********************************************************************
* File			    HALCyon cortisol syntax_BoydOrr.do
* BY				Mike Gardner, University of Bristol
* FOR				HALCyon cross-cohort collaboration (funded by the New Dynamics of Ageing (RES-353-25-0001))
* DATASET			Boyd Orr Cohort study
* Date Created 		24/03/2010 
* last modified	    24/03/2010 

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

set more off

** clean cortisol.

sum b3cortisol
li uniq_id b3cortisol if b3cortisol==0 & b3cortisol!=.
** variable "601904" had cortisol values as "0" and hence replaced as missing
replace b3cortisol=. if b3cortisol==0
sum b3cortisol


**PHASE 3 TIME ADJUSTED CORTISOL VALUES
**Generate time in hours when cortisol sampled
generate time=((b3hrs_blood__taken*60) + (b3min_blood__taken))/60
sum time, detail
**Need recode cortisol and time so omit those 35 out of 405 not fasting
sum b3cortisol
sum time
gen b3cortisolfast=b3cortisol if b3fast6==1
gen timefast=time if b3fast6==1
sum b3cortisolfast
sum timefast
scatter b3cortisolfast timefast
**As want morning cortisol and to be comparable with CaPS phase 1,
**limit cortisol and time to morning
gen b3morncortisol=b3cortisolfast if timefast<12
gen morntime=timefast if timefast<12
scatter b3morncortisol morntime
**Distribution of morning cortisol is not skewed and approx. normal hence not transform
sum b3morncortisol, detail
hist b3morncortisol
**Now need to adjust cortisol for time of day by fitting linear and fractional polynomial
**First Linear
regress b3morncortisol morntime
predict res1, residual
hist res1
qnorm res1

fracpoly, compare: regress b3morncortisol morntime
fracplot morntime
fracpred resfp, dresid
hist resfp
qnorm resfp

**There is a significant negative linear fit and fractional polynomial fit 
**where p1=-2 and p2=-2 wasn't significantly better.  However use fractional
**polynomial fit (as in case of phase 1 fasting morning cortisol in CaPS)

**Now generate time adjusted cortisol.  Mean of b3morncortisol is 441.94
gen b3cortadj=resfp+441.94
sum b3cortadj, detail
**Minimum value is greater than 0 (159.23)


**Need to replace those participants taking oral corticosteroids
**li uniq_id b3medcode if( b3medcode=="06.03.02") was used in file


  *   uniq_id   b3medc~e |
  * |--------------------|
  * |  403307   06.03.02 |
  * |  411009   06.03.02 |
  * | 1106803   06.03.02 |
  * | 1381307   06.03.02 |
  * |  600407   06.03.02 |
  * |--------------------|
  * | 1100206   06.03.02 |
  * |  802907   06.03.02 |
  * | 1109907   06.03.02 |
  * |  209403   06.03.02 |
  * |  900304   06.03.02 |
  * |--------------------|
  * |  804403   06.03.02 |
  * | 1508105   06.03.02 |
  * | 1505005   06.03.02 |
  * +--------------------+
  
replace b3cortadj=. if(uniq_id==403307)
replace b3cortadj=. if(uniq_id==411009)
replace b3cortadj=. if(uniq_id==1106803)
replace b3cortadj=. if(uniq_id==1381307)
replace b3cortadj=. if(uniq_id==600407)
replace b3cortadj=. if(uniq_id==1100206)
replace b3cortadj=. if(uniq_id==802907)
replace b3cortadj=. if(uniq_id==1109907)
replace b3cortadj=. if(uniq_id==209403)
replace b3cortadj=. if(uniq_id==900304)
replace b3cortadj=. if(uniq_id==804403)
replace b3cortadj=. if(uniq_id==1508105)
replace b3cortadj=. if(uniq_id==1505005)

sum b3cortadj, detail

**Label morning adjusted cortisol variable and morning time
label variable b3cortadj "Time adjusted morning cortisol"
label variable morntime "Morning b3 cortisol time"

**Now zscore phase 3 morning cortisol
zscore b3cortadj

**Now put phase 3 time adjusted morning cortisol into quartiles
xtile b3cortquart=b3cortadj, nq(4)
table b3cortquart, c(n b3cortadj min b3cortadj max b3cortadj)


**Smoking status to
**Never, ex and current.
tab b3smokingstatus
gen b3smokeindex1 = b3smokingstatus
recode b3smokeindex1 (1 = 6)(2 = 5)(3 = 4), generate (b3smokeindex2) 
tab b3smokeindex2
recode b3smokeindex2 (4 = 0)(5 = 1)(6 = 2), generate (b3smokeindex3)
tab b3smokeindex3