********************************************************************
* File			    HALCyon PC covariate syntax_NSHD.do
* BY				Rachel Cooper, MRC Unit for Lifelong Health and Ageing at UCL
* 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 		24/08/2009
* last modified	    12/12/2012

* PURPOSE			Recodes and derives physical capability variables, basic sociodemographic variables 
*					and covariates (indicators of socioeconomic position, health status, living alone, neuroticism and BMI) for use in cross-cohort analyses
*************************************************************************************


# delimit;
set more off;

/*********************************************************************************/
/*Standard names and categories for demographic variables */

/* SEX */
/*labelling existing sex variable */
label variable sex "Sex of study member" ;
label define genderlab 1 "Male" 2 "Female" ;
label values sex genderlab ;

/*AGE */
/*age at time of assessment not applicable up to 60-64y collection*/
gen age_clinic09=agen09/12 ;

label variable age_clinic09 "Age (y) at time of clinic visit" ;

gen age_99=age99/12 ;
label variable age_99 "Age (y) at time of 1999 home visit" ;



/*********************************************************************************/
/* PHYSICAL CAPABILITY MEASURES */

/* GRIP STRENGTH */
/*At age 53y */
/*4 trials performed at age 53y (2 in each hand), using an electronic dynamometer */

/*Best of 4 */
gen bestgrip_53=grip53x ;
label variable bestgrip_53 "Grip strength (kg), best of 4, age 53" ;


/*At age 60-64y */
/*6 trials performed (2 in each hand), using an electronic dynamometer */

/*Use best of 4 for comparability with age 53y */
gen bestgrip_60=grip4max09 ;
replace bestgrip_60=. if grip4max09>776 ;
label variable bestgrip_60 "Grip strength (kg), best of 4, age 60-64" ;



/* STANDING BALANCE */
/* 2 trials performed at age 53 and then again at age 60-64y - time up to a max of 30s that a person could balance on 1 leg, 1 trial with eyes open, 1 with eyes closed */

/* Age 53y */
/*Eyes open */
gen balance_eo_53=legbp ;
label variable balance_eo_53 "Balance time(s), eyes open, 53y" ;

/*Eyes closed */
gen balance_ec_53=legbc ;
label variable balance_ec_53 "Balance time(s), eyes closed, 53y" ;

/*Natural log transformations */
gen lnbalance_eo_53=ln(balance_eo_53) ;
label variable lnbalance_eo_53 "ln(Balance time, eyes open), 53y" ;

gen lnbalance_ec_53=ln(balance_ec_53) ;
label variable lnbalance_ec_53 "ln(Balance time, eyes closed), 53y" ;


/*Binary categorisations of 'eyes open' variable */
/*Able to balance for 30s or not */
gen balance_30_eo_53=balance_eo_53 ;
recode balance_30_eo_53 (min/29.99=0) (30=1) ;
label variable balance_30_eo_53 "Able to balance for 30s eyes open at age 53?" ;
label define yeslab 0 "No" 1 "Yes" ;
label values balance_30_eo_53 yeslab ;

/*Able to complete at least 5 seconds */
gen balance_5_eo_53=balance_eo_53 ;
recode balance_5_eo_53 (min/4.99=0) (5/30=1) ;
label variable balance_5_eo_53 "Able to balance for at least 5s eyes open? age 53" ;
label values balance_5_eo_53 yeslab ;

/*Coding balance the alternative way so that inability to balance is the 'positive' outcome */
gen balance_30_eo_opp_53=. ;
replace balance_30_eo_opp_53=1 if balance_30_eo_53==0 ;
replace balance_30_eo_opp_53=0 if balance_30_eo_53==1 ;
label variable balance_30_eo_opp_53 "Able to balance for 30s eyes open? age 53" ;
label define nolab 1 "No" 0 "Yes" ;
label values balance_30_eo_opp_53 nolab ;

gen balance_5_eo_opp_53=. ;
replace balance_5_eo_opp_53=1 if balance_5_eo_53==0 ;
replace balance_5_eo_opp_53=0 if balance_5_eo_53==1 ;
label variable balance_5_eo_opp_53 "Able to balance for at least 5s eyes open? age 53" ;
label values balance_5_eo_opp_53 nolab ;


/*Creating a categorisation of balance (eyes open) which instead of using a specific time as a cut-point, identifies those in the bottom */
/*20% of performance by sex */
egen bal20m_eo_53=cut(balance_eo_53) if sex==1, group(5) ;
egen bal20f_eo_53=cut(balance_eo_53) if sex==2, group(5) ;
table bal20m_eo_53, c(min  balance_eo_53 max balance_eo_53) ;
table bal20f_eo_53, c(min  balance_eo_53 max balance_eo_53) ;

gen balance_b20_eo_53=. ;
replace balance_b20_eo_53=bal20m_eo_53 if sex==1 & bal20m_eo_53!=. ;
replace balance_b20_eo_53=bal20f_eo_53 if sex==2 & bal20f_eo_53!=. ;
recode balance_b20_eo_53 1/4=0 0=1 ;
label variable balance_b20_eo_53 "In bottom 20% of balance times, eyes open, 53" ;
label define b20lab 0 "Top 80%" 1 "Bottom 20%" ;
label values balance_b20_eo_53 b20lab ;

label variable bal20m_eo_53 "Quintiles of balance time, eyes open, men, 53y" ;
label variable bal20f_eo_53 "Quintiles of balance time, eyes open, women, 53y" ;



/*Binary categorisations of 'eyes closed' variable */
/*Able to balance for 30s or not */
gen balance_30_ec_53=balance_ec_53 ;
recode balance_30_ec_53 (min/29.99=0) (30=1) ;
label variable balance_30_ec_53 "Able to balance for 30s eyes closed? 53y" ;
label values balance_30_ec_53 yeslab ;

/*Able to complete at least 5 seconds */
gen balance_5_ec_53=balance_ec_53 ;
recode balance_5_ec_53 (min/4.99=0) (5/30=1) ;
label variable balance_5_ec_53 "Able to balance for at least 5s eyes closed? 53y" ;
label values balance_5_ec_53 yeslab ;



/* Age 60-64y */
/*Eyes open */
gen balance_eo_60=legbp09 ;
replace balance_eo_60=. if legbp09>776 ;
label variable balance_eo_60 "Balance time(s), eyes open, 60-64y" ;

/*Eyes closed */
gen balance_ec_60=legbc09 ;
replace balance_ec_60=. if legbc09>776 ;
label variable balance_ec_60 "Balance time(s), eyes closed, 60-64y" ;

/*Natural log transformations */
gen lnbalance_eo_60=ln(balance_eo_60) ;
label variable lnbalance_eo_60 "ln(Balance time, eyes open), 60-64y" ;

gen lnbalance_ec_60=ln(balance_ec_60) ;
label variable lnbalance_ec_60 "ln(Balance time, eyes closed), 60-64y" ;


/*Binary categorisations of 'eyes open' variable */
/*Able to balance for 30s or not */
gen balance_30_eo_60=balance_eo_60 ;
recode balance_30_eo_60 (min/29.99=0) (30=1) ;
label variable balance_30_eo_60 "Able to balance for 30s eyes open at age 60-64?" ;
label values balance_30_eo_60 yeslab ;

/*Able to complete at least 5 seconds */
gen balance_5_eo_60=balance_eo_60 ;
recode balance_5_eo_60 (min/4.99=0) (5/30=1) ;
label variable balance_5_eo_60 "Able to balance for at least 5s eyes open? age 60-64" ;
label values balance_5_eo_60 yeslab ;

/*Coding balance the alternative way so that inability to balance is the 'positive' outcome */
gen balance_30_eo_opp_60=. ;
replace balance_30_eo_opp_60=1 if balance_30_eo_60==0 ;
replace balance_30_eo_opp_60=0 if balance_30_eo_60==1 ;
label variable balance_30_eo_opp_60 "Able to balance for 30s eyes open? age 60-64" ;
label values balance_30_eo_opp_60 nolab ;

gen balance_5_eo_opp_60=. ;
replace balance_5_eo_opp_60=1 if balance_5_eo_60==0 ;
replace balance_5_eo_opp_60=0 if balance_5_eo_60==1 ;
label variable balance_5_eo_opp_60 "Able to balance for at least 5s eyes open? age 60-64" ;
label values balance_5_eo_opp_60 nolab ;


/*Creating a categorisation of balance (eyes open) which instead of using a specific time as a cut-point, identifies those in the bottom */
/*20% of performance by sex */
egen bal20m_eo_60=cut(balance_eo_60) if sex==1, group(5) ;
egen bal20f_eo_60=cut(balance_eo_60) if sex==2, group(5) ;
table bal20m_eo_60, c(min  balance_eo_60 max balance_eo_60) ;
table bal20f_eo_60, c(min  balance_eo_60 max balance_eo_60) ;

gen balance_b20_eo_60=. ;
replace balance_b20_eo_60=bal20m_eo_60 if sex==1 & bal20m_eo_60!=. ;
replace balance_b20_eo_60=bal20f_eo_60 if sex==2 & bal20f_eo_60!=. ;
recode balance_b20_eo_60 1/4=0 0=1 ;
label variable balance_b20_eo_60 "In bottom 20% of balance times, eyes open, 60-64" ;
label values balance_b20_eo_60 b20lab ;

label variable bal20m_eo_60 "Quintiles of balance time, eyes open, men, 60-64y" ;
label variable bal20f_eo_60 "Quintiles of balance time, eyes open, women, 60-64y" ;



/*Binary categorisations of 'eyes closed' variable */
/*Able to balance for 30s or not */
gen balance_30_ec_60=balance_ec_60 ;
recode balance_30_ec_60 (min/29.99=0) (30=1) ;
label variable balance_30_ec_60 "Able to balance for 30s eyes closed? 60-64y" ;
label values balance_30_ec_60 yeslab ;

/*Able to complete at least 5 seconds */
gen balance_5_ec_60=balance_ec_60 ;
recode balance_5_ec_60 (min/4.99=0) (5/30=1) ;
label variable balance_5_ec_60 "Able to balance for at least 5s eyes closed? 60-64y" ;
label values balance_5_ec_60 yeslab ;





/*CHAIR RISES */
/*1 trial of 10 chair rises at age 53y */

gen chairtime_53=chrstfc ;
label variable chairtime_53 "Chair rise time (s), 10 rises, age 53" ;

/*coding to missing people with values <1s per chair rise */
replace chairtime_53=. if chairtime_53<10 ;

/*Natural log transformation */
gen lnchairtime_53=ln(chairtime_53) ;
label variable lnchairtime_53 "ln(chair rise time, age 53)" ;

/*Reciprocal of chair rise time */
gen rpchairtime_53=(1/chairtime_53)*100 ;
label variable rpchairtime_53 "Reciprocal of chair rise time, age 53" ;

/*Chair rise speed */
/*Chair rises per second */
gen chairspeed53_s=10/chairtime_53 ;
label variable chairspeed53_s "Chair rise speed (stands/sec), 53y" ;

/*per minute */
gen chairspeed53_m=chairspeed53_s*60 ;
label variable chairspeed53_m "Chair rise speed (stands/min), 53y" ;


/* Rebecca's conversion of 10 chair rises to 5 chair rises - using ELSA 50-59 years sex specific data*/
gen estchairtime5_53=. ;
replace estchairtime5_53=0.51+0.46*chrstfc if sex==1 & chrstfc!=. ;
replace estchairtime5_53=0.63+0.44*chrstfc if sex==2 & chrstfc!=. ;

label variable estchairtime5_53 "Estimated chair rise time for 5 rises, age 53" ;

/*coding to missing people with values <1s per chair rise */
replace estchairtime5_53=. if estchairtime5_53<5 ;

/*Natural log transformation */
gen lnchairtime5_53=ln(estchairtime5_53) ;
label variable lnchairtime5_53 "ln(chair rise time (estimate for 5 rises), age 53)" ;



/*1 trial of 10 chair rises at age 60-64y */

gen chairtime_60=chrst09 ;
replace chairtime_60=. if chrst09>776 ;
label variable chairtime_60 "Chair rise time (s), 10 rises, age 60-64" ;

/*coding to missing people with values <1s per chair rise */
replace chairtime_60=. if chairtime_60<10 ;


/*Natural log transformation */
gen lnchairtime_60=ln(chairtime_60) ;
label variable lnchairtime_60 "ln(chair rise time, age 60-64)" ;

/*Reciprocal of chair rise time */
gen rpchairtime_60=(1/chairtime_60)*100 ;
label variable rpchairtime_60 "Reciprocal of chair rise time, age 60-64" ;

/*Chair rise speed */
/*Chair rises per second */
gen chairspeed60_s=10/chairtime_60 ;
label variable chairspeed60_s "Chair rise speed (stands/sec), 60-4y" ;

/*per minute */
gen chairspeed60_m=chairspeed60_s*60 ;
label variable chairspeed60_m "Chair rise speed (stands/min), 60-4y" ;



/* Rebecca's conversion of 10 chair rises to 5 chair rises - using ELSA 50-59 years sex specific data*/
gen estchairtime5_60=. ;
replace estchairtime5_60=0.51+0.46*chairtime_60 if sex==1 & chairtime_60!=. ;
replace estchairtime5_60=0.63+0.44*chairtime_60 if sex==2 & chairtime_60!=. ;

label variable estchairtime5_60 "Estimated chair rise time for 5 rises, age 60-64" ;

/*coding to missing people with values <1s per chair rise */
replace estchairtime5_60=. if estchairtime5_60<5 ;

/*Natural log transformation */
gen lnchairtime5_60=ln(estchairtime5_60) ;
label variable lnchairtime5_60 "ln(chair rise time (estimate for 5 rises), age 60-64)" ;


/*TUG speed at 60 */
gen tugspeed_60=tugspeed09 ;
replace tugspeed_60=. if tugspeed09>776 ;
label variable tugspeed_60 "TUG speed (m/s), 60-64y" ;

/*Unables at 53*/
gen gripunable_53=. ;
replace gripunable_53=1 if grip53g==996 ;
replace gripunable_53=0 if grip53g==1 ;

label variable gripunable_53 "Unable to perform grip test? age 53y" ;
label define unablelab 0 "Able" 1 "Unable" ;
label values gripunable_53 unablelab ;

gen chairunable_53=. ;
replace chairunable_53=1 if chrst53g==995 | chrst53g==997 ;
replace chairunable_53=0 if chrst53g==1 ;
label variable chairunable_53 "Unable to perform chair rise test? age 53y" ;
label values chairunable_53 unablelab ;



/***************************************************************************************/
/*SOCIOECONOMIC POSITION */

/*Childhood SEP */
/*Occupational class of male head of household at age 4y */
gen occ_fath_4=fsc50t ;
/*coding to missing those unclassified (incl missing) */
recode occ_fath_4 66=. 99=. ;
label variable occ_fath_4 "Father's occupation at age 4y" ;
label define seplab 1 "I" 2 "II" 3 "IIINM" 4 "IIIM" 5 "IV" 6 "V"  ;
label values occ_fath_4 seplab ;


/*Adult SEP */

/*Own occupational class in adulthood -taking information from age 53 if available, from 43 if not and so on */
gen occ_adult_own=sc1553 ;
recode occ_adult_own 999=. ;
label variable occ_adult_own "Own adult occupational class (53-15)" ;
label values occ_adult_own seplab ;

/*Binary categorisation in line with other studies */
gen occ_adult_2cat=occ_adult_own ;
recode occ_adult_2cat 1/2=1 3/6=2 ;
label variable occ_adult_2cat "Adult occupational class (binary)" ;
label define occcatlab 1 "I or II" 2 "III, IV or V" ;
label values occ_adult_2cat occcatlab ;


/*Occupational class in adulthood of spouse in adulthood (53-15)*/
gen occ_adult_sp=spsc1553 ;
recode occ_adult_sp 999=. ;
label variable occ_adult_sp "Spouse adult occupational class (53-15)" ;
label values occ_adult_sp seplab ;


/*Education variables */
gen highestqual=lhqr ;
recode highestqual 0=0 1=1 2=1 3=2 4=3 5=3 6/8=4 88=. 99=. ;
label variable highestqual "Highest qualification achieved" ;
label define edulab 0 "None" 1 "Sub GCE or vocational course" 2 "GCE O level or Burnham C" 3 "GCE 'A' level, Burnham B or Burnham A2" 4 "Degree or higher" ;
label values highestqual edulab ;

/*Binary categorisation as per other cohorts */
gen highestqual_2cat=highestqual ;
recode highestqual_2cat 0/2=1 3/4=2 ;
label define quallab 1 "O level or lower" 2 "A level or higher" ;
label values highestqual_2cat quallab ;


/*OTHER COVARIATES */
/*Neuroticism */
/*Recoding missing values to . for neuroticism at age 26y */
recode neur72 19=. ;

/*Living alone */
/*Creating a variable to identify people living alone at baseline based on their marital status at age 53y (need to check that this is best measure) */
gen livealn=. ;
replace livealn=1 if marstats==1 | marstats==3 | marstats==4 | marstats==5 ;
replace livealn=2 if marstats==2  ;
label define alonelab 1 "Living alone" 2 "Not living alone" ;
label values livealn alonelab ;

/*Height, weight and BMI */
/*Recoding missing values to . for height and weight at age 53y */
recode ht99u 7777=. 9997=. 9999=. ;
recode wt99u 7777=. 9997=. 9999=. ;
recode bmi99u 7777=. 9997=. 9999=. ;

/*Health status */
/*Health status (renaming it to be consistent with other cohort analyses) */
gen hp_w1=hp99l1 ;
recode hp_w1 8=. ;
label variable hp_w1 "Health status" ;
label define hplab 0 "No" 1 "Yes"  ;
label values hp_w1 hplab ;