* >

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found it! Re: EpiData-list Digest, Vol 55, Issue 20
by epidata-list＠lists.umanitoba.ca 10 Jun '08

10 Jun '08

Hello! managed to sort it out, pasting below the proper one if something fyi! DISP1 AFTER ENTRY IF (DRUG1="EFV") and (DOS1=600) and (DISP1>28) and (DISP1<101) THEN DAILYD1=1 GOTO DRUG2 ENDIF IF (DRUG1="EFV") and (DOS1=200) and (DISP1>118) and (DISP1<181) THEN DAILYD1=4 GOTO DRUG2 ENDIF IF (DRUG1="EFV") and (DOS1=200) and (DISP1>88) and (DISP1<110) THEN DAILYD1=3 GOTO DRUG2 ENDIF END END best regards ziad On Tue, Jun 10, 2008 at 12:08 PM, Ziad El-Khatib <ziad.khatib(a)gmail.com> wrote: > Hi again, > another question inline with previous query i posted last month, to > have different -if..then- conditions (pasted below), when i test it, > it does not write anything under DAILYD1 cell, as instructed below, > any tips? > > DISP1 > AFTER ENTRY > IF (DRUG1="EFV" & DOS1=600 & DISP1>29 & DISP1<101) THEN > DAILYD1=1 > ELSE > IF (DRUG1="EFV" & DOS1=200 & DISP1>119 & DISP1<181) THEN > DAILYD1=4 > ELSE > IF (DRUG1="EFV" & DOS1=200 & DISP1>89 & DISP1<110) THEN > DAILYD1=3 > GOTO DRUG2 > ENDIF > ENDIF > ENDIF > END > END > > > > > > Thank you and best regards > ziad > > > On Thu, May 29, 2008 at 10:03 AM, > <epidata-list-request(a)lists.umanitoba.ca> wrote: >> Send EpiData-list mailing list submissions to >> epidata-list(a)lists.umanitoba.ca >> >> To subscribe or unsubscribe via the World Wide Web, visit >> http://lists.umanitoba.ca/mailman/listinfo/epidata-list >> or, via email, send a message with subject or body 'help' to >> epidata-list-request(a)lists.umanitoba.ca >> >> You can reach the person managing the list at >> epidata-list-owner(a)lists.umanitoba.ca >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of EpiData-list digest..." >> >> EpiData-list mailing list >> ___________________________________ >> >> Today's Topics: >> >> 1. Re: If..then (epidata-list(a)lists.umanitoba.ca) >> 2. re: If..then (epidata-list(a)lists.umanitoba.ca) >> 3. Re: EpiData-list Digest, Vol 55, Issue 19 Missing values is >> not NA (epidata-list(a)lists.umanitoba.ca) >> >> >> ---------- Forwarded message ---------- >> From: epidata-list(a)lists.umanitoba.ca >> To: epidata-list(a)lists.umanitoba.ca >> Date: Wed, 28 May 2008 20:33:07 +0200 >> Subject: Re: [EpiData-list] If..then >> Perhaps: >> >> AFTER ENTRY >> IF v64="NA" THEN >> V65=9 >> V66=9 >> goto V67 >> ENDIF >> END >> >> >> Regards, >> >> Hans >> >> >> epidata-list(a)lists.umanitoba.ca wrote: >>> >>> Hi, >>> might be easy question, i am trying to write condition under check >>> file to write value of 9 in 2 places if one cell equal to NA (code >>> below), it does not work (and no error message), any tips? >>> >>> >>> >>> Thank you in advance >>> best regards >>> ziad >>> >>> >> >> -- >> Hans L Rieder, MD, MPH >> Jetzikofenstr. 12 >> 3038 Kirchlindach >> Switzerland >> >> Tel: +41 31 829 4577 >> Mob: +41 79 321 9122 >> Web: http://www.tbrieder.org >> >> >> >> >> >> ---------- Forwarded message ---------- >> From: epidata-list(a)lists.umanitoba.ca >> To: epidata-list(a)lists.umanitoba.ca >> Date: Wed, 28 May 2008 23:33:56 +0200 >> Subject: [EpiData-list] re: If..then >> Just split in three lines: >> >> after entry >> IF v64=NA THEN >> LET V65=9 >> V66=9 >> goto V67 >> ENDIF >> >> >> regards >> Jens Lauritsen >> EpiData Association >> >> >> >> ---------- Forwarded message ---------- >> From: epidata-list(a)lists.umanitoba.ca >> To: epidata-list(a)lists.umanitoba.ca >> Date: Thu, 29 May 2008 09:05:47 -0300 >> Subject: [EpiData-list] Re: EpiData-list Digest, Vol 55, Issue 19 Missing values is not NA >> Dear friend Ziad, >> >> NA is common expression to identify missing values. If you are working with >> R or S-Plus then NA is NA. That means that all functions or commands that >> you want to specify NA, the expression is also NA. However, in Stata or >> Epidata entry the NAs are epecified by dots (.) and sometimes by empty >> quotes (" ") depending if the variable of interest is formated as numeric or >> text. So, my guess is that your check command will work fine if do like >> this... >> >> AFTER ENTRY >> IF v64=. THEN >> LET V65=9 & V66=9 & goto V67 >> ENDIF >> END >> >> Best regards, >> Pedro Emmanuel >> >> >> >>> Today's Topics: >>> >>> 1. If..then (epidata-list(a)lists.umanitoba.ca) >>> >>> >>> ---------------------------------------------------------------------- >>> >>> Message: 1 >>> Date: Wed, 28 May 2008 08:47:34 -0700 >>> From: epidata-list(a)lists.umanitoba.ca >>> Subject: [EpiData-list] If..then >>> To: epidata-list(a)lists.umanitoba.ca >>> Message-ID: >>> <897a5cf60805280847u3b99c66ak6f49e3855b879141(a)mail.gmail.com> >>> Content-Type: text/plain; charset=ISO-8859-1 >>> >>> Hi, >>> might be easy question, i am trying to write condition under check >>> file to write value of 9 in 2 places if one cell equal to NA (code >>> below), it does not work (and no error message), any tips? >>> >>> AFTER ENTRY >>> IF v64=NA THEN >>> LET V65=9 & V66=9 & goto V67 >>> ENDIF >>> >>> >>> Thank you in advance >>> best regards >>> ziad >>> >>> >>> ------------------------------ >>> >>> ________________________________________ >>> EpiData-list(a)lists.umanitoba.ca >>> http://lists.umanitoba.ca/mailman/listinfo/epidata-list >>> >>> >>> End of EpiData-list Digest, Vol 55, Issue 19 >>> ******************************************** >>> >> >> >> ________________________________________ >> EpiData-list(a)lists.umanitoba.ca >> http://lists.umanitoba.ca/mailman/listinfo/epidata-list >> >> >

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Re: EpiData-list Digest, Vol 55, Issue 20
by epidata-list＠lists.umanitoba.ca 10 Jun '08

10 Jun '08

Hi again, another question inline with previous query i posted last month, to have different -if..then- conditions (pasted below), when i test it, it does not write anything under DAILYD1 cell, as instructed below, any tips? DISP1 AFTER ENTRY IF (DRUG1="EFV" & DOS1=600 & DISP1>29 & DISP1<101) THEN DAILYD1=1 ELSE IF (DRUG1="EFV" & DOS1=200 & DISP1>119 & DISP1<181) THEN DAILYD1=4 ELSE IF (DRUG1="EFV" & DOS1=200 & DISP1>89 & DISP1<110) THEN DAILYD1=3 GOTO DRUG2 ENDIF ENDIF ENDIF END END Thank you and best regards ziad On Thu, May 29, 2008 at 10:03 AM, <epidata-list-request(a)lists.umanitoba.ca> wrote: > Send EpiData-list mailing list submissions to > epidata-list(a)lists.umanitoba.ca > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.umanitoba.ca/mailman/listinfo/epidata-list > or, via email, send a message with subject or body 'help' to > epidata-list-request(a)lists.umanitoba.ca > > You can reach the person managing the list at > epidata-list-owner(a)lists.umanitoba.ca > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of EpiData-list digest..." > > EpiData-list mailing list > ___________________________________ > > Today's Topics: > > 1. Re: If..then (epidata-list(a)lists.umanitoba.ca) > 2. re: If..then (epidata-list(a)lists.umanitoba.ca) > 3. Re: EpiData-list Digest, Vol 55, Issue 19 Missing values is > not NA (epidata-list(a)lists.umanitoba.ca) > > > ---------- Forwarded message ---------- > From: epidata-list(a)lists.umanitoba.ca > To: epidata-list(a)lists.umanitoba.ca > Date: Wed, 28 May 2008 20:33:07 +0200 > Subject: Re: [EpiData-list] If..then > Perhaps: > > AFTER ENTRY > IF v64="NA" THEN > V65=9 > V66=9 > goto V67 > ENDIF > END > > > Regards, > > Hans > > > epidata-list(a)lists.umanitoba.ca wrote: >> >> Hi, >> might be easy question, i am trying to write condition under check >> file to write value of 9 in 2 places if one cell equal to NA (code >> below), it does not work (and no error message), any tips? >> >> >> >> Thank you in advance >> best regards >> ziad >> >> > > -- > Hans L Rieder, MD, MPH > Jetzikofenstr. 12 > 3038 Kirchlindach > Switzerland > > Tel: +41 31 829 4577 > Mob: +41 79 321 9122 > Web: http://www.tbrieder.org > > > > > > ---------- Forwarded message ---------- > From: epidata-list(a)lists.umanitoba.ca > To: epidata-list(a)lists.umanitoba.ca > Date: Wed, 28 May 2008 23:33:56 +0200 > Subject: [EpiData-list] re: If..then > Just split in three lines: > > after entry > IF v64=NA THEN > LET V65=9 > V66=9 > goto V67 > ENDIF > > > regards > Jens Lauritsen > EpiData Association > > > > ---------- Forwarded message ---------- > From: epidata-list(a)lists.umanitoba.ca > To: epidata-list(a)lists.umanitoba.ca > Date: Thu, 29 May 2008 09:05:47 -0300 > Subject: [EpiData-list] Re: EpiData-list Digest, Vol 55, Issue 19 Missing values is not NA > Dear friend Ziad, > > NA is common expression to identify missing values. If you are working with > R or S-Plus then NA is NA. That means that all functions or commands that > you want to specify NA, the expression is also NA. However, in Stata or > Epidata entry the NAs are epecified by dots (.) and sometimes by empty > quotes (" ") depending if the variable of interest is formated as numeric or > text. So, my guess is that your check command will work fine if do like > this... > > AFTER ENTRY > IF v64=. THEN > LET V65=9 & V66=9 & goto V67 > ENDIF > END > > Best regards, > Pedro Emmanuel > > > >> Today's Topics: >> >> 1. If..then (epidata-list(a)lists.umanitoba.ca) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Wed, 28 May 2008 08:47:34 -0700 >> From: epidata-list(a)lists.umanitoba.ca >> Subject: [EpiData-list] If..then >> To: epidata-list(a)lists.umanitoba.ca >> Message-ID: >> <897a5cf60805280847u3b99c66ak6f49e3855b879141(a)mail.gmail.com> >> Content-Type: text/plain; charset=ISO-8859-1 >> >> Hi, >> might be easy question, i am trying to write condition under check >> file to write value of 9 in 2 places if one cell equal to NA (code >> below), it does not work (and no error message), any tips? >> >> AFTER ENTRY >> IF v64=NA THEN >> LET V65=9 & V66=9 & goto V67 >> ENDIF >> >> >> Thank you in advance >> best regards >> ziad >> >> >> ------------------------------ >> >> ________________________________________ >> EpiData-list(a)lists.umanitoba.ca >> http://lists.umanitoba.ca/mailman/listinfo/epidata-list >> >> >> End of EpiData-list Digest, Vol 55, Issue 19 >> ******************************************** >> > > > ________________________________________ > EpiData-list(a)lists.umanitoba.ca > http://lists.umanitoba.ca/mailman/listinfo/epidata-list > >

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Re: [EpiData-list] Re: Outbreak analysis diary - multiple data sets
by epidata-list＠lists.umanitoba.ca 10 Jun '08

10 Jun '08

Hi Jamie Sorry I sent the message without finishing my section on multiple data sets. Working with Multiple data sets in Epidata Analysis What I was going to say was our first attempt at working with several copies of an outbreak dataset had been sucessful. This was a timing thing - we wanted to get the data in more quickly. We had already entered 150 records when we decided to use another data entry person, but that was Ok the process still worked. Our steps were 1. Created a file and entered records (outbreak1) 2. Used Tools copy structure to create a new file (outbreak 2) 3. Entered records in both outbreak 1 and outbreak 2 4. Used Data in/out then Append/merge option B to create a new file outbreak_final, that was outbreak1 and outbreak 2 combined. What was good about this was that it was easy, and I also really liked the option to copy the check file we had set up for the first file to use with the new file when you copied the structure. The only thing I didn't like so much was we ended up with a duplicate ID which we wouldn't get with an autoID (which we usually use for our ID field) but I used a number field rather than AutoID this time as I thought it would be a problem with the merge to have auto ID. Using Multiple data sets in Epidata Analysis - READ and multiple data sets Could you explain a bit more about how to do this. When I try and READ more than one data set it says "no data will be lost close first". Then - what does the SAVEDATA do - create a new file like MERGE does? Which do you recommend to combine data - Merging in Epidata entry or in Analysis. Using Epidata analysis in a field epidemilogy course I'm very interested in how you use Epidata Analysis in your field epidemiology course . Would I be able to find out a bit more about this from you - perhaps off the list to avoid taking up too much time on this topic? As I am involved in teaching courses using epidata/epi info to support field epi I am very interested in what you cover in your courses but realise others may not have the same interest Many thanks Christine For multiple data sets (we do this every year in our Field Epidemiology Course), you can use Merge in EpiData Entry or just READ multiple data sets on one line in Analysis and then SAVEDATA. Jamie Christine wrote: > 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 Christine Roseveare Analyst Regional Public Health 570 9194 027 495 9671 -- The information contained in this email and 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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If..then
by epidata-list＠lists.umanitoba.ca 10 Jun '08

10 Jun '08

Hi, might be easy question, i am trying to write condition under check file to write value of 9 in 2 places if one cell equal to NA (code below), it does not work (and no error message), any tips? AFTER ENTRY IF v64=NA THEN LET V65=9 & V66=9 & goto V67 ENDIF Thank you in advance best regards ziad

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EpiData Analysis notes
by epidata-list＠lists.umanitoba.ca 10 Jun '08

10 Jun '08

Dear Christine We do have notes (although different trainers have different notes to reflect their own style). If you wish we can discuss further off-list (e-mail neville.verlander(a)hpa.org.uk). Regards, Neville ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ----------------------------- Neville Verlander Statistics Unit Statistics, Modelling and Bioinformatics Department Health Protection Agency Centre for Infections 61 Colindale Avenue London NW9 5EQ Tel: (direct) (+44) (0)208 3277426 Fax: (+44) (0)208 200 7868 ----------------------------------------- ************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of the HPA, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses, but please re-sweep any attachments before opening or saving. HTTP://www.HPA.org.uk **************************************************************************

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RE: [EpiData-list] Outbreak analysis diary - Defining cases as a newvariable
by epidata-list＠lists.umanitoba.ca 09 Jun '08

09 Jun '08

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(a)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(a)uwic.ac.uk -----Original Message----- From: epidata-list(a)lists.umanitoba.ca [mailto:epidata-list@lists.umanitoba.ca] Sent: 05 June 2008 06:05 To: epidata-list(a)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 -- The information contained in this email and 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 ** Christine Roseveare Analyst Regional Public Health 570 9194 027 495 9671 -- The information contained in this email and 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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Re: Outbreak analysis diary - attack rate table
by epidata-list＠lists.umanitoba.ca 09 Jun '08

09 Jun '08

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 as below: 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. Christine 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 Christine Roseveare Analyst Regional Public Health 570 9194 027 495 9671 >>> <epidata-list(a)lists.umanitoba.ca> 6/06/2008 8:56 a.m. >>> Dear Christine: 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 continents. Regards, Hans epidata-list(a)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. > > 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 =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 > > thanks > > Christine > > > -- Hans L Rieder, MD, MPH Jetzikofenstr. 12 3038 Kirchlindach Switzerland Tel: +41 31 829 4577 Mob: +41 79 321 9122 Web: http://www.tbrieder.org -- The information contained in this email and 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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Epidata analysis on a network with restricted access to c drive
by epidata-list＠lists.umanitoba.ca 09 Jun '08

09 Jun '08

Just a quick question re an issue I have with Epidata analysis and the C drive default directories it uses for some functions. This is the message I get when I load Epidata Analyis * EpiData Analysis default settings file * Edit the next lines to change size or font . set echo=off Access is denied Operation aborted Although I can still use Epidata Analysis I do not get the option to change the settings, I don't see the results of the read command displayed or information about how many records are in the file. I also have to change the default I send the output to as I can not access the default directory. I asked our IT help desk and they say the reason this happens is that I am now allowed access to one of the directories Epidata looks for - an administrator folder in the C drive. I wonder if this might be a problem for others who are in organisations/working on networks where users are not allowed access to administrator folders. Do you have a suggested workaround? thanks Christine Christine Roseveare Analyst Regional Public Health 570 9194 027 495 9671 >>> <epidata-list-request(a)lists.umanitoba.ca> 7/06/2008 5:04 a.m. >>> Send EpiData-list mailing list submissions to epidata-list(a)lists.umanitoba.ca To subscribe or unsubscribe via the World Wide Web, visit http://lists.umanitoba.ca/mailman/listinfo/epidata-list or, via email, send a message with subject or body 'help' to epidata-list-request(a)lists.umanitoba.ca You can reach the person managing the list at epidata-list-owner(a)lists.umanitoba.ca When replying, please edit your Subject line so it is more specific than "Re: Contents of EpiData-list digest..." -- The information contained in this email and 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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Outbreak analysis diary - Defining cases as a new variable
by epidata-list＠lists.umanitoba.ca 06 Jun '08

06 Jun '08

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 -- The information contained in this email and 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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