*Code for point estimates for the burden of GBS in pregnant women, stillbirths and infants ***control directory for data files insert cd "" set more off *bring in file of regions, live and stillbirths for 2015 use GBSest_input_data.dta, clear *add in components fo the model *generate inputs for maternal cols gen matcol=. replace matcol=0.184 if UNSUBREGI=="South America" replace matcol=0.171 if UNSUBREGI=="Central America" replace matcol=0.347 if UNSUBREGI=="Caribbean" replace matcol=0.147 if UNSUBREGI=="Western Asia" replace matcol=0.125 if UNSUBREGI=="Southern Asia" replace matcol=0.144 if UNSUBREGI=="South-eastern Asia" replace matcol=0.111 if UNSUBREGI=="Eastern Asia" *for Oceania use Asia replace matcol=0.128 if UNSUBREGI=="Oceania" *Use Asia for Central Asia replace matcol=0.128 if UNSUBREGI=="Central Asia" replace matcol=0.229 if UNSUBREGI=="Northern Africa" replace matcol=0.175 if UNSUBREGI=="Western Africa" replace matcol=0.194 if UNSUBREGI=="Eastern Africa" replace matcol=0.289 if UNSUBREGI=="Southern Africa" replace matcol=0.239 if UNSUBREGI=="Middle Africa" replace matcol=0.192 if UNSUBREGI=="Developed countries" **for those with country data replace matcol=0.179 if un_iso=="centamMEX" replace matcol=0.238 if un_iso=="devAUS" replace matcol=0.146 if un_iso=="devAUT" replace matcol=0.205 if un_iso=="devCAN" replace matcol=0.187 if un_iso=="devCHE" replace matcol=0.184 if un_iso=="devDEU" replace matcol=0.155 if un_iso=="devESP" replace matcol=0.156 if un_iso=="devFRA" replace matcol=0.228 if un_iso=="devGBR" replace matcol=0.134 if un_iso=="devGRC" replace matcol=0.232 if un_iso=="devITA" replace matcol=0.162 if un_iso=="devJPN" replace matcol=0.214 if un_iso=="devNLD" replace matcol=0.261 if un_iso=="devNOR" replace matcol=0.231 if un_iso=="devPOL" replace matcol=0.202 if un_iso=="devSVN" replace matcol=0.227 if un_iso=="devSWE" replace matcol=0.247 if un_iso=="devUSA" *east africa replace matcol=0.135 if un_iso=="eastafETH" replace matcol=0.115 if un_iso=="eastafKEN" replace matcol=0.212 if un_iso=="eastafMWI" replace matcol=0.346 if un_iso=="eastafZWB" *east asia replace matcol=0.083 if un_iso=="eastasiaPRK" replace matcol=0.113 if un_iso=="eastasiaCHN" *se asia replace matcol=0.157 if un_iso=="seasiaTHA" *southern africa replace matcol=0.289 if un_iso=="souafZAF" *south america replace matcol=0.064 if un_iso=="souamARG" replace matcol=0.208 if un_iso=="souamBRA" replace matcol=0.141 if un_iso=="souamCHL" *south asia replace matcol=0.096 if un_iso=="souasIND" replace matcol=0.157 if un_iso=="souasIRN" replace matcol=0.112 if un_iso=="souasBGD" *west af replace matcol=0.145 if un_iso=="westafNGA" *west asia replace matcol=0.158 if un_iso=="westasARE" replace matcol=0.121 if un_iso=="westasISR" replace matcol=0.148 if un_iso=="westasKWT" replace matcol=0.262 if un_iso=="westasLBN" replace matcol=0.221 if un_iso=="westasSAU" replace matcol=0.105 if un_iso=="westasTUR" **** add in risk gen IAPgroup=1 replace IAPgroup=4 if UNSUBREGI=="Developed countries" replace IAPgroup=4 if un_iso=="caribGRD" replace IAPgroup=2 if un_iso=="centamerBLZ" replace IAPgroup=4 if un_iso=="centamerMEX" replace IAPgroup=3 if un_iso=="devFIN" replace IAPgroup=3 if un_iso=="devDNK" replace IAPgroup=3 if un_iso=="devGBR" replace IAPgroup=1 if un_iso=="devHRV" replace IAPgroup=1 if un_iso=="devIRL" replace IAPgroup=3 if un_iso=="devISL" replace IAPgroup=3 if un_iso=="devNLD" replace IAPgroup=3 if un_iso=="devNOR" replace IAPgroup=3 if un_iso=="devNZL" replace IAPgroup=1 if un_iso=="devUKR" replace IAPgroup=3 if un_iso=="eastafMUS" replace IAPgroup=3 if un_iso=="eastasiaKOR" replace IAPgroup=4 if un_iso=="seasiaSGP" replace IAPgroup=4 if un_iso=="souamARG" replace IAPgroup=4 if un_iso=="souamBRA" replace IAPgroup=4 if un_iso=="souamCHL" replace IAPgroup=2 if un_iso=="souasIRN" replace IAPgroup=2 if un_iso=="westasJOR" replace IAPgroup=2 if un_iso=="westasOMN" gen IAPrisk=. replace IAPrisk=0.011 if IAPgroup==1 replace IAPrisk=0.0094 if IAPgroup==2 replace IAPrisk=0.00788 if IAPgroup==3 replace IAPrisk=0.0032 if IAPgroup==4 *add in high IAP coverage for clinical risk factors gen IAPhighall=0.0032 gen IAPnoneall=0.011 gen IAPmedall=0.00788 gen IAPclinall=0.00788 *replace IAPclinall=0.0094 if IAPgroup==2 replace IAPclinall=0.0032 if IAPgroup==4 ****LOD rati gen lodratio=. replace lodratio=1.82 if super_region=="Developed countries" replace lodratio=1.90 if super_region=="Latin_America" replace lodratio=5.599 if super_region=="Asia" replace lodratio=1.02 if super_region=="Africa" replace lodratio=5.599 if super_region=="Oceania" gsort un_iso save point1a.dta, replace ****bring in facility delivery clear import excel "skilled_birth_attendance.xls", firstrow keep iso3 sab gsort iso3 gen skillbirth=sab/100 gen homebirth=1-sab/100 drop sab merge 1:1 iso3 using point1a.dta keep if _merge==3 save point1b.dta, replace ****add in CFRs gen deathhome=0.9 replace deathhome=0 if super_region=="Developed countries" gen deathearly=0.05 if super_region=="Developed countries" replace deathearly=0.14 if super_region=="Asia" replace deathearly=0.17 if super_region=="Latin_America" replace deathearly=0.27 if super_region=="Africa" replace deathearly=0.14 if super_region=="Oceania" gen deathlate=0.04 if super_region=="Developed countries" replace deathlate=0.05 if super_region=="Asia" replace deathlate=0.06 if super_region=="Latin_America" replace deathlate=0.12 if super_region=="Africa" replace deathlate=0.05 if super_region=="Oceania" **meningitis cases gen earmen=0.12 gen latmen=0.42 *impairment gen imp=0.18 *triangulation for neonatal disease incidence (early) gen eoninc=. replace eoninc=0.00147 if UNSUBREGI=="Caribbean" replace eoninc=0.00077 if UNSUBREGI=="Central America" replace eoninc=0.00037 if UNSUBREGI=="Developed countries" replace eoninc=0.00034 if UNSUBREGI=="South America" replace eoninc=0.00024 if UNSUBREGI=="South-eastern Asia" replace eoninc=0.00106 if UNSUBREGI=="Southern Africa" replace eoninc=0.00020 if UNSUBREGI=="Southern Asia" replace eoninc=0.00025 if UNSUBREGI=="Western Africa" replace eoninc=0.00046 if UNSUBREGI=="Eastern Africa" replace eoninc=0.00058 if UNSUBREGI=="Western Asia" replace eoninc=0.00098 if UNSUBREGI=="Northern Africa" replace eoninc=0.00025 if UNSUBREGI=="Eastern Asia" *use Asia replace eoninc=0.00032 if UNSUBREGI=="Oceania" *use asia replace eoninc=0.00032 if UNSUBREGI=="Central Asia" *use africa replace eoninc=0.00071 if UNSUBREGI=="Middle Africa" *triangulation for neonatal disease incidence (late) gen loninc=. replace loninc=0.00019 if UNSUBREGI=="Caribbean" replace loninc=0.00058 if UNSUBREGI=="Central America" replace loninc=0.00018 if UNSUBREGI=="Developed countries" *use latin america replace loninc=0.00022 if UNSUBREGI=="South America" replace loninc=0.00003 if UNSUBREGI=="South-eastern Asia" replace loninc=0.00093 if UNSUBREGI=="Southern Africa" replace loninc=0.00003 if UNSUBREGI=="Southern Asia" replace loninc=0.00055 if UNSUBREGI=="Eastern Africa" replace loninc=0.00038 if UNSUBREGI=="Eastern Asia" *use Africa replace loninc=0.00065 if UNSUBREGI=="Western Africa" *use asia replace loninc=0.00004 if UNSUBREGI=="Western Asia" replace loninc=0.00004 if UNSUBREGI=="Oceania" *use africa replace loninc=0.00065 if UNSUBREGI=="Northern Africa" *use asia replace loninc=0.00004 if UNSUBREGI=="Central Asia" *use africa replace loninc=0.00065 if UNSUBREGI=="Middle Africa" *pregnancy gen gbspreg=0.00023 *stillbirth gen gbsstill=0.010 replace gbsstill=0.037 if super_regio=="Africa" *ne gen ne=0.0058 replace ne=0.00510 if UNSUBREGI=="Developed countries" drop _merge order super_reg UNSUBREG un_iso iso3 tot_births lbirths sbirths save gbs_data_inputs.dta, replace ******calculations use gbs_data_inputs.dta, clear *mothers exposed with live births gen no_exposed=lbirths*matcol *mothers exposed with live and stillbirths gen no_exposedtot=tot_births*matcol *infants estimated with early onset disease gen no_eod=IAPrisk*no_exposed *scenarios gen no_IAPall=IAPhighall*no_exposed gen no_IAPnone=IAPnoneall*no_exposed gen no_IAPmed=IAPmedall*no_exposed gen no_IAPclin=IAPclinall*no_exposed *deaths gen no_lod=(1/lodratio)*no_eod gen no_hdeath=deathhome*(no_eod*homebirth) gen no_fedeath=deathearly*(no_eod*skillbirth) gen no_fldeath=deathlate*no_lod gen no_IAPalldeath=deathearly*no_IAPall gen no_IAPmeddeath=deathearly*no_IAPmed gen no_IAPnonehdeath=deathhome*(no_IAPnone*homebirth) gen no_IAPnonefdeath=deathearly*(no_IAPnone*skillbirth) gen no_IAPclinhdeath=deathhome*(no_IAPclin*homebirth) gen no_IAPclinfdeath=deathearly*(no_IAPclin*skillbirth) gen no_IAPclindeath=no_IAPclinhdeath+no_IAPclinfdeath *impairment gen surv_early=no_eod-no_hdeath-no_fedeath gen surv_late=no_lod-no_fldeath gen mensurvearly=surv_early*earmen gen mensurvelate=surv_late*latmen gen impearmen=mensurvearly*imp gen implatemen=mensurvelate*imp gen totimp=impearmen+implatemen *triangulation gen no_eoninc=lbirths*eoninc gen no_loninc=lbirths*loninc *single cause estimates gen nopreggbs=tot_births*gbspreg gen nigbsstill=sbirth*gbsstill gen no_ne=ne2015*ne gen nonegbs=no_ne*ne *infant cases totals gen tot_infantca=no_eod + no_lod *infant death totals gen tot_infant_death=no_hdeath+no_fedeath+no_fldeath save pointest2a.dta, replace *compartmental data inputs use pointest2a.dta, clear keep super_region UNSUBREGIO1 un_iso country lbirths ne2015 sbirths skillbirth matcol IAPrisk lodratio deathearly deathhome deathlate earmen latmen imp order super_region UNSUBREGIO1 un_iso country lbirths sbirths matcol IAPrisk lodratio skillbirth deathhome deathearly deathlate earmen latmen imp gsort super_region un_iso save datainputsgbs.dta, replace *single cause data inputs use pointest2a.dta, clear keep super_region UNSUBREGIO1 un_iso country lbirths sbirths eoninc loninc gbspreg gbsstill ne2015 ne order super_region UNSUBREGIO1 un_iso country lbirths sbirths eoninc loninc gbspreg gbsstill ne gsort super_region un_iso save datainputsgbs_singlecause.dta, replace *compartmental outputs use pointest2a.dta, clear keep super_region UNSUBREGIO1 un_iso country lbirths sbirths no_exposed no_eod no_lod no_hdeath no_fedeath no_fldeath surv_early surv_late mensurvearly mensurvelate impearmen implatemen totimp tot_infantca tot_infant_dea order super_region UNSUBREGIO1 un_iso country lbirths sbirths no_exposed no_eod no_lod no_hdeath no_fedeath no_fldeath surv_early surv_late mensurvearly mensurvelate impearmen implatemen totimp tot_infantca tot_infant_dea gsort un_iso save dataoutputgbscompart.dta, replace *leading countries use dataoutputgbscompart.dta, clear gsort -tot_infantca use dataoutputgbscompart.dta, clear gsort -tot_infant_death *single cause outputs use pointest2a.dta, clear keep super_region UNSUBREGIO1 un_iso country lbirths sbirths no_eoninc no_loninc nopreggbs nigbsstill no_ne no_exposedtot order super_region UNSUBREGIO1 un_iso country lbirths sbirths no_eoninc no_loninc nopreggbs nigbsstill no_ne no_exposedtot gsort un_iso save dataoutputsgbssingcause.dta, replace *summaries of data use pointest2a.dta, clear gsort un_iso egen sumtotexp = sum(no_exposedtot), by(UNSUBRE) egen sumexp = sum(no_exposed), by(UNSUBRE) egen sumeogbs=sum(no_eod), by(UNSUBRE) egen sumlogbs=sum(no_lod), by(UNSUBRE) egen sumhdeath=sum(no_hdeath), by(UNSUBRE) egen sumfedeath=sum(no_fedeath), by(UNSUBRE) egen sumfldeath=sum(no_fldeath), by(UNSUBRE) egen sumimp = sum(totimp), by(UNSUBRE) egen sumeoinc = sum(no_eoninc), by(UNSUBRE) egen sumloinc = sum(no_loninc), by(UNSUBRE) egen sumne2015 = sum(ne2015), by(UNSUBRE) egen sumno_ne = sum(no_ne), by(UNSUBRE) egen sumno_IAPhigh=sum(no_IAPall), by(UNSUBRE) egen sumno_IAPclin=sum(no_IAPclin), by(UNSUBRE) egen sumno_IAPclindeath=sum(no_IAPclindeath), by(UNSUBRE) egen sumno_IAPnone=sum(no_IAPnone), by(UNSUBRE) egen sumno_IAPmed=sum(no_IAPmed), by(UNSUBRE) egen sumno_IAPalldeath=sum(no_IAPalldeath), by(UNSUBRE) egen sumno_IAPnonehdeath=sum(no_IAPnonehdeath), by(UNSUBRE) egen sumno_IAPnonefdeath=sum(no_IAPnonefdeath), by(UNSUBRE) egen sumno_IAPmeddeath=sum(no_IAPmeddeath), by(UNSUBRE) duplicates drop UNSUB, force save subregional_pointest.dta, replace use subregional_pointest.dta, clear list sumtotexp UNSUB list sumexp UNSUB list sumeogbs UNSUBR list sumlogbs UNSUBR list sumhdeath UNSUBR list sumfedeath UNSUBR list sumfldeath UNSUBR list sumimp UNSUBR list sumeoinc UNSUBR list sumloinc UNSUBR list sumno_ne UNSUBR list sumne2015 UNSUBR list sumno_IAPhigh UNSUBR list sumno_IAPnone UNSUBR list sumno_IAPalldeath UNSUBR list sumno_IAPnonehdeath UNSUBR list sumno_IAPnonefdeath UNSUBR list sumno_IAPmeddeath UNSUBR list sumno_IAPmed UNSUBR list sumno_IAPclin UNSUBR list sumno_IAPclindeath UNSUBR *******preterm birth estimates********************************* *ranges of possible numbers of preterm birth associated with maternal GBS colonization based on risk ratio range from 0-2.8 *indicate working directory for files cd "" set more off use GBSest_preterm_input_data.dta, replace gen matgbs=0.2 replace matgbs=0.347 if UNSUBREGIO1=="Carib" replace matgbs=0.171 if UNSUBREGIO1=="Central America" replace matgbs=0.145 if UNSUBREGIO1=="Central Asia" replace matgbs=0.22 if UNSUBREGIO1=="Developed countries" replace matgbs=0.194 if UNSUBREGIO1=="Eastern Africa" replace matgbs=0.194 if UNSUBREGIO1=="Middle Africa" replace matgbs=0.229 if UNSUBREGIO1=="Northern Africa" replace matgbs=0.144 if UNSUBREGIO1=="Oceania" replace matgbs=0.184 if UNSUBREGIO1=="South America" replace matgbs=0.144 if UNSUBREGIO1=="South-eastern Asia" replace matgbs=0.289 if UNSUBREGIO1=="Southern Africa" replace matgbs=0.125 if UNSUBREGIO1=="Southern Asia" replace matgbs=0.175 if UNSUBREGIO1=="Western Africa" replace matgbs=0.147 if UNSUBREGIO1=="Western Asia" * for RR=1.1, 1.6 gen RRa=1.0 gen RRb=1.2 gen RRc=1.4 gen RRd=1.6 gen RRe=1.8 gen RRf=2.0 gen RRg=2.2 gen RRh=2.4 gen RRi=2.6 gen RRj=2.8 gen PARa=(matgbs*(RRa-1))/(1+matgbs*(RRa-1)) gen PARb=(matgbs*(RRb-1))/(1+matgbs*(RRb-1)) gen PARc=(matgbs*(RRc-1))/(1+matgbs*(RRc-1)) gen PARd=(matgbs*(RRd-1))/(1+matgbs*(RRd-1)) gen PARe=(matgbs*(RRe-1))/(1+matgbs*(RRe-1)) gen PARf=(matgbs*(RRf-1))/(1+matgbs*(RRf-1)) gen PARg=(matgbs*(RRg-1))/(1+matgbs*(RRg-1)) gen PARh=(matgbs*(RRh-1))/(1+matgbs*(RRh-1)) gen PARi=(matgbs*(RRi-1))/(1+matgbs*(RRi-1)) gen PARj=(matgbs*(RRj-1))/(1+matgbs*(RRj-1)) gen preva=PARa*pretermno gen prevb=PARb*pretermno gen prevc=PARc*pretermno gen prevd=PARd*pretermno gen preve=PARe*pretermno gen prevf=PARf*pretermno gen prevg=PARg*pretermno gen prevh=PARh*pretermno gen previ=PARi*pretermno gen prevj=PARj*pretermno egen totalprem=total(pretermno) egen totalpreva=total(preva) egen totalprevb=total(prevb) egen totalprevc=total(prevc) egen totalprevd=total(prevd) egen totalpreve=total(preve) egen totalprevf=total(prevf) egen totalprevg=total(prevg) egen totalprevh=total(prevh) egen totalprevi=total(previ) egen totalprevj=total(prevj) egen regionpreva = total(preva), by(UNSUBREGIO1) egen regionprevb = total(prevb), by(UNSUBREGIO1) egen regionprevc = total(prevc), by(UNSUBREGIO1) egen regionprevd = total(prevd), by(UNSUBREGIO1) egen regionpreve = total(preve), by(UNSUBREGIO1) egen regionprevf = total(prevf), by(UNSUBREGIO1) egen regionprevg = total(prevg), by(UNSUBREGIO1) egen regionprevh = total(prevh), by(UNSUBREGIO1) egen regionprevi = total(previ), by(UNSUBREGIO1) egen regionprevj = total(prevj), by(UNSUBREGIO1) duplicates drop UNSUBREGIO1, force list UNSUB regionpreva list UNSUB regionprevb list UNSUB regionprevc list UNSUB regionprevd list UNSUB regionpreve list UNSUB regionprevf list UNSUB regionprevg list UNSUB regionprevh list UNSUB regionprevi list UNSUB regionprevj