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ASCVD_cohort_creation.do
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cd "/home/steve/phd/ASCVD/ASCVD/"
* ASCVD recal
* ARIC
/*Visit1 */
import delimited "aric/V1/csv/derive13.csv", clear
keep id_c centerid cholmdcode01 cholmdcode02 cursmk01 diabts02 diabts03 gender hdl01 hyptmd01 racegrp cigt01 cigtyr01 glucos01 clvh01 v1age01 enroll_yr prevmi05 prvchd05 prevhf01 forsmk01 fast1202 fast0802 ldl02 bmi01 wsthpr01 tglefh01 momhistorystr dadhistorystr momhistorychd dadhistorychd dadhistorydia momhistorydia rangna01
sort id_c
save "pooled_data/aric_v1.dta", replace
import delimited "aric/V1/csv/sbpa02.csv", clear
keep id_c sbpa21 sbpa22
sort id_c
merge 1:1 id_c using "pooled_data/aric_v1.dta"
drop _merge
sort id_c
save "pooled_data/aric_v1.dta", replace
import delimited "aric/V1/csv/lipa.csv", clear
keep id_c lipa01 lipa02 lipa08
sort id_c
merge 1:1 id_c using "pooled_data/aric_v1.dta"
drop _merge
sort id_c
save "pooled_data/aric_v1.dta", replace
import delimited "aric/V1/csv/hom.csv", clear
keep id_c hom10d hom10e hom29 hom31 hom32 hom35 hom10a hom54 hom12 hom13 hom14 hom15e hom15d hom16d hom16e hom18d hom18e hom19d hom19e hom20 hom21 hom22 hom23e hom23d hom24d hom24e hom26d hom26e hom27d hom27e hom55 hom56
sort id_c
merge 1:1 id_c using "pooled_data/aric_v1.dta"
drop _merge
sort id_c
save "pooled_data/aric_v1.dta", replace
import delimited "aric/V1/csv/msra.csv", clear
keep id_c msra01 msra02 msra08f
sort id_c
merge 1:1 id_c using "pooled_data/aric_v1.dta"
drop _merge
sort id_c
save "pooled_data/aric_v1.dta", replace
import delimited "aric/V1/csv/anta.csv", clear
keep id_c anta01 anta07a anta04
sort id_c
merge 1:1 id_c using "pooled_data/aric_v1.dta"
drop _merge
sort id_c
save "pooled_data/aric_v1.dta", replace
import delimited "aric/V1/csv/stroke01.csv", varnames(1) clear
keep id_c tia01 stroke01 stia01
sort id_c
merge 1:1 id_c using "pooled_data/aric_v1.dta"
drop _merge
sort id_c
save "pooled_data/aric_v1.dta", replace
import delimited "aric/V1/csv/phea.csv", varnames(1) clear
keep id_c phea06 phea07a phea08 phea09a
sort id_c
merge 1:1 id_c using "pooled_data/aric_v1.dta"
drop _merge
sort id_c
save "pooled_data/aric_v1.dta", replace
g brngmeds = 1 if msra01=="Y"
replace brngmeds = 2 if msra01=="N" & msra02=="T"
replace brngmeds = 3 if msra01=="S"
g cholmed1 = cholmdcode01
g sysbp=sbpa21
g cholmed2=cholmdcode02
g diabp=sbpa22
g age=v1age01
g hyptmdsr=hyptmd01
g hyptmdml=.
g cursmoke=cursmk01
g smokstat=cigt01
g cigpday=hom32 if smokstat==1
replace cigpday=0 if smokstat>=2 & smokstat<=3
g avgsmoke=hom35 if smokstat>=1 & smokstat<=2
replace avgsmoke=0 if smokstat==3
g packyrs=cigtyr01/20
g strtsmk=hom29
g stopsmk=hom31
g bmi=bmi01
g wsthip=wsthpr01
g waist=anta07a
g weight=0.45*anta04
g height=anta01
g fast08=fast0802
g fast12=fast1202
g ldlc=ldl02
g tglefh=tglefh01
g glucose=glucos01
g hdlc=hdl01
g totchol=lipa01
g trigly=lipa02
g apolpa=lipa08
g prevmi=prevmi05
g prevchd=prvchd05
g prevstrk=1 if stroke01=="Y" | hom10d=="Y"
replace prevstrk=0 if stroke01!="Y" & hom10d=="N"
g prevchf=prevhf01
g prevap=1 if rangna01==1
replace prevap=0 if rangna01==4
replace prevap=. if rangna01>1 & rangna01<4
g prevproc =0 if phea06=="N"
replace prevproc=1 if phea06=="Y" & (phea07a=="Y" | phea09a=="Y")
replace prevproc=0 if phea06=="Y" & (phea07a=="N" & phea09a=="N")
/* Diabetes Definitions */
g study_dm=diabts03
g diabmed=0 if msra08f=="N" | msra02=="T"
replace diabmed=1 if msra08f=="Y"
g diabtsr=0 if hom10e=="N"
replace diabtsr=1 if hom10e=="Y"
replace diabtsr=. if hom10e!="N" & hom10e!="Y"
g diabhx=1 if (glucose >=200) | (glucose>=126 & fast08>=1) | diabtsr==1 | diabmed==1
replace diabhx=0 if glucose>0 & glucose<126 & diabtsr==0 & (diabmed==0 | diabmed==.)
g diabt126=1 if (glucose >=200) | (glucose>=126 & fast08>=1) | diabmed==1
replace diabt126=0 if glucose>0 & glucose<126 & diabmed!=1
replace diabt126=. if glucose>=126 & glucose<200 & fast08<=0 & diabmed==.
/* End Diabetes defintion */
g exam=1
keep id_c enroll_yr age gender racegrp centerid bmi totchol ldlc tglefh hdlc trigly cholmed1 cholmed2 sysbp diabp hyptmdsr hyptmdml cursmoke smokstat cigpday strtsmk stopsmk packyrs avgsmoke fast08 fast12 glucose diabt126 diabtsr brngmeds diabmed prevmi prevchd prevstrk wsthip apolpa height exam waist weight prevchf study_dm diabhx prevap prevproc
save "pooled_data/aric_v1.dta", replace
g aricid_c=id_c
replace smokstat=. if smokstat==4
label variable height "Standing height in cm"
label variable weight "Weight in Kg"
label variable waist "Waist circumference (cm)"
label variable study_dm "Study defined Diabetes"
label variable diabhx "Diabetes history: self-report or exam"
label variable id_c "Pooling study id_c"
label variable aricid_c "ARIC orginal id_c"
label variable age "Participant age (years)"
label variable gender "Participant sex"
label variable racegrp "Race group of participant"
label variable centerid "Baseline exam centerid"
label variable totchol "Total Chol (mg/dL)"
label variable ldlc "LDL chol (mg/dL)"
label variable tglefh "Triglycerid_ces LE 400"
label variable hdlc "HDL chol (mg/dL)"
label variable trigly "Triglycerid_ces (mg/dL)"
label variable cholmed1 "Chol lowering Medications"
label variable cholmed2 "Meds secondarily lower Cholesterol"
label variable sysbp "Avg systolic BP"
label variable diabp "Avg diastolic BP"
label variable hyptmdsr "High BP+meds or Self report of BP meds"
label variable hyptmdml "Coded Hypertension meds"
label variable cursmoke "Current cigarette smoking"
label variable smokstat "1 cur, 2 For, 3 Never"
label variable strtsmk "Age started smoking"
label variable stopsmk "Age stopped smoking"
label variable packyrs "Pack years of cigarette smoking"
label variable study "ARIC, CHS, FCOH, FOFF or SHS"
label variable fast08 "8 hour fast indicator"
label variable fast12 "12 hour fast indicator"
label variable glucose "Blood glucose (mg/dL)"
label variable diabt126 "Diabetes by 126 cutoff"
label variable prevmi "Prevalent MI by history or ECG"
label variable prevchd "Prevalent CHD (MI, SMI, Procedures)"
label variable prevstrk "Prevalent Stroke"
label variable exam "Clinic exam number"
label variable bmi "Body Mass Index (kg/M*M)"
label variable cigpday "Cig per day, Cur Smokers"
label variable avgsmoke "Avg cigs/day lifetime"
label variable diabtsr "Diabetes self-report"
label variable brngmeds "Brought all Meds for past 2 wks"
label variable diabmed "Meds for Diabetes past 2 wks"
label variable prevproc "Prevalent Cor Revas procedure"
label variable prevchf "Prevalent Congestive Heart Failure"
label variable prevap "Prevalent Angina (Study)"
replace hyptmdml=0 if hyptmdsr==0
replace hyptmdml=1 if hyptmdsr==1
sort id_c
save "pooled_data/aric.dta", replace
insheet using "aric/cohort_Stroke/csv/cderps10.csv", clear
sort id_c
* From data dictionary: For these reasons, all time-to-event analysis (except time to death) should be censored at last contact as defined by CENSDAT7 and in corresponding variables with the prefix C7_. Events identified after CENSDAT7, including those identified through linkage with registries, should be excluded from analysis.
* unforunately, we dont have CENSDAT7...
g upperdx = upper(finaldx)
* https://www2.cscc.unc.edu/aric/sites/default/files/public/datasets/Data%20Dictionary%20C12DERV1%20Cohort%20Surv%20Stroke%20Derived%20Variables.pdf
g defstroke = 1 if inrange(upperdx, "A", "D")
replace defstroke = 0 if defstroke != 1
collapse (max) defstroke=defstroke, by(id_c)
merge 1:1 id_c using "pooled_data/aric.dta"
drop _merge
sort id_c
save "pooled_data/aric.dta", replace
insheet using "aric/cohort_CHD/csv/cevtps10.csv", clear
sort id_c
* From data dictionary: For these reasons, all time-to-event analysis (except time to death) should be censored at last contact as defined by CENSDAT7 and in corresponding variables with the prefix C7_. Events identified after CENSDAT7, including those identified through linkage with registries, should be excluded from analysis.
* unforunately, we dont have CENSDAT7...
g defmi = 1 if cmidx=="DEFMI"
replace defmi = 0 if defmi != 1
collapse (max) defmi=defmi, by(id_c)
merge 1:1 id_c using "pooled_data/aric.dta"
drop _merge
sort id_c
save "pooled_data/aric.dta", replace
insheet using "aric/cohort_Incident/csv/ichdps10.csv", clear
sort id_c
merge 1:1 id_c using "pooled_data/aric.dta"
drop _merge
sort id_c
save "pooled_data/aric.dta", replace
* mi's/strokes/deaths
* let's try getting the mi directly from event coding, so that we can only use "definite" ones...
g mi = 1 if mi10==1
*& defmi==1
replace mi = 0 if mi!=1
g str = 1 if indp10 == 1
*& defstroke == 1
replace str = 0 if str != 1
g chddeath = fatchd10
g strdeath = .
g timetomi = fuinc10/365.25 if mi==1
g timetostr = ftdp10/365.25 if str==1
g timetochddeath = fuinc10/365.25 if chddeath==1
g timetostrdeath = .
g censored = 1 if yrdth10<2010
g timecensored = (yrdth10-enroll_yr) if censored==1
save "pooled_data/aric.dta", replace
encode id_c, gen(id)
g grp = 1 if racegrp=="B" & gender=="F"
replace grp =2 if racegrp=="W" & gender=="F"
replace grp =3 if racegrp=="B" & gender=="M"
replace grp =4 if racegrp=="W" & gender=="M"
g unrxsbp = sysbp if hyptmdsr==0
g rxsbp = sysbp if hyptmdsr==1
by grp, sort: su id age totchol hdl unrxsbp rxsbp hyptmdsr cursmo diabt126
save "pooled_data/aric.dta", replace
* CHS
/* BASELINE */
insheet using "CHS_2015a/BASELINE/basebothfinal.csv", clear
destring, replace force
g gender = "F" if gend01==0
replace gender="M" if gend01==1
drop cohort
g cohort="ORG"
g racegrp = "W" if race01==1
replace racegrp = "B" if race01==2
g id=idno
g smokstat=3 if smoke==1
replace smokstat=2 if smoke==2
replace smokstat=1 if smoke==3
g cursmoke=1 if smoke==3
replace cursmoke=0 if smoke==1 | smoke==2
g cigpday = amount if smoke==3
replace cigpday=0 if smoke==1 | smoke==2
g avgsmoke=amount
g totchol=choladj
g trigly=trig44
g hdlc=hdl44
g sercreat=cre44
g ldlc=ldladj
g glucose=glu44
g lvh=ecglvh
g age = (age2*2)+63.5
g sysbp=avzmsys
g diabp=avzmdia
g diabetes=diabada
g diab = 1 if diabetes==3 | diabetes==4
replace diab = 0 if diabetes==1 | diabetes==2
drop diabetes
g diabt126 = diab
g cholmed1=1 if sttn06==1 | lipid06==1 | mlpd06==1
replace cholmed1=0 if (sttn06==0 & lipid06==0 & mlpd06==0)
g hyptmdml=1 if htnmed06==1 | beta06==1 | betad06==1 | ccb06==1 | ace06==1 | aced06==1 | vaso06==1 | vasod06==1 | diuret06==1 | loop06==1 | hctz06==1 | hctzk06==1 | ccbir06==1 | ccbsr06==1 | alpha06==1 | alphad06==1 | ccbt06==1
replace hyptmdml=0 if htnmed06==0 & ( beta06==0 | betad06==0 | ccb06==0 | ace06==0 | aced06==0 | vaso06==0 | vasod06==0 | diuret06==0 | loop06==0 | hctz06==0 | hctzk06==0 | ccbir06==0 | ccbsr06==0 | alpha06==0 | alphad06==0 | ccbt06==0)
g hyptmdsr = hyptmdml
* g hyptmdsr = 1 if bp07==1 & hyptmdml==1
* replace hyptmdsr = 0 if bp07==0 | hyptmdml==0
g prevmi=miblmod
g prevchd=1 if prevmi==1 | bpssur==1 | corart==1
replace prevchd=0 if prevchd!=1
g prevchf=chblmod
g prevstrk=stblmod
g prevap=anblmod
g prevafib=afib
g prevproc=1 if bpssur==1 | corart==1
replace prevproc=0 if bpssur==0 & corart==0
g exam=1
save "pooled_data/chs.dta", replace
/* YEAR 5 */
import delimited "CHS_2015a/YEAR5/yr5newfinal.csv", clear
destring, replace force
g gender = "F" if gend01==0
replace gender="M" if gend01==1
g racegrp = "W" if race01==1
replace racegrp = "B" if race01==2
replace racegrp = "A" if race01==3
replace racegrp = "0" if race01==4 | race01==5
drop cohort
g cohort="NEW"
g id=idno
g totchol=choladj
g trigly=trig44
g hdlc=hdl44
g sercreat=cre44
g ldlc=ldl44
g glucose=glu44
g lvh=ecglvh
g age = (age2*2)+63.5
g sysbp=avesys
g diabp=avedia
g diabetes=diabada
g diab = 1 if diabetes==3 | diabetes==4
replace diab = 0 if diabetes==1 | diabetes==2
drop diabetes
g diabt126 = diab
g cholmed1=1 if sttn06==1 | lipid06==1 | mlpd06==1
replace cholmed1=0 if (sttn06==0 & lipid06==0 & mlpd06==0)
g hyptmdml=1 if htnmed06==1 | beta06==1 | betad06==1 | ccb06==1 | ace06==1 | aced06==1 | vaso06==1 | vasod06==1 | diuret06==1 | loop06==1 | hctz06==1 | hctzk06==1 | ccbir06==1 | ccbsr06==1 | alpha06==1 | alphad06==1 | ccbt06==1
replace hyptmdml=0 if htnmed06==0 & ( beta06==0 | betad06==0 | ccb06==0 | ace06==0 | aced06==0 | vaso06==0 | vasod06==0 | diuret06==0 | loop06==0 | hctz06==0 | hctzk06==0 | ccbir06==0 | ccbsr06==0 | alpha06==0 | alphad06==0 | ccbt06==0)
g hyptmdsr = 1 if bp57==1 & hyptmdml==1
replace hyptmdsr = 0 if bp57==0 | hyptmdml==0
g prevmi=1 if miblmod==1
replace prevmi=0 if prevmi!=1
g prevchd=1 if prevmi==1
replace prevchd=0 if prevchd!=1
g prevchf=1 if chblmod==1
replace prevchf = 0 if prevchf!=1
g prevstrk=1 if stblmod==1
replace prevstrk = 0 if prevstrk!=1
g prevap=anblmod
g prevafib=atrfib21
g prevproc=1 if corart==1
replace prevproc=0 if corart==0
g exam=5
g smokstat=3 if smoke==1
replace smokstat=2 if smoke==2
replace smokstat=1 if smoke==3
g cursmoke=1 if smoke==3
replace cursmoke=0 if smoke==1 | smoke==2
g cigpday = amount if smoke==3
replace cigpday=0 if smoke==1 | smoke==2
g avgsmoke=amount
merge 1:1 id using "pooled_data/chs.dta"
drop _merge
save "pooled_data/chs.dta", replace
insheet using "CHS_2015a/EVENTS/eventsfinal.csv", clear
encode perstat, g(perstat1)
drop perstat
rename perstat1 perstat
destring, replace force
g mi = 1 if (evtype==1 | evtype==10) & increc==1
replace mi = 0 if mi!=1
g str= 1 if evtype==3 & increc==1
replace str = 0 if str!=1
g chddeath = 1 if (evtype==11 | evtype==4 | evtype==7 | evtype==8) & fatal==1 & increc!=0
replace chddeath = 0 if chddeath!=1
g strdeath = 1 if evtype==11 & fatal==1 & defprob!=0
replace strdeath = 0 if strdeath!=1
g timetomi = ttoevent/365.25 if mi==1
g timetostr = ttoevent/365.25 if str==1
g timetochddeath = ttoevent/365.25 if chddeath==1
g timetostrdeath = .
g censored = 1 if evtype==9
g timecensored = (ttoevent/365.25) if censored==1
collapse (max) mi str chddeath strdeath censored (min) timetomi timetostr timetochddeath timetostrdeath timecensored, by(id)
sort id
merge 1:1 id using "pooled_data/chs.dta"
drop _merge
save "pooled_data/chs.dta", replace
g grp = 1 if racegrp=="B" & gender=="F"
replace grp =2 if racegrp=="W" & gender=="F"
replace grp =3 if racegrp=="B" & gender=="M"
replace grp =4 if racegrp=="W" & gender=="M"
g unrxsbp = sysbp if hyptmdsr==0
g rxsbp = sysbp if hyptmdsr==1
by grp, sort: su id age totchol hdlc unrxsbp rxsbp hyptmdsr cursmoke diabt126
save "pooled_data/chs.dta", replace
* CARDIA
*******baseline exam;
insheet using "cardia/Y00/DATA/aaf05.csv", clear
keep pid a05fstmn
sort pid
save "pooled_data/cardia.dta", replace
insheet using "cardia/Y00/DATA/aaf09med.csv", clear
keep if a09mdtyp=="HBP"
keep pid a09mdtyp a09mdnow
sort pid
merge m:1 pid using "pooled_data/cardia.dta"
drop _merge
sort pid
save "pooled_data/cardia.dta", replace
insheet using "cardia/Y00/DATA/aaf08v2.csv", clear
keep pid a08hbp a08heart a08diab a08bpmed a08preg
sort pid
merge m:m pid using "pooled_data/cardia.dta"
drop _merge
sort pid
save "pooled_data/cardia.dta", replace
insheet using "cardia/Y00/DATA/aalip.csv", clear
keep pid al1chol al1hdl al1ntrig al1ldl
sort pid
merge m:m pid using "pooled_data/cardia.dta"
drop _merge
sort pid
save "pooled_data/cardia.dta", replace
insheet using "cardia/Y00/DATA/aaf02.csv", clear
keep pid a02sbp a02dbp a02pulse
sort pid
merge m:m pid using "pooled_data/cardia.dta"
drop _merge
sort pid
save "pooled_data/cardia.dta", replace
insheet using "cardia/Y00/DATA/aaf10.csv", clear
keep pid a10cigs
sort pid
merge m:m pid using "pooled_data/cardia.dta"
drop _merge
sort pid
save "pooled_data/cardia.dta", replace
insheet using "cardia/Y00/DATA/aaf09tob.csv", clear
keep pid a09smknw a09cgtdy
sort pid
merge m:m pid using "pooled_data/cardia.dta"
drop _merge
sort pid
save "pooled_data/cardia.dta", replace
insheet using "cardia/Y00/DATA/aaref.csv", clear
keep pid race sex examage a02date a03ed
sort pid
merge m:m pid using "pooled_data/cardia.dta"
drop _merge
sort pid
save "pooled_data/cardia.dta", replace
insheet using "cardia/Y00/DATA/aaf09gen.csv", clear
keep pid a09dibst a09hrtak a09angin a09chf
sort pid
merge m:m pid using "pooled_data/cardia.dta"
drop _merge
sort pid
save "pooled_data/cardia.dta", replace
insheet using "cardia/Y00/DATA/aaf09gen.csv", clear
keep pid a09dibst a09hrtak a09angin
sort pid
merge m:m pid using "pooled_data/cardia.dta"
drop _merge
sort pid
save "pooled_data/cardia.dta", replace
insheet using "cardia/Y00/DATA/aachem.csv", clear
keep pid al3_glu al3creat al3album
sort pid
merge m:m pid using "pooled_data/cardia.dta"
drop _merge
sort pid
save "pooled_data/cardia.dta", replace
insheet using "cardia/Y00/DATA/aaf20.csv", clear
keep pid a20bmi a20wgt a20wst1
sort pid
merge m:m pid using "pooled_data/cardia.dta"
drop _merge
sort pid
save "pooled_data/cardia.dta", replace
insheet using "cardia/Y00/DATA/aains.csv", clear
keep pid al4ins
sort pid
merge m:m pid using "pooled_data/cardia.dta"
drop _merge
sort pid
save "pooled_data/cardia.dta", replace
insheet using "cardia/Y00/DATA/aains.csv", clear
keep pid al4ins
sort pid
merge m:m pid using "pooled_data/cardia.dta"
drop _merge
sort pid
save "pooled_data/cardia.dta", replace
destring, replace force
g gender="M" if sex==1
replace gender="F" if sex==2
g racegrp="B" if race==4
replace racegrp="W" if race==5
g id=int(pid/1000000)
g cardid=pid
g weight=a20wgt*0.45
g waist=a20wst1
g bmi=a20bmi
g pregnant = 1 if a08preg==2
replace pregnant = 0 if a08preg==1
g smokstat = 3 if a10cigs==1
replace smokstat = 2 if a10cigs==2 & a09smknw==1
replace smokstat = 1 if a10cigs==2 & a09smknw==2
g cursmoke =1 if smokstat==1
replace cursmoke = 0 if smokstat==2 | smokstat==3
g cigpday = a09cgtdy if cursmoke==1
replace cigpday = 0 if cursmoke==0
g hyptmdsr=. if a08bpmed==8
replace hyptmdsr=0 if a08bpmed==1
replace hyptmdsr=1 if a08bpmed==2 & a09mdnow==2
replace hyptmdsr=0 if a08bpmed==2 & a09mdnow==1
g totchol=al1chol
g trigly=al1ntrig
g hdlc=al1hdl
g ldlc=al1ldl
g tglefh=1 if al1ntrig<=400
replace tglefh=0 if tglefh!=1
g glucose=al3_glu
g sercreat=0.2159+(0.6867*al3creat)
g albumin=al3album
g fast08=0 if a05fstmn/60 <8
replace fast08=1 if a05fstmn/60 >=8
g fast12=0 if a05fstmn/60 <12
replace fast12=1 if a05fstmn/60 >=12
g age = examage
g exmdate=a02date
g sysbp=a02sbp
g diabp=a02dbp
g finsulin=al4ins
g heartrte=a02pulse*2
/* Diabetes Definitions */
**history or self report;
g diabhx=1 if (a08diab==2 & (a09dibst>=3 | a09dibst<=4))
replace diabhx=0 if (a08diab==1 | (a08diab==2 & a09dibst==5))
**status at exam;
g diabt126=1 if (glucose >=200) | (glucose>=126 & fast08>=1) | diabhx==1
replace diabt126=0 if glucose>0 & glucose<126 & (diabhx==. | diabhx==0)
replace diabt126=. if glucose>=126 & glucose<200 & fast08<=0 & diabhx==.
/* End Diabetes defintion */
* Prevalent Disease ;
g prevchd=0 if a09hrtak==1 | a08heart==1
replace prevchd=1 if a09hrtak==2
replace prevchd=. if a08heart==8
g prevap=0 if a09angin==1 | a08heart==1
replace prevap=1 if a09angin==2
replace prevap=. if a08heart==8
g prevmi=prevchd
g study="CARD"
g exam=0
save "pooled_data/cardia_yr1.dta", replace
*******year 2 exam;
g diabhx1=diabhx
g diabt1261=diabt126
g prevap1=prevap
g prevchd1=prevchd
g prevmi1=prevmi
keep pid cardid diabhx1 diabt1261 prevchd1 prevmi1 prevap1
save "pooled_data/cardia_yr2.dta", replace
insheet using "cardia/Y02/DATA/baf05.csv", clear
keep pid b05fstmn
sort pid
merge m:m pid using "pooled_data/cardia_yr2.dta"
drop _merge
sort pid
save "pooled_data/cardia_yr2.dta", replace
insheet using "cardia/Y02/DATA/baf09mhb.csv", clear
keep pid b09hbnow
drop if b09hbnow=="1"
sort pid
merge m:m pid using "pooled_data/cardia_yr2.dta"
drop _merge
sort pid
save "pooled_data/cardia_yr2.dta", replace
insheet using "cardia/Y02/DATA/baf08v2.csv", clear
keep pid b08hbp b08heart b08diab b08bpmed b08preg
sort pid
merge m:m pid using "pooled_data/cardia_yr2.dta"
drop _merge
sort pid
save "pooled_data/cardia_yr2.dta", replace
insheet using "cardia/Y02/DATA/baf02.csv", clear
keep pid b02avgsy b02avgdi b02pulse
sort pid
merge m:m pid using "pooled_data/cardia_yr2.dta"
drop _merge
sort pid
save "pooled_data/cardia_yr2.dta", replace
insheet using "cardia/Y02/DATA/baf10.csv", clear
keep pid b10cigs b10tobac
sort pid
merge m:m pid using "pooled_data/cardia_yr2.dta"
drop _merge
sort pid
save "pooled_data/cardia_yr2.dta", replace
insheet using "cardia/Y02/DATA/baf09tob.csv", clear
keep pid b09smknw b09cgtdy
sort pid
merge m:m pid using "pooled_data/cardia_yr2.dta"
drop _merge
sort pid
save "pooled_data/cardia_yr2.dta", replace
insheet using "cardia/Y02/DATA/baref.csv", clear
keep pid race sex ex2_age x2date
sort pid
merge m:m pid using "pooled_data/cardia_yr2.dta"
drop _merge
sort pid
save "pooled_data/cardia_yr2.dta", replace
insheet using "cardia/Y02/DATA/baf09dib.csv", clear
keep pid b09dibst
sort pid
merge m:m pid using "pooled_data/cardia_yr2.dta"
drop _merge
sort pid
save "pooled_data/cardia_yr2.dta", replace
insheet using "cardia/Y02/DATA/baf20.csv", clear
keep pid b20bmi b20wgt b20wst1
sort pid
merge m:m pid using "pooled_data/cardia_yr2.dta"
drop _merge
sort pid
save "pooled_data/cardia_yr2.dta", replace
destring, replace force
g idno=pid
g short_id=int(id/10000000)
replace cardid=pid
g gender="M" if sex==1
replace gender="F" if sex==2
g racegrp="B" if race==4
replace racegrp="W" if race==5
g id=int(pid/1000000)
g weight=b20wgt*0.45
g waist=b20wst1
g bmi=b20bmi
g pregnant = 1 if b08preg==2
replace pregnant = 0 if b08preg==1
g smokstat = 3 if b10cigs==1
replace smokstat = 2 if b10cigs==2 & b09smknw==1
replace smokstat = 1 if b10cigs==2 & b09smknw==2
g cursmoke =1 if smokstat==1
replace cursmoke = 0 if smokstat==2 | smokstat==3
g cigpday = b09cgtdy if cursmoke==1
replace cigpday = 0 if cursmoke==0
g hyptmdsr=. if b08bpmed==8
replace hyptmdsr=0 if b08bpmed==1
replace hyptmdsr=1 if b08bpmed==2 & b09hbnow==2
replace hyptmdsr=0 if b08bpmed==2 & b09hbnow==1
g fast08=0 if b05fstmn/60 <8
replace fast08=1 if b05fstmn/60 >=8
g fast12=0 if b05fstmn/60 <12
replace fast12=1 if b05fstmn/60 >=12
g age = ex2_age
g exmdate=x2date
g sysbp=b02avgsy
g diabp=b02avgdi
g heartrte=b02pulse*2
g diabhx=1 if diabhx1==1 | diabt1261==1
replace diabhx=0 if (diabhx1==0 | diabhx1==.) & (diabt1261==0 | diabt1261==.)
g study="CARD"
g exam=2
save "pooled_data/cardia_yr2.dta", replace
*******year 5 exam;
g diabhx2=diabhx
keep pid cardid diabhx2 diabt1261
sort pid
save "pooled_data/cardia_yr5.dta", replace
insheet using "cardia/Y05/DATA/caf05.csv", clear
keep pid c05fstmn
sort pid
merge m:m pid using "pooled_data/cardia_yr5.dta"
drop _merge
sort pid
save "pooled_data/cardia_yr5.dta", replace
insheet using "cardia/Y05/DATA/caf08.csv", clear
keep pid c08hbp c08hbnow c08diab c08chnow c08preg c08diab
sort pid
merge m:m pid using "pooled_data/cardia_yr5.dta"
drop _merge
sort pid
save "pooled_data/cardia_yr5.dta", replace
insheet using "cardia/Y05/DATA/calip.csv", clear
keep pid cl1chol cl1hdl cl1ntrig cl1ldl
sort pid
merge m:m pid using "pooled_data/cardia_yr5.dta"
drop _merge
sort pid
save "pooled_data/cardia_yr5.dta", replace
insheet using "cardia/Y05/DATA/caf02.csv", clear
keep pid c02avgsy c02avgdi c02pulse
sort pid
merge m:m pid using "pooled_data/cardia_yr5.dta"
drop _merge
sort pid
save "pooled_data/cardia_yr5.dta", replace
insheet using "cardia/Y05/DATA/caf10.csv", clear
keep pid c10cigs c10tobac
sort pid
merge m:m pid using "pooled_data/cardia_yr5.dta"
drop _merge
sort pid
save "pooled_data/cardia_yr5.dta", replace
insheet using "cardia/Y05/DATA/caf09tob.csv", clear
keep pid c09smknw c09cgtdy
sort pid
merge m:m pid using "pooled_data/cardia_yr5.dta"
drop _merge
sort pid
save "pooled_data/cardia_yr5.dta", replace
insheet using "cardia/Y05/DATA/caref.csv", clear
keep pid race sex ex3_age c02date c03ed
sort pid
merge m:m pid using "pooled_data/cardia_yr5.dta"
drop _merge
sort pid
save "pooled_data/cardia_yr5.dta", replace
insheet using "cardia/Y05/DATA/caf20.csv", clear
keep pid c20bmi c20wgt c20wst1
sort pid
merge m:m pid using "pooled_data/cardia_yr5.dta"
drop _merge
sort pid
save "pooled_data/cardia_yr5.dta", replace
insheet using "cardia/Y05/DATA/caf11.csv", clear
keep pid c11momlv c11mage c11mdth c11mhage c11dadlv c11fage c11fdth c11fhage c11bdiab c11fdiab c11mdiab c11sdiab c11bstrk c11fstrk c11mstrk c11sstrk
sort pid
merge m:m pid using "pooled_data/cardia_yr5.dta"
drop _merge
sort pid
save "pooled_data/cardia_yr5.dta", replace
destring, replace force
replace cardid=pid
g gender="M" if sex==1
replace gender="F" if sex==2
g racegrp="B" if race==4
replace racegrp="W" if race==5
g id=int(pid/1000000)
g weight=c20wgt*0.45
g waist=c20wst1
g bmi=c20bmi
g pregnant = 1 if c08preg==2
replace pregnant = 0 if c08preg==1
g smokstat = 3 if c10cigs==1
replace smokstat = 2 if c10cigs==2 & c09smknw==1
replace smokstat = 1 if c10cigs==2 & c09smknw==2
g cursmoke =1 if smokstat==1
replace cursmoke = 0 if smokstat==2 | smokstat==3
g cigpday = c09cgtdy if cursmoke==1
replace cigpday = 0 if cursmoke==0
g hyptmdsr=. if c08hbnow==8
replace hyptmdsr=0 if c08hbnow==1
replace hyptmdsr=1 if c08hbnow==2 & c08hbp==2
replace hyptmdsr=0 if c08hbnow==2 & c08hbp==1
g cholmed1=0 if c08chnow==1
replace cholmed1=1 if c08chnow==2
g fast08=0 if c05fstmn/60 <8
replace fast08=1 if c05fstmn/60 >=8
g fast12=0 if c05fstmn/60 <12
replace fast12=1 if c05fstmn/60 >=12
g age = ex3_age
g exmdate=c02date
g sysbp=c02avgsy
g diabp=c02avgdi
g heartrte=c02pulse*2
g diabhx=1 if diabhx2==1 | diabt1261==1
replace diabhx=0 if (diabhx2==0 | diabhx2==.) & (diabt1261==0 | diabt1261==.)
g study="CARD"
g exam=5
g totchol=cl1chol
g trigly=cl1ntrig
g hdlc=cl1hdl
g ldlc=cl1ldl
save "pooled_data/cardia_yr5.dta", replace
g diabhx3=diabhx
keep pid cardid diabhx3 diabt1261
save "pooled_data/cardia_yr7.dta", replace
*******year 7 exam;
insheet using "cardia/Y07/DATA/daf05a.csv", clear
keep pid d05fstmn
sort pid
merge m:m pid using "pooled_data/cardia_yr7.dta"
drop _merge
sort pid
save "pooled_data/cardia_yr7.dta", replace
insheet using "cardia/Y07/DATA/daf08.csv", clear
keep pid d08hbp d08hbnow d08diab d08chnow d08preg d08diab
sort pid
merge m:m pid using "pooled_data/cardia_yr7.dta"
drop _merge
sort pid
save "pooled_data/cardia_yr7.dta", replace
insheet using "cardia/Y07/DATA/dalip.csv", clear
keep pid dl1chol dl1hdl dl1ntrig dl1ldl
sort pid
merge m:m pid using "pooled_data/cardia_yr7.dta"
drop _merge
sort pid
save "pooled_data/cardia_yr7.dta", replace
insheet using "cardia/Y07/DATA/daf02.csv", clear
keep pid d02avgsy d02avgdi d02pulse
sort pid
merge m:m pid using "pooled_data/cardia_yr7.dta"
drop _merge
sort pid
save "pooled_data/cardia_yr7.dta", replace
insheet using "cardia/Y07/DATA/daf10.csv", clear
keep pid d10cigs d10tobac
sort pid
merge m:m pid using "pooled_data/cardia_yr7.dta"
drop _merge
sort pid
save "pooled_data/cardia_yr7.dta", replace
insheet using "cardia/Y07/DATA/daf09tob.csv", clear
keep pid d09smknw d09cgtdy
sort pid
merge m:m pid using "pooled_data/cardia_yr7.dta"
drop _merge
sort pid
save "pooled_data/cardia_yr7.dta", replace
insheet using "cardia/Y07/DATA/daref.csv", clear
keep pid race sex ex4_age d02date d03ed
sort pid
merge m:m pid using "pooled_data/cardia_yr7.dta"
drop _merge
sort pid
save "pooled_data/cardia_yr7.dta", replace
insheet using "cardia/Y07/DATA/daglu.csv", clear
keep pid dl7glu
sort pid