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pr_cvd_female_raw_bmirep_qrisk2.do

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+*use a dataset including 
+cap prog drop cvd_female_raw_qrisk2
+program define cvd_female_raw_qrisk2
+
+noi di "Variables you need:"
+noi di "age -- age as integer"
+noi di	"b_AF -- atrial fibrilation as binary 01"
+noi di "b_ra -- rheumatoid arthritis as binary 01"
+noi di "b_renal -- rename disease as binary 01"
+noi di "b_treatedhyp -- hypertension treatment as binary 01"
+noi di "b_type1 -- type 1 diabetes as binary 01"
+noi di "b_type2 -- type 2 diabetes as binary 01"
+noi di "bmi -- bmi as continuous numeric, replaced with 20 if below 20"
+noi di "ethrisk -- ethnicity as categorical integer (0-9)"
+noi di "fh_cvd -- family history as binary 01"
+noi di "rati -- HDL LDL cholesterol ratio as continuous numeric"
+noi di "sbp -- systolic blood pressure as continuous numeric"
+noi di "smoke_cat -- smoking as integer category (0-4)"
+noi di "sex  -- sex as 1=male 2=female"
+
+
+
+cap gen score=.
+gen double rec_num = _n
+preserve
+
+keep if sex==2
+*replace bmi=20 if bmi<20
+
+
+local surv=10
+forvalues i = 0/15 {
+	gen survivor`i'=0
+}
+replace survivor10=0.989747583866119
+*this part is added in incase they want to do risk scores over a different number of years but they haven't actually done the groundwork yet.
+
+gen Iethrisk0 = 0
+gen Iethrisk1 = 0 /*5*/
+gen Iethrisk2 = 0.2574099349831925900000000 /*3*/
+gen Iethrisk3 = 0.6129795430571779400000000 /*1*/
+gen Iethrisk4 = 0.3362159841669621300000000 /*2*/
+gen Iethrisk5 = 0.1512517303224336400000000 /*4*/
+gen Iethrisk6 = -0.1794156259657768100000000 /*7*/
+gen Iethrisk7 = -0.3503423610057745400000000 /*9*/
+gen Iethrisk8 = -0.2778372483233216800000000 /*8*/
+gen Iethrisk9 = -0.1592734122665366000000000 /*6*/
+
+gen Ismoke0=0
+gen Ismoke1=0.2119377108760385200000000
+gen Ismoke2=0.6618634379685941500000000
+gen Ismoke3=0.7570714587132305600000000
+gen Ismoke4=0.9496298251457036000000000
+
+gen double dage = age
+replace dage=dage/10
+gen double age_2 = dage
+gen double age_1 = dage^0.5
+gen double dbmi = bmi
+replace dbmi=dbmi/10
+gen double bmi_2 = ln(dbmi)*dbmi^(-2)
+gen double bmi_1 = dbmi^(-2)
+
+replace age_1 = age_1 - 2.086397409439087
+replace age_2 = age_2 - 4.353054523468018
+replace bmi_1 = bmi_1 - 0.152244374155998
+replace bmi_2 = bmi_2 - 0.143282383680344
+replace rati = rati - 3.506655454635620
+replace sbp = sbp - 125.040039062500000
+replace town = town - 0.416743695735931
+
+gen double a=0
+
+
+
+
+
+
+/* The conditional sums */
+forvalues i=1/9 {
+replace a = a+ Iethrisk`i' if ethrisk==`i'
+} 
+forvalues i=0/4{
+replace a = a+ Ismoke`i' if smoke_cat==`i' 
+}
+
+	/* Sum from continuous values */
+
+
+ replace a = a+ age_1 * 4.4417863976316578000000000 
+ replace a = a+ age_2 * 0.0281637210672999180000000 
+ replace a = a+ bmi_1 * 0.8942365304710663300000000 
+ replace a = a+ bmi_2 * -6.5748047596104335000000000 
+ replace a = a+ rati * 0.1433900561621420900000000 
+ replace a = a+ sbp * 0.0128971795843613720000000 
+ replace a = a+ town * 0.0664772630011438850000000 
+
+
+
+	/* Sum from boolean values */
+
+ replace a = a+ b_AF * 1.6284780236484424000000000 
+ replace a = a+ b_ra * 0.2901233104088770700000000 
+ replace a = a+ b_renal * 1.0043796680368302000000000 
+ replace a = a+ b_treatedhyp * 0.6180430562788129500000000 
+ replace a = a+ b_type1 * 1.8400348250874599000000000 
+ replace a = a+ b_type2 * 1.1711626412196512000000000 
+ replace a = a+ fh_cvd * 0.5147261203665195500000000 
+
+	/* Sum from interaction terms */
+
+ replace a = a+ age_1 * 1 * 0.7464406144391666500000000 if smoke_cat==1 
+ replace a = a+ age_1 * 1 * 0.2568541711879666600000000 if smoke_cat==2
+ replace a = a+ age_1 * 1 * -1.5452226707866523000000000 if smoke_cat==3
+ replace a = a+ age_1 * 1 * -1.7113013709043405000000000 if smoke_cat==4
+ replace a = a+ age_1 * b_AF * -7.0177986441269269000000000 
+ replace a = a+ age_1 * b_renal * -2.9684019256454390000000000 
+ replace a = a+ age_1 * b_treatedhyp * -4.2219906452967848000000000 
+ replace a = a+ age_1 * b_type1 * 1.6835769546040080000000000 
+ replace a = a+ age_1 * b_type2 * -2.9371798540034648000000000 
+ replace a = a+ age_1 * bmi_1 * 0.1797196207044682300000000 
+ replace a = a+ age_1 * bmi_2 * 40.2428166760658140000000000 
+ replace a = a+ age_1 * fh_cvd * 0.1439979240753906700000000 
+ replace a = a+ age_1 * sbp * -0.0362575233899774460000000 
+ replace a = a+ age_1 * town * 0.3735138031433442600000000 
+ replace a = a+ age_2 * 1 * -0.1927057741748231000000000 if smoke_cat==1
+ replace a = a+ age_2 * 1 * -0.1526965063458932700000000 if smoke_cat==2
+ replace a = a+ age_2 * 1 * 0.2313563976521429400000000 if smoke_cat==3
+ replace a = a+ age_2 * 1 * 0.2307165013868296700000000 if smoke_cat==4
+ replace a = a+ age_2 * b_AF * 1.1395776028337732000000000 
+ replace a = a+ age_2 * b_renal * 0.4356963208330940600000000 
+ replace a = a+ age_2 * b_treatedhyp * 0.7265947108887239600000000 
+ replace a = a+ age_2 * b_type1 * -0.6320977766275653900000000 
+ replace a = a+ age_2 * b_type2 * 0.4023270434871086800000000 
+ replace a = a+ age_2 * bmi_1 * 0.1319276622711877700000000 
+ replace a = a+ age_2 * bmi_2 * -7.3211322435546409000000000 
+ replace a = a+ age_2 * fh_cvd * -0.1330260018273720400000000 
+ replace a = a+ age_2 * sbp * 0.0045842850495397955000000 
+ replace a = a+ age_2 * town * -0.0952370300845990780000000 
+
+
+ gen double scoref = exp(a)
+ replace scoref=survivor`surv'^scoref
+ replace  scoref = 1-scoref
+ replace  scoref=100*scoref
+ *gen double scoref = 100.0 * (1 - survivor`surv'^(exp(a)))
+
+keep scoref patid rec_num
+
+tempfile temper
+save `temper' , replace
+restore
+merge 1:1 patid rec_num using `temper' , nogen
+drop rec_num
+
+replace score=scoref if scoref!=.
+drop scoref
+
+end
+
+
+
+
+
+
+
+
+
+
+
+
+

pr_cvd_female_raw_bmirep_qrisk3.do

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+*use a dataset including 
+cap prog drop cvd_female_raw_qrisk3
+program define cvd_female_raw_qrisk3
+
+noi di "Variables you need:"
+noi di "age -- age as integer"
+noi di	"b_AF -- atrial fibrilation as binary 01"
+noi di "b_ra -- rheumatoid arthritis as binary 01"
+noi di "b_renal -- rename disease as binary 01"
+noi di "b_treatedhyp -- hypertension treatment as binary 01"
+noi di "b_type1 -- type 1 diabetes as binary 01"
+noi di "b_type2 -- type 2 diabetes as binary 01"
+noi di "bmi -- bmi as continuous numeric, replaced with 20 if below 20"
+noi di "ethrisk -- ethnicity as categorical integer (0-9)"
+noi di "fh_cvd -- family history as binary 01"
+noi di "rati -- HDL LDL cholesterol ratio as continuous numeric"
+noi di "sbp -- systolic blood pressure as continuous numeric"
+noi di "smoke_cat -- smoking as integer category (0-4)"
+noi di "sex  -- sex as 1=male 2=female"
+
+noi di "b_atypicalantipsy -- atypical antipsychotic prescribing as binary 01"
+noi di "b_semi - severe mental illness as binary 01"
+noi di "sbp_s5 - systolic blood pressure variability as continuous numeric"
+noi di "b_impotence2 - erectile dysfunction as binary 01"
+noi di "b_sle - systemic lupus erythematosus as binary 01"
+noi di "b_corticosteroids - corticosteroid prescribing as binary 01"
+
+
+cap gen score=.
+gen double rec_num = _n
+preserve
+
+keep if sex==2
+*replace bmi=20 if bmi<20
+
+
+local surv=10
+forvalues i = 0/15 { 
+	gen survivor`i'=0
+}
+replace survivor10=0.988876402378082
+*this part is added in incase they want to do risk scores over a different number of years but they haven't actually done the groundwork yet.
+
+gen Iethrisk0 = 0
+gen Iethrisk1 = 0
+gen Iethrisk2 = 0.2804031433299542500000000
+gen Iethrisk3 = 0.5629899414207539800000000
+gen Iethrisk4 = 0.2959000085111651600000000
+gen Iethrisk5 = 0.0727853798779825450000000
+gen Iethrisk6 = -0.1707213550885731700000000
+gen Iethrisk7 = -0.3937104331487497100000000
+gen Iethrisk8 = -0.3263249528353027200000000 
+gen Iethrisk9 = -0.1712705688324178400000000
+
+gen Ismoke0=0
+gen Ismoke1=0.1338683378654626200000000
+gen Ismoke2=0.5620085801243853700000000
+gen Ismoke3=0.6674959337750254700000000
+gen Ismoke4=0.8494817764483084700000000
+
+gen double dage = age
+replace dage=dage/10
+gen double age_1 = dage^(-2)
+gen double age_2 = dage
+gen double dbmi = bmi
+replace dbmi=dbmi/10
+gen double bmi_1 = dbmi^(-2)
+gen double bmi_2 = ln(dbmi)*dbmi^(-2)
+
+replace age_1 = age_1 - 0.053274843841791
+replace age_2 = age_2 - 4.332503318786621
+replace bmi_1 = bmi_1 - 0.154946178197861
+replace bmi_2 = bmi_2 - 0.144462317228317
+replace rati = rati - 3.476326465606690
+replace sbp = sbp - 123.130012512207030
+replace sbps5 = sbps5 - 9.002537727355957
+replace town = town - 0.392308831214905
+
+/* Start of Sum */
+gen double a=0
+
+
+/* The conditional sums */
+forvalues i=1/9 {
+replace a = a+ Iethrisk`i' if ethrisk==`i'
+} 
+forvalues i=0/4{
+replace a = a+ Ismoke`i' if smoke_cat==`i' 
+}
+
+	/* Sum from continuous values */
+
+
+ replace a = a+ age_1 * -8.1388109247726188000000000 
+ replace a = a+ age_2 * 0.7973337668969909800000000 
+ replace a = a+ bmi_1 * 0.2923609227546005200000000 
+ replace a = a+ bmi_2 * -4.1513300213837665000000000 
+ replace a = a+ rati * 0.1533803582080255400000000 
+ replace a = a+ sbp * 0.0131314884071034240000000
+ replace a = a+ sbps5 * 0.0078894541014586095000000 if sbps5 != .
+ replace a = a+ town * 0.0772237905885901080000000 
+
+
+
+	/* Sum from boolean values */
+
+ replace a = a+ b_AF * 1.5923354969269663000000000
+ replace a = a+ b_atypicalantipsy * 0.2523764207011555700000000
+ replace a = a+ b_corticosteroids * 0.5952072530460185100000000
+ replace a = a+ b_migraine * 0.3012672608703450000000000
+ replace a = a+ b_ra * 0.2136480343518194200000000 
+ replace a = a+ b_renal * 0.6519456949384583300000000
+ replace a = a+ b_semi * 0.1255530805882017800000000
+ replace a = a+ b_sle * 0.7588093865426769300000000
+ replace a = a+ b_treatedhyp * 0.5093159368342300400000000 
+ replace a = a+ b_type1 * 1.7267977510537347000000000 
+ replace a = a+ b_type2 * 1.0688773244615468000000000 
+ replace a = a+ fh_cvd * 0.4544531902089621300000000 
+
+	/* Sum from interaction terms */
+
+ replace a = a+ age_1 * -4.7057161785851891000000000 if smoke_cat==1 
+ replace a = a+ age_1 * -2.7430383403573337000000000 if smoke_cat==2
+ replace a = a+ age_1 * -0.8660808882939218200000000 if smoke_cat==3
+ replace a = a+ age_1 * 0.9024156236971064800000000 if smoke_cat==4
+ replace a = a+ age_1 * b_AF * 19.9380348895465610000000000
+ replace a = a+ age_1 * b_corticosteroids * -0.9840804523593628100000000
+ replace a = a+ age_1 * b_migraine * 1.7634979587872999000000000
+ replace a = a+ age_1 * b_renal * -3.5874047731694114000000000
+ replace a = a+ age_1 * b_sle * 19.6903037386382920000000000
+ replace a = a+ age_1 * b_treatedhyp * 11.8728097339218120000000000 
+ replace a = a+ age_1 * b_type1 * -1.2444332714320747000000000 
+ replace a = a+ age_1 * b_type2 * 6.8652342000009599000000000 
+ replace a = a+ age_1 * bmi_1 * 23.8026234121417420000000000 
+ replace a = a+ age_1 * bmi_2 * -71.1849476920870070000000000 
+ replace a = a+ age_1 * fh_cvd * 0.9946780794043512700000000 
+ replace a = a+ age_1 * sbp * 0.0341318423386154850000000 
+ replace a = a+ age_1 * town * -1.0301180802035639000000000 
+ replace a = a+ age_2 * -0.0755892446431930260000000 if smoke_cat==1
+ replace a = a+ age_2 * -0.1195119287486707400000000 if smoke_cat==2
+ replace a = a+ age_2 * -0.1036630639757192300000000 if smoke_cat==3
+ replace a = a+ age_2 * -0.1399185359171838900000000 if smoke_cat==4
+ replace a = a+ age_2 * b_AF * -0.0761826510111625050000000
+ replace a = a+ age_2 * b_corticosteroids * -0.1200536494674247200000000
+ replace a = a+ age_2 * b_migraine * -0.0655869178986998590000000
+ replace a = a+ age_2 * b_renal * -0.2268887308644250700000000
+ replace a = a+ age_2 * b_sle * 0.0773479496790162730000000
+ replace a = a+ age_2 * b_treatedhyp * 0.0009685782358817443600000 
+ replace a = a+ age_2 * b_type1 * -0.2872406462448894900000000 
+ replace a = a+ age_2 * b_type2 * -0.0971122525906954890000000 
+ replace a = a+ age_2 * bmi_1 * 0.5236995893366442900000000 
+ replace a = a+ age_2 * bmi_2 * 0.0457441901223237590000000 
+ replace a = a+ age_2 * fh_cvd * -0.0768850516984230380000000 
+ replace a = a+ age_2 * sbp * -0.0015082501423272358000000 
+ replace a = a+ age_2 * town * -0.0315934146749623290000000 
+
+
+ gen double scoref = exp(a)
+ replace scoref=survivor`surv'^scoref
+ replace  scoref = 1-scoref
+ replace  scoref=100*scoref
+ *gen double scoref = 100.0 * (1 - survivor`surv'^(exp(a)))
+
+keep scoref patid rec_num
+
+tempfile temper
+save `temper' , replace
+restore
+merge 1:1 patid rec_num using `temper' , nogen
+drop rec_num
+
+replace score=scoref if scoref!=.
+drop scoref
+
+end
+
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