capture log close _all clear * Define some variables; local today=subinstr("`c(current_date)'"," ","",.) local time=subinstr("`c(current_time)'",":","",.) * stata version compatibility version 16.0 * log file number local vnum="1_10" * Syntax name local syntax "Analyses01" * Projectname local project "C19a" * Open log file; log using "$logfilepath/StataLog_AW_`project'_`syntax'_`vnum'_`today'_`time'", replace text name(Merge`syntax') local logname=r(name) timer clear 1 * Change Log ******************************** * 1.01: Add age split * 1.02: Moved all data preparation to separate file * 1.05: Changed sun and dispink reference groups * 1.06: Changed reference groups for gender (to women) * 1.07: Added bivariate regression for covid covariates * 1.08: Added comments for public extraction * 1.09: Added analyses for all causes of death following Reviewer comments * 1.09: Added tests for proportional hazards assumption back into syntax * 1.09: Added tests for multicollinearity * 1.10: Re-added models for total population clear use "$datafilepath/AW_`project'_Prepare01" *sample 1 cd "$outputpath" * Replace event variable with only the deaths we care about and save all others for possible later use gen codhold=. replace codhold=0 if _d==0 replace codhold=1 if _d==1 * all cause without Covid replace _d=0 if cod_cov==1 & _d==1 * Main effect models stratified by sex stcox b1.marital_status b3.sun3 b3.dispink2018_3 i.mena stolan if sex==1 eststo mainmenmenaall, title("Main Models, Men, 6-controls") estat vce, corr estat phtest, detail stcox b1.marital_status b3.sun3 b3.dispink2018_3 i.mena stolan if sex==2 eststo mainwomenmenaall, title("Main Models, Women, 6-controls") estat vce, corr estat phtest, detail esttab mainmenmenaall mainwomenmenaall using "$outputpath/mainAllC_`project'_`today'_`time'.rtf", mtitles b(3) ci eform nogaps scalars(N_fail risk) compress replace label * Bivariate regressions stcox b2.sex if dispink2018_3!=. eststo bivasexall stcox b1.marital_status if dispink2018_3!=. eststo bivamarstatall stcox b3.sun3 if dispink2018_3!=. eststo bivasun3all stcox b3.dispink2018_3 if dispink2018_3!=. eststo bivadispink3all stcox i.lmic if dispink2018_3!=. eststo bivalmicall stcox i.mena if dispink2018_3!=. eststo bivamenaall stcox stolan if dispink2018_3!=. eststo bivastolanall esttab bivasexall bivamarstatall bivasun3all bivadispink3all bivalmicall bivamenaall bivastolanall using "$outputpath/mainbivarall_`project'_`today'_`time'.rtf", mtitles b(3) ci eform nogaps scalars(N_fail risk) compress replace label stcox b2.sex b1.marital_status b3.sun3 b3.dispink2018_3 i.mena stolan eststo maincov, title("Main Models Covid, Both Sexes, 6-controls") estat vce, corr estat phtest, detail stcox b2.sex b1.marital_status b3.sun3 b3.dispink2018_3 i.mena stolan if age<66 eststo agestratAll2less66 estat vce, corr estat phtest, detail stcox b2.sex b1.marital_status b3.sun3 b3.dispink2018_3 i.mena stolan if age>=66 eststo agestratAll2more66 estat vce, corr estat phtest, detail esttab agestratAll2less66 agestratAll2less66m agestratAll2less66f agestratAll2more66 agestratAll2more66m agestratAll2more66f using "$outputpath/agestratAll_`project'_`today'_`time'.rtf", mtitles b(3) ci eform nogaps scalars(N_fail risk) compress replace label * Analyses for COVID-19 deaths replace _d=codhold replace _d=0 if cod_cov!=1 & _d==1 stcox b2.sex b1.marital_status b3.sun3 b3.dispink2018_3 i.mena stolan eststo mainall, title("Main Models All, Both Sexes, 6-controls") estat vce, corr estat phtest, detail esttab maincov mainall using "$outputpath/mainNoSexSep_`project'_`today'_`time'.rtf", mtitles b(3) ci eform nogaps scalars(N_fail risk) compress replace label * Main effect models stcox b1.marital_status b3.sun3 b3.dispink2018_3 i.mena stolan if sex==1 eststo mainmenmena, title("Main Models, Men, 6-controls") estat vce, corr estat phtest, detail stcox b1.marital_status b3.sun3 b3.dispink2018_3 i.mena stolan if sex==2 eststo mainwomenmena, title("Main Models, Women, 6-controls") estat vce, corr estat phtest, detail esttab mainmenmena mainwomenmena using "$outputpath/main_`project'_`today'_`time'.rtf", mtitles b(3) ci eform nogaps scalars(N_fail risk) compress replace label * Bivariate regressions stcox b2.sex if dispink2018_3!=. eststo bivasex stcox b1.marital_status if dispink2018_3!=. eststo bivamarstat stcox b3.sun3 if dispink2018_3!=. eststo bivasun3 stcox b3.dispink2018_3 if dispink2018_3!=. eststo bivadispink3 stcox i.lmic if dispink2018_3!=. eststo bivalmic stcox i.mena if dispink2018_3!=. eststo bivamena stcox stolan if dispink2018_3!=. eststo bivastolan esttab bivasex bivamarstat bivasun3 bivadispink3 bivalmic bivamena bivastolan using "$outputpath/mainbivar_`project'_`today'_`time'.rtf", mtitles b(3) ci eform nogaps scalars(N_fail risk) compress replace label stcox b2.sex b1.marital_status b3.sun3 b3.dispink2018_3 i.mena stolan if age<66 eststo agestratCovless66 estat vce, corr estat phtest, detail stcox b2.sex b1.marital_status b3.sun3 b3.dispink2018_3 i.mena stolan if age>=66 eststo agestratCovmore66 estat vce, corr estat phtest, detail esttab agestratCovless66 agestratCovless66m agestratCovless66f agestratCovmore66 agestratCovmore66m agestratCovmore66f using "$outputpath/agestratCovid_`project'_`today'_`time'.rtf", mtitles b(3) ci eform nogaps scalars(N_fail risk) compress replace label timer list 1 log close `logname'