*2007-xxx.pgm
*Intended for use with EpiInfo 6 or EpiData (http://www.epidata.dk).

*This program analyzes the basic DBF file exported from the FileMaker
*outbreak data entry file, aka "DataEntry.fp7".

*For more information, contact Bill Keene (keene@cluemail.com; 971.673.1111)

*This template program last updated 29 Jan 2007.

*Note that all variable names in EpiInfo are truncated at 10 characters.
*If you added or renamed any variables you will need to modify this accordingly.

*None of the generic text, numeric, or date fields (e.g., numeric1, numeric2)
*are referred to in this program, so if you used those and want to analyze by
*them, you will need to modify this accordingly.

*Lines that begin with asterisks (*) are ignored in running, and hence can be
*used to store comments or to temporarily inactive sections of code.

*TO SAVE PAPER and TIME, DELETE UNUSED VARIABLES BEFORE RUNNING PROGRAM

*You must specify the correct file names and paths to read from and write to.
*Two models are provided. Clean up whichever you prefer, but don't forget
*to remove the leading asterisks from the operative lines.

*For Mac users-----------------------------------
*read  o:\2007-xxx.dbf
*erase o:\2007-xxx.out
*route o:\2007-xxx.out

*For PC users working on Stash-------------------
*read  i:\Outbreak\2007\2007-xxx\2007-xxx.dbf
*erase i:\Outbreak\2007\2007-xxx\2007-xxx.out
*route i:\Outbreak\2007\2007-xxx\2007-xxx.out

*------------------------------------------------

*NOTE: The FM template allows the user to choose how they label people.

*"LabelSick" is a variable defined in FM as "case", "ill", "sick", whatever
*"LabelWell" is a variable defined in FM as "control", "well", "not sick"...
*"LabelExclu" is a variable defined in FM as "excluded or ...

*This program refers to those labels generically, i.e., instead of
*selecting records where 'status = "case" or status = "control"', for example,
*it goes for 'status = LabelSick or status = LabelWell'. Note that those
*generic labels are NOT in quotes, because they in turn refer to variables in
*the DBF file, and not to absolute text.

*Blank values in FM-calculated fields export to DBFs as "0.000" instead of 
* missing, so the following statements just recodes those to blank.

***************************************************************************

if durationSx = 0 then durationSx = .
if durationVD = 0 then durationVD = .

if incubVD1_D  = 0 then incubVD1_D  = .
if incubVD1_H  = 0 then incubVD1_H  = .
if incubVD2_D  = 0 then incubVD2_D  = .
if incubVD2_H  = 0 then incubVD2_H  = .
if incubVD3_D  = 0 then incubVD3_D  = .
if incubVD3_H  = 0 then incubVD3_H  = .
if incubVD4_D  = 0 then incubVD4_D  = .
if incubVD4_H  = 0 then incubVD4_H  = .
if incubVD5_D  = 0 then incubVD5_D  = .
if incubVD5_H  = 0 then incubVD5_H  = .

*List the outbreak ID and name from an arbitrarily chosen record qua header.

select recnumber = 1
list OutbreakID OutbreakNa

set ignore = off
select
freq status

select status = LabelSick
set statistics = on
type " "
type "DEMOGRAPHICS OF CASES"
freq sex
freq agegroup

type " "
type "SYMPTOM PROFILE FOR CASES"
freq cramps
type "NB: diarrhea3x means ³3 loose stools in <24 hr."
freq Diarrhea3x
freq vomiting
freq fever
freq bloodyD
freq headache
freq myalgia
freq nausea
freq fatigue
freq chills
freq gas
type "Loosestool means any reported self-defined diarrhea"
type "This is rarely used in any case definition"
freq loosestool

type " "
type "MD means any clinician visit."
freq MD
freq ER
freq hospital
freq died
type " "
type "MISSWORK means missing some school or work."
freq misswork

type " "
type "DAYS_OFF is the number of days of work/school missed."
type "Note that it only includes people who had recovered"
type "by the time they were interviewed."
freq days_off

type "SPECIMEN means a stool sample was already given."
freq specimen
type " "
type "CONFIRMED means already known lab+; this may change."
freq confirmed
type " "
type "WILLING means would (in concept) donate stool."
freq willing

type "DURATION (IN DAYS) OF ANY SYMPTOMS"
means durationSx

type "DURATION (IN DAYS) OF VOMITING OR DIARRHEA"
means durationVD

type " "
type "The following is an ordered list of onset times for cases."
type "OnsetX is the onset of any symptoms, whereas OnsetVD is the"
type "first onset of vomiting or diarrhea. For most GI illness"
type "outbreaks the latter may be more meaningful."
type " "
type "For your graphing convenience, onset times are also grouped"
type "into 6, 8, 12, and 24-hour blocks. Pick whichever"
type "grouping seems most informative."

sort OnsetXDate OnsetXTime
list PersonID initials OnsetXDate OnsetXTime

sort onsetVD_Da onsetVD_Ti
list PersonID initials onsetVD_Da onsetVD_Ti

type "******************"
type "ONSET OF FIRST SYMPTOMS (ONSET 1) BY DAY"
sort OnsetXDate OnsetXTime
freq OnsetXDate
type "FIRST SX ONSETS BY 12-HOUR BLOCK"
freq OnsetX_12H
type "FIRST SX ONSETS BY 8-HOUR BLOCK"
freq OnsetX_8H
type "FIRST SX ONSETS BY 6-HOUR BLOCK"
freq OnsetX_6H

type " "
type "******************"
type "ONSET OF VOMITING/DIARRHEA (ONSET 2) BY DAY"
sort onsetVD_Da onsetVD_Ti
freq onsetVD_Da
type "VD ONSETS BY 12-HOUR BLOCK"
freq OnsetVD12H
type "VD ONSETS BY 8-HOUR BLOCK"
freq OnsetVD8H
type "VD ONSETS BY 6-HOUR BLOCK"
freq OnsetVD6H

type "******************"
type "INCUBATION is only valid if a single defined exposure time."
type "IncubVD is time to first vomit or diarrhea"
type "(i.e., OnsetVD) and is shown both in hours and in days."
type "******************"

**Delete the stuff referring to meals not being considered as a source

**BY DEFAULT, only incubations based on OnsetVD (V or D) are shown.
*To use OnsetX (any sx), activate the following steps by removing
*the leading asterisks

*select
*select status = LabelSick
*select incubX1_D  <>.
*sort incubX1_H 
*type "INCUBATION (to V or D) ASSUMING MEAL1 IS SOLE SOURCE"
*freq incubX1_D 
*freq incubX1_H 
*
*select
*select status = LabelSick
*select incubX2_D  <>.
*sort incubX2_H 
*type "INCUBATION (to V or D) ASSUMING MEAL2 IS SOLE SOURCE"
*freq incubX2_D 
*freq incubX2_H 
*
*select
*select status = LabelSick
*select incubX3_D  <>.
*sort incubX3_H 
*type "INCUBATION (to V or D) ASSUMING MEAL3 IS SOLE SOURCE"
*freq incubX3_D 
*freq incubX3_H 
*
*select
*select status = LabelSick
*select incubX4_D  <>.
*sort incubX4_H 
*type "INCUBATION (to V or D) ASSUMING MEAL4 IS SOLE SOURCE"
*freq incubX4_D 
*freq incubX4_H 
*
*select
*select status = LabelSick
*select incubX5_D  <>.
*sort incubX5_H 
*type "INCUBATION (to V or D) ASSUMING MEAL5 IS SOLE SOURCE"
*freq incubX5_D 
*freq incubX5_H 

*type "******************"


select
select status = LabelSick
select incubVD1_D  <>.
sort incubVD1_H 
type "INCUBATION (to V or D) ASSUMING MEAL1 IS SOLE SOURCE"
type "NB: this is meaningless if meal1 was not the exposure"
type " "
type "Incubation to first V or D in days"
freq incubVD1_D 
type "Incubation to first V or D in hours"
freq incubVD1_H 

select
select status = LabelSick
select incubVD2_D  <>.
sort incubVD2_H 
type "INCUBATION (to V or D) ASSUMING MEAL2 IS SOLE SOURCE"
type "NB: this is meaningless if meal2 was not the exposure"
type "Incubation to first V or D in days"
freq incubVD2_D 
type "Incubation to first V or D in hours"
freq incubVD2_H 

*select
*select status = LabelSick
*select incubVD3_D  <>.
*sort incubVD3_H 
*type "INCUBATION (to V or D) ASSUMING MEAL3 IS SOLE SOURCE"
*type "NB: this is meaningless if meal3 was not the exposure"
*freq incubVD3_D 
*freq incubVD3_H 
*
*select
*select status = LabelSick
*select incubVD4_D  <>.
*sort incubVD4_H 
*type "INCUBATION (to V or D) ASSUMING MEAL4 IS SOLE SOURCE"
*type "NB: this is meaningless if meal4 was not the exposure"
*freq incubVD4_D 
*freq incubVD4_H 
*
*select
*select status = LabelSick
*select incubVD5_D  <>.
*sort incubVD5_H 
*type "INCUBATION (to V or D) ASSUMING MEAL5 IS SOLE SOURCE"
*type "NB: this is meaningless if meal5 was not the exposure"
*freq incubVD5_D 
*freq incubVD5_H 

type "******************"
select
select status <> LabelExclu
set ignore = on

set statistics = on
tables sex status
means age status

***DON'T FORGET TO DELETE UNUSED VARIABLES BEFORE RUNNING PROGRAM

type " "
type "****************************"
type "EXPOSURE-SPECIFIC 2x2 TABLES"
type "****************************"
tables item01a status
tables item01b status
tables item01c status
tables item01d status
tables item01e status
tables item01f status
tables item01g status
tables item01h status
tables item01i status
tables item01j status
tables item01k status
tables item01l status
tables item01m status
tables item01n status
tables item01o status
tables item01p status
tables item01q status
tables item01r status
tables item01s status
tables item01t status
tables item01u status
tables item01v status
tables item01w status
tables item01x status
tables item01y status
tables item01z status

type "******************"
tables item02a status
tables item02b status
tables item02c status
tables item02d status
tables item02e status
tables item02f status
tables item02g status
tables item02h status
tables item02i status
tables item02j status
tables item02k status
tables item02l status
tables item02m status
tables item02n status
tables item02o status
tables item02p status
tables item02q status
tables item02r status
tables item02s status
tables item02t status
tables item02u status
tables item02v status
tables item02w status
tables item02x status
tables item02y status
tables item02z status

type "******************"
tables item03a status
tables item03b status
tables item03c status
tables item03d status
tables item03e status
tables item03f status
tables item03g status
tables item03h status
tables item03i status
tables item03j status
tables item03k status
tables item03l status
tables item03m status
tables item03n status
tables item03o status
tables item03p status
tables item03q status
tables item03r status
tables item03s status
tables item03t status
tables item03u status
tables item03v status
tables item03w status
tables item03x status
tables item03y status
tables item03z status

type "******************"
tables item04a status
tables item04b status
tables item04c status
tables item04d status
tables item04e status
tables item04f status
tables item04g status
tables item04h status
tables item04i status
tables item04j status
tables item04k status
tables item04l status
tables item04m status
tables item04n status
tables item04o status
tables item04p status
tables item04q status
tables item04r status
tables item04s status
tables item04t status
tables item04u status
tables item04v status
tables item04w status
tables item04x status
tables item04y status
tables item04z status

type "******************"
tables item05a status
tables item05b status
tables item05c status
tables item05d status
tables item05e status
tables item05f status
tables item05g status
tables item05h status
tables item05i status
tables item05j status
tables item05k status
tables item05l status
tables item05m status
tables item05n status
tables item05o status
tables item05p status
tables item05q status
tables item05r status
tables item05s status
tables item05t status
tables item05u status
tables item05v status
tables item05w status
tables item05x status
tables item05y status
tables item05z status

type "******************"
tables item06a status
tables item06b status
tables item06c status
tables item06d status
tables item06e status
tables item06f status
tables item06g status
tables item06h status
tables item06i status
tables item06j status
tables item06k status
tables item06l status
tables item06m status
tables item06n status
tables item06o status
tables item06p status
tables item06q status
tables item06r status
tables item06s status
tables item06t status
tables item06u status
tables item06v status
tables item06w status
tables item06x status
tables item06y status
tables item06z status

type "******************"
tables item07a status
tables item07b status
tables item07c status
tables item07d status
tables item07e status
tables item07f status
tables item07g status
tables item07h status
tables item07i status
tables item07j status
tables item07k status
tables item07l status
tables item07m status
tables item07n status
tables item07o status
tables item07p status
tables item07q status
tables item07r status
tables item07s status
tables item07t status
tables item07u status
tables item07v status
tables item07w status
tables item07x status
tables item07y status
tables item07z status

type "******************"
tables item08a status
tables item08b status
tables item08c status
tables item08d status
tables item08e status
tables item08f status
tables item08g status
tables item08h status
tables item08i status
tables item08j status
tables item08k status
tables item08l status
tables item08m status
tables item08n status
tables item08o status
tables item08p status
tables item08q status
tables item08r status
tables item08s status
tables item08t status
tables item08u status
tables item08v status
tables item08w status
tables item08x status
tables item08y status
tables item08z status

type "******************"
tables item09a status
tables item09b status
tables item09c status
tables item09d status
tables item09e status
tables item09f status
tables item09g status
tables item09h status
tables item09i status
tables item09j status
tables item09k status
tables item09l status
tables item09m status
tables item09n status
tables item09o status
tables item09p status
tables item09q status
tables item09r status
tables item09s status
tables item09t status
tables item09u status
tables item09v status
tables item09w status
tables item09x status
tables item09y status
tables item09z status

type "******************"
tables item10a status
tables item10b status
tables item10c status
tables item10d status
tables item10e status
tables item10f status
tables item10g status
tables item10h status
tables item10i status
tables item10j status
tables item10k status
tables item10l status
tables item10m status
tables item10n status
tables item10o status
tables item10p status
tables item10q status
tables item10r status
tables item10s status
tables item10t status
tables item10u status
tables item10v status
tables item10w status
tables item10x status
tables item10y status
tables item10z status

type "******************"
tables item11a status
tables item11b status
tables item11c status
tables item11d status
tables item11e status
tables item11f status
tables item11g status
tables item11h status
tables item11i status
tables item11j status
tables item11k status
tables item11l status
tables item11m status
tables item11n status
tables item11o status
tables item11p status
tables item11q status
tables item11r status
tables item11s status
tables item11t status
tables item11u status
tables item11v status
tables item11w status
tables item11x status
tables item11y status
tables item11z status

type "******************"
tables item12a status
tables item12b status
tables item12c status
tables item12d status
tables item12e status
tables item12f status
tables item12g status
tables item12h status
tables item12i status
tables item12j status
tables item12k status
tables item12l status
tables item12m status
tables item12n status
tables item12o status
tables item12p status
tables item12q status
tables item12r status
tables item12s status
tables item12t status
tables item12u status
tables item12v status
tables item12w status
tables item12x status
tables item12y status
tables item12z status

type "******************"
tables item13a status
tables item13b status
tables item13c status
tables item13d status
tables item13e status
tables item13f status
tables item13g status
tables item13h status
tables item13i status
tables item13j status
tables item13k status
tables item13l status
tables item13m status
tables item13n status
tables item13o status
tables item13p status
tables item13q status
tables item13r status
tables item13s status
tables item13t status
tables item13u status
tables item13v status
tables item13w status
tables item13x status
tables item13y status
tables item13z status

type "******************"
tables item14a status
tables item14b status
tables item14c status
tables item14d status
tables item14e status
tables item14f status
tables item14g status
tables item14h status
tables item14i status
tables item14j status
tables item14k status
tables item14l status
tables item14m status
tables item14n status
tables item14o status
tables item14p status
tables item14q status
tables item14r status
tables item14s status
tables item14t status
tables item14u status
tables item14v status
tables item14w status
tables item14x status
tables item14y status
tables item14z status

type "******************"
tables item15a status
tables item15b status
tables item15c status
tables item15d status
tables item15e status
tables item15f status
tables item15g status
tables item15h status
tables item15i status
tables item15j status
tables item15k status
tables item15l status
tables item15m status
tables item15n status
tables item15o status
tables item15p status
tables item15q status
tables item15r status
tables item15s status
tables item15t status
tables item15u status
tables item15v status
tables item15w status
tables item15x status
tables item15y status
tables item15z status

type "******************"
tables item16a status
tables item16b status
tables item16c status
tables item16d status
tables item16e status
tables item16f status
tables item16g status
tables item16h status
tables item16i status
tables item16j status
tables item16k status
tables item16l status
tables item16m status
tables item16n status
tables item16o status
tables item16p status
tables item16q status
tables item16r status
tables item16s status
tables item16t status
tables item16u status
tables item16v status
tables item16w status
tables item16x status
tables item16y status
tables item16z status

type "******************"
tables item17a status
tables item17b status
tables item17c status
tables item17d status
tables item17e status
tables item17f status
tables item17g status
tables item17h status
tables item17i status
tables item17j status
tables item17k status
tables item17l status
tables item17m status
tables item17n status
tables item17o status
tables item17p status
tables item17q status
tables item17r status
tables item17s status
tables item17t status
tables item17u status
tables item17v status
tables item17w status
tables item17x status
tables item17y status
tables item17z status

type "******************"
tables item18a status
tables item18b status
tables item18c status
tables item18d status
tables item18e status
tables item18f status
tables item18g status
tables item18h status
tables item18i status
tables item18j status
tables item18k status
tables item18l status
tables item18m status
tables item18n status
tables item18o status
tables item18p status
tables item18q status
tables item18r status
tables item18s status
tables item18t status
tables item18u status
tables item18v status
tables item18w status
tables item18x status
tables item18y status
tables item18z status

type "******************"
tables item19a status
tables item19b status
tables item19c status
tables item19d status
tables item19e status
tables item19f status
tables item19g status
tables item19h status
tables item19i status
tables item19j status
tables item19k status
tables item19l status
tables item19m status
tables item19n status
tables item19o status
tables item19p status
tables item19q status
tables item19r status
tables item19s status
tables item19t status
tables item19u status
tables item19v status
tables item19w status
tables item19x status
tables item19y status
tables item19z status

type "******************"
tables item20a status
tables item20b status
tables item20c status
tables item20d status
tables item20e status
tables item20f status
tables item20g status
tables item20h status
tables item20i status
tables item20j status
tables item20k status
tables item20l status
tables item20m status
tables item20n status
tables item20o status
tables item20p status
tables item20q status
tables item20r status
tables item20s status
tables item20t status
tables item20u status
tables item20v status
tables item20w status
tables item20x status
tables item20y status
tables item20z status

type "******************"
tables item21a status
tables item21b status
tables item21c status
tables item21d status
tables item21e status
tables item21f status
tables item21g status
tables item21h status
tables item21i status
tables item21j status
tables item21k status
tables item21l status
tables item21m status
tables item21n status
tables item21o status
tables item21p status
tables item21q status
tables item21r status
tables item21s status
tables item21t status
tables item21u status
tables item21v status
tables item21w status
tables item21x status
tables item21y status
tables item21z status

type "******************"
tables item22a status
tables item22b status
tables item22c status
tables item22d status
tables item22e status
tables item22f status
tables item22g status
tables item22h status
tables item22i status
tables item22j status
tables item22k status
tables item22l status
tables item22m status
tables item22n status
tables item22o status
tables item22p status
tables item22q status
tables item22r status
tables item22s status
tables item22t status
tables item22u status
tables item22v status
tables item22w status
tables item22x status
tables item22y status
tables item22z status

type "******************"
tables item23a status
tables item23b status
tables item23c status
tables item23d status
tables item23e status
tables item23f status
tables item23g status
tables item23h status
tables item23i status
tables item23j status
tables item23k status
tables item23l status
tables item23m status
tables item23n status
tables item23o status
tables item23p status
tables item23q status
tables item23r status
tables item23s status
tables item23t status
tables item23u status
tables item23v status
tables item23w status
tables item23x status
tables item23y status
tables item23z status

type "******************"
tables item24a status
tables item24b status
tables item24c status
tables item24d status
tables item24e status
tables item24f status
tables item24g status
tables item24h status
tables item24i status
tables item24j status
tables item24k status
tables item24l status
tables item24m status
tables item24n status
tables item24o status
tables item24p status
tables item24q status
tables item24r status
tables item24s status
tables item24t status
tables item24u status
tables item24v status
tables item24w status
tables item24x status
tables item24y status
tables item24z status

type "******************"
tables item25a status
tables item25b status
tables item25c status
tables item25d status
tables item25e status
tables item25f status
tables item25g status
tables item25h status
tables item25i status
tables item25j status
tables item25k status
tables item25l status
tables item25m status
tables item25n status
tables item25o status
tables item25p status
tables item25q status
tables item25r status
tables item25s status
tables item25t status
tables item25u status
tables item25v status
tables item25w status
tables item25x status
tables item25y status
tables item25z status

*Sample syntax for matched analyses and stratified analyses
*where "match" is the match link field (e.g., case household name, whatever)---
*the variable that links the case and controls who are being matched.
*type " "
*type "******************"
*type "MATCHED 2x2 TABLES"
*type "******************"
*match match status item01a
*match match status item01b


*tables item01c status item02d



type "THE END"
*END