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* File      HALCyon cognitive syntax_Caerphilly.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   Caerphilly Prospective Study
* Date Created    07/04/2010
* Date Modified     27/06/2011	
* 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_Caerphilly.do


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

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

/*Crystallized cognitive ability*/
/*nart*/ 
/* range 0-50*/
mvdecode c3cq73ascorecorrectpronounce c4cq73ascorecorrectpronounce, mv(99);

gen nart_w3= c3cq73ascorecorrectpronounce ;
label variable nart_w3 "NART at wave 3" ;
gen nart_w4= c4cq73ascorecorrectpronounce ;
label variable nart_w4 "NART at wave 4" ;
gen nart_w5=c5_nart ;
label variable nart_w5 "NART at wave 5" ;

/*standardise NART to whole sample*/
egen nartz_w3=std(nart_w3) ;
label variable nartz_w3 "standardised NART at wave 3" ;
egen nartz_w4=std(nart_w4) ;
label variable nartz_w4 "standardised NART at wave 4" ;
egen nartz_w5=std(nart_w5) ;
label variable nartz_w5 "standardised NART at wave 5" ;

/*age-standardised NART - standardised residuals from regression on age*/
xi: regress nart_w3 age_w3;
predict nartzage_w3, rstandard ;
label variable nartzage_w3 "age-standardised NART at wave 3" ;
xi: regress nart_w4 age_w4 ;
predict nartzage_w4, rstandard ;
label variable nartzage_w4 "age-standardised NART at wave 4" ;
xi: regress nart_w5 age_w5 ;
predict nartzage_w5, rstandard ;
label variable nartzage_w5 "age-standardised NART at wave 5" ;

/*reaction time*/
gen crt_w3=c3crt ;
label variable crt_w3 "Reaction time at wave 3" ;
gen crt_w4=c4crt ;
label variable crt_w4 "Reaction time at wave 4" ;
gen crt_w5=c5crt ;
label variable crt_w5 "Reaction time at wave 5" ;

gen lncrt_w3=ln(crt_w3) ;
gen lncrt_w4=ln(crt_w4) ;
gen lncrt_w5=ln(crt_w5) ;

/*standardise ln(reaction time)*/
egen lncrtz_w3=std(lncrt_w3) ;
label variable lncrtz_w3 "standardised ln(reaction time) at wave 3" ;
egen lncrtz_w4=std(lncrt_w4) ;
label variable lncrtz_w4 "standardised ln(reaction time) at wave 4" ;
egen lncrtz_w5=std(lncrt_w5) ;
label variable lncrtz_w5 "standardised ln(reaction time) at wave 5" ;

/*age-standardised ln(reaction time) - standardised residuals from regression on age*/
xi: regress lncrt_w3 age_w3 ;
predict lncrtzage_w3, rstandard ;
label variable lncrtzage_w3 "age-standardised ln(reaction time) at wave 3" ;
xi: regress lncrt_w4 age_w4 ;
predict lncrtzage_w4, rstandard ;
label variable lncrtzage_w4 "age-standardised ln(reaction time) at wave 4" ;
xi: regress lncrt_w5 age_w5 ;
predict lncrtzage_w5, rstandard ;
label variable lncrtzage_w5 "age-standardised ln(reaction time) at wave 5" ;

/*ah4*/
/*range 0-61*/
gen ah4_w3=c3ah4 ;
label variable ah4_w3 "AH4 at wave 3" ;
gen ah4_w4=c4ah4 ;
label variable ah4_w4 "AH4 at wave 4" ;
gen ah4_w5=c5ah4 ;
label variable ah4_w5 "AH4 at wave 5" ;

/*standardise AH4*/
egen ah4z_w3=std(ah4_w3) ;
label variable ah4z_w3 "standardised AH4 at wave 3" ;
egen ah4z_w4=std(ah4_w4) ;
label variable ah4z_w4 "standardised AH4 at wave 4" ;
egen ah4z_w5=std(ah4_w5) ;
label variable ah4z_w5 "standardised AH4 at wave 5" ;

/*age-standardised AH4 - standardised residuals from regression on age*/
xi: regress ah4_w3 age_w3 ;
predict ah4zage_w3, rstandard ;
label variable ah4zage_w3 "age-standardised AH4 at wave 3" ;
xi: regress ah4_w4 age_w4 ;
predict ah4zage_w4, rstandard ;
label variable ah4zage_w4 "age-standardised AH4 at wave 4" ;
xi: regress ah4_w5 age_w5 ;
predict ah4zage_w5, rstandard ;
label variable ah4zage_w5 "age-standardised AH4 at wave 5" ;

/*derive fluid cognitive performance variable - Gf*/
factor ah4z_w3 lncrtz_w3, factors(1) pcf ;
predict Gf_w3 ;
label variable Gf_w3 "Gf at wave 3" ;
factor ah4z_w4 lncrtz_w4, factors(1) pcf ;
predict Gf_w4 ;
label variable Gf_w4 "Gf at wave 4" ;
factor ah4z_w5 lncrtz_w5, factors(1) pcf ;
predict Gf_w5 ;
label variable Gf_w5 "Gf at wave 5" ;

/*age-standardised scores*/
factor ah4zage_w3 lncrtzage_w3, factors(1) pcf ;
predict Gfage_w3 ;
label variable Gfage_w3 "Gf (age adjusted) at wave 3" ;
factor ah4zage_w4 lncrtzage_w4, factors(1) pcf ;
predict Gfage_w4 ;
label variable Gfage_w4 "Gf (age adjusted) at wave 4" ;
factor ah4zage_w5 lncrtzage_w5, factors(1) pcf ;
predict Gfage_w5 ;
label variable Gfage_w5 "Gf (age adjusted) at wave 5" ;

/*other cognitive tests*/
/*MMSE*/
gen mmse_w3=c3mmseindex ;
label variable mmse_w3 "MMSE at wave 3" ;
gen mmse_w4=c4mmseindex ;
label variable mmse_w4 "MMSE at wave 4" ;
gen mmse_w5=c5_mmse ;
label variable mmse_w5 "MMSE at wave 5" ;