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* File      HALCyon cognitive syntax_HAS.do
* BY        Rebecca Hardy, 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   Hertfordshire Ageing Study (HAS)
* Date Created    07/04/2010
* PURPOSE         Recodes and derives cognitive variables for use in cross-cohort analyses
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# delimit;
set more off;

*To obtain age variables, please first run HALCyon PC covariate syntax_HAS.do

/*Creating break between newly recoded cognitive variables and variables in existing dataset with a blank variable */
gen cogrecodes_below=. ;

/*********************************************************************************/

/*Crystallized cognitive ability*/
/*Mill Hill vocabulary*/
/*range 0-35*/
gen mh_w1=numcorr9 ;
label variable mh_w1 "Mill Hill at wave 1" ;
gen mh_w2=mhncorr ;
label variable mh_w2 "Mill Hill at wave 2" ;

/*standardised Mill Hill score to whole sample*/
egen mhz_w1=std(mh_w1) ;
egen mhz_w2=std(mh_w2) ;
label variable mhz_w1 "standardised Mill Hill at wave 1" ;
label variable mhz_w2 "standardised Mill Hill at wave 2" ;

/*standardise Mill Hill for men and women seprately*/
egen mhzm_w1=std(mh_w1) if sex==1;
egen mhzf_w1=std(mh_w1) if sex==2;
label variable mhzm_w1 "standardised Mill Hill for men at wave 1" ;
label variable mhzf_w1 "standardised Mill Hill for women at wave 1" ;
egen mhzm_w2=std(mh_w2) if sex==1;
egen mhzf_w2=std(mh_w2) if sex==2;
label variable mhzm_w2 "standardised Mill Hill for men at wave 2" ;
label variable mhzf_w2 "standardised Mill Hill for women at wave 2" ;
/*combine in one variable*/
gen mhzs_w1=. ;
replace mhzs_w1=mhzm_w1 if sex==1;
replace mhzs_w1=mhzf_w1 if sex==2;
label variable mhzs_w1 "sex-standardised Mill Hill at wave 1" ;
gen mhzs_w2=. ;
replace mhzs_w2=mhzm_w2 if sex==1;
replace mhzs_w2=mhzf_w2 if sex==2;
label variable mhzs_w2 "sex-standardised Mill Hill at wave 2" ;

/*age and sex-standardised Mill Hill - standardised residuals from regression on age and sex*/
xi: regress mh_w1 age_w1 i.sex ;
predict mhzage_w1, rstandard ;
label variable mhzage_w1 "age and sex-standardised Mill Hill at wave 1" ;
xi: regress mh_w2 age_w2 i.sex ;
predict mhzage_w2, rstandard ;
label variable mhzage_w2 "age and sex-standardised Mill Hill at wave 2" ;

/*AH4*/
/*range 0-50*/
gen ah4_w1=numcorr ;
label variable ah4_w1 "AH4 at wave 1" ;
gen ah4_w2=hnumcorr ;
label variable ah4_w2 "AH4 at wave 2" ;

/*Gf includes only AH4*/
/*standadised AH4*/
egen ah4z_w1=std(ah4_w1);
egen ah4z_w2=std(ah4_w2);
label variable ah4z_w1 "standardised AH4 at wave 1 (Gf)" ;
label variable ah4z_w2 "standardised AH4 at wave 2 (Gf)" ;

/*standardise AH4 for men and women seprately*/
egen ah4zm_w1=std(ah4_w1) if sex==1;
egen ah4zf_w1=std(ah4_w1) if sex==2;
label variable ah4zm_w1 "standardised AH4 for men at wave 1 (Gf)" ;
label variable ah4zf_w1 "standardised AH4 for women at wave 1 (Gf)" ;
egen ah4zm_w2=std(ah4_w2) if sex==1;
egen ah4zf_w2=std(ah4_w2) if sex==2;
label variable mhzm_w2 "standardised AH4 for men at wave 2 (Gf)" ;
label variable mhzf_w2 "standardised AH4 for women at wave 2 (Gf)" ;
/*combine in one variable*/
gen ah4zs_w1=. ;
replace ah4zs_w1=ah4zm_w1 if sex==1;
replace ah4zs_w1=ah4zf_w1 if sex==2;
label variable ah4zs_w1 "sex-standardised AH4 at wave 1 (Gf)" ;
gen ah4zs_w2=. ;
replace ah4zs_w2=ah4zm_w2 if sex==1;
replace ah4zs_w2=ah4zf_w2 if sex==2;
label variable ah4zs_w2 "sex-standardised AH4 at wave 2 (Gf)" ;

/*age and sex-standardised AH4 - standardised residuals from regression on age and sex*/
xi: regress ah4_w1 age_w1 i.sex ;
predict ah4zage_w1, rstandard ;
label variable ah4zage_w1 "age and sex-standardised AH4 at wave 1 (Gf)" ;
xi: regress ah4_w2 age_w2 i.sex ;
predict ah4zage_w2, rstandard ;
label variable ah4zage_w2 "age and sex-standardised AH4 at wave 2 (Gf)" ;

/*MMSE*/
gen mmse_w2=mmtotsc
label variable mmse_w2 "MMSE total score at wave 2"

/*AMT*/
gen amt_w1=amtotsc
label variable amt_w1 "AMT at wave 1"