********************************************************************
* File			    HALCyon cortisol syntax_NSHD.do
* BY				Mike Gardner, University of Bristol
* FOR				HALCyon cross-cohort collaboration (funded by the New Dynamics of Ageing (RES-353-25-0001))
* DATASET			MRC National Survey of Health and Development
* Date Created 		25/03/2010 
* last modified	    25/03/2010 

* PURPOSE			Cleans and derives cortisol variables
*************************************************************************************


*************************************************************************************
*    Cleans cortisol to less than 100nmol/L and derives morning, CAR and diurnaldrop*
*    Derives z scored cortisol measures and cortisol variables in quartiles         *
*************************************************************************************

**NSHD data had 9999 coded for unknown, 7777 for not attending clinic and 9998 for empty
mvdecode cortt106, mv(9999)
mvdecode cortt206, mv(9999)
mvdecode cortt306, mv(9999)
mvdecode cortt406, mv(9999)

mvdecode cortt106, mv(7777)
mvdecode cortt206, mv(7777)
mvdecode cortt306, mv(7777)
mvdecode cortt406, mv(7777)

mvdecode cortt106, mv(9998)
mvdecode cortt206, mv(9998)
mvdecode cortt306, mv(9998)
mvdecode cortt406, mv(9998)

rename cortt306 cortisoltime1
rename cortt406 cortisoltime2
rename cortt106 cortisoltime3
rename cortt206 cortisoltime4

sum cortisoltime1 cortisoltime2 cortisoltime3 cortisoltime4
replace cortisoltime1=. if cortisoltime1>100
replace cortisoltime2=. if cortisoltime2>100
replace cortisoltime3=. if cortisoltime3>100
replace cortisoltime4=. if cortisoltime4>100
sum cortisoltime1 cortisoltime2 cortisoltime3 cortisoltime4

**Now generate cortisol variables
**Average morning cortisol for waking and 30 mins after waking
egen cortmornavg=rowmean(cortisoltime1 cortisoltime2)
**Now generate CAR
gen deltaavg = (cortisoltime2 - cortisoltime1)
gen diurnaldropavg = (cortmornavg - cortisoltime4)

**Lable cortisol variables
label variable cortisoltime1 "Cortisol on waking"
label variable cortisoltime2 "Cortisol 30 minutes after waking"
label variable cortisoltime3 "Mid-morning clinic cortisol"
label variable cortisoltime4 "Night time cortisol 9.30pm"
label variable cortmornavg "Morning Cortisol"
label variable deltaavg "CAR"
label variable diurnaldropavg "Diurnal cortisol slope"

**zscore cortisol variables
zscore cortisoltime1
zscore cortisoltime2
zscore cortisoltime3
zscore cortisoltime4
zscore cortmornavg
zscore deltaavg
zscore diurnaldropavg

**put cortisol variables into quartiles
xtile morncortquart=cortmornavg, nq(4)
table morncortquart, c(n cortmornavg min cortmornavg max cortmornavg)
xtile nightcortquart=cortisoltime4, nq(4)
table nightcortquart, c(n cortisoltime4 min cortisoltime4 max cortisoltime4)
xtile nightcortbin=cortisoltime4, nq(2)
xtile deltacortquart=deltaavg, nq(4)
table deltacortquart, c(n deltaavg min deltaavg max deltaavg)
xtile diurnalcortquart=diurnaldropavg, nq(4)
table diurnalcortquart, c(n diurnaldropavg min diurnaldropavg max diurnaldropavg)