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08b_an_model_checks.do
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08b_an_model_checks.do
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/*==============================================================================
DO FILE NAME: 08b_an_model_checks
PROJECT: Anticoagulant in COVID-19
AUTHOR: A Wong (modified from NSAID study by A Schultze)
DATE: 2 Nov 2020
DESCRIPTION OF FILE: program 08b
check the PH assumption, produce graphs
Objective 2: comparing warfarin vs DOACs in people
with atrial fibrillation
DATASETS USED: data in memory ($tempdir/analysis_dataset_STSET_outcome)
DATASETS CREATED: none
OTHER OUTPUT: logfiles, printed to folder analysis/$logdir
table5_`outcome' & table6_`outcome', printed to analysis/$outdir
schoenplots1-x, printed to analysis?$outdir
==============================================================================*/
local outcome `1'
local global_option `2'
do `c(pwd)'/analysis/global_`global_option'.do
* Open a log file
cap log close
log using $logdir/08b_an_model_checks_`outcome', replace t
/*==============================================================================*/
* Open Stata dataset
use $tempdir/analysis_dataset_STSET_`outcome', clear
/* In full cohort*/
/* Quietly run models, perform test and store results in local macro==========*/
qui stcox i.exposure
estat phtest, detail
local univar_p = round(r(p),0.001)
di `univar_p'
estat phtest, plot(1.exposure) ///
graphregion(fcolor(white)) ///
ylabel(, nogrid labsize(small)) ///
xlabel(, labsize(small)) ///
xtitle("Time", size(small)) ///
ytitle("Scaled Schoenfeld Residuals", size(small)) ///
msize(small) ///
mcolor(gs6) ///
msymbol(circle_hollow) ///
scheme(s1mono) ///
title ("Schoenfeld residuals against time, univariable", position(11) size(medsmall))
graph export "$tabfigdir/`outcome'_schoenplot1.svg", as(svg) replace
* Close window
graph close
stcox i.exposure i.male age1 age2 age3
estat phtest, detail
local multivar1_p = round(r(phtest)[2,4],0.001)
estat phtest, plot(1.exposure) ///
graphregion(fcolor(white)) ///
ylabel(, nogrid labsize(small)) ///
xlabel(, labsize(small)) ///
xtitle("Time", size(small)) ///
ytitle("Scaled Schoenfeld Residuals", size(small)) ///
msize(small) ///
mcolor(gs6) ///
msymbol(circle_hollow) ///
scheme(s1mono) ///
title ("Schoenfeld residuals against time, age and sex adjusted", position(11) size(medsmall))
graph export "$tabfigdir/`outcome'_schoenplot2.svg", as(svg) replace
* Close window
graph close
stcox i.exposure i.male age1 age2 age3 $dagvarlist ,strata(practice_id)
estat phtest, detail
local multivar2_p = round(r(phtest)[2,4],0.001)
estat phtest, plot(1.exposure) ///
graphregion(fcolor(white)) ///
ylabel(, nogrid labsize(small)) ///
xlabel(, labsize(small)) ///
xtitle("Time", size(small)) ///
ytitle("Scaled Schoenfeld Residuals", size(small)) ///
msize(small) ///
mcolor(gs6) ///
msymbol(circle_hollow) ///
scheme(s1mono) ///
title ("Schoenfeld residuals against time, DAG adjusted", position(11) size(medsmall))
graph export "$tabfigdir/`outcome'_schoenplot3.svg", as(svg) replace
stcox i.exposure i.male age1 age2 age3 $fullvarlist, strata(practice_id)
estat phtest, detail
local multivar3_p = round(r(phtest)[2,4],0.001)
estat phtest, plot(1.exposure) ///
graphregion(fcolor(white)) ///
ylabel(, nogrid labsize(small)) ///
xlabel(, labsize(small)) ///
xtitle("Time", size(small)) ///
ytitle("Scaled Schoenfeld Residuals", size(small)) ///
msize(small) ///
mcolor(gs6) ///
msymbol(circle_hollow) ///
scheme(s1mono) ///
title ("Schoenfeld residuals against time, fully adjusted", position(11) size(medsmall))
graph export "$tabfigdir/`outcome'_schoenplot4.svg", as(svg) replace
* Close window
graph close
* Print table of results======================================================*/
cap file close tablecontent
file open tablecontent using $tabfigdir/table5_`outcome'.txt, write text replace
* Column headings
file write tablecontent ("Table 5: Testing the PH assumption - `outcome' - $population Population in Full cohort") _n
file write tablecontent _tab ("Univariable") _tab ("Age/Sex Adjusted") _tab ///
("DAG Adjusted") _tab ("Fully Adjusted") _tab _n
file write tablecontent _tab ("p-value") _tab ("p-value") _tab ("p-value") _tab ///
("p-value") _tab _n
* Row heading and content
file write tablecontent ("Treatment Exposure") _tab
file write tablecontent ("`univar_p'") _tab ("`multivar1_p'") ///
_tab ("`multivar2_p'") _tab ("`multivar3_p'")
file write tablecontent _n
file close tablecontent
* =============================================================================*/
/* In complete case cohort - restrict to people with known ethnicity*/
* Open Stata dataset
use $tempdir/analysis_dataset_STSET_`outcome', clear
drop if ethnicity == .u
/* Quietly run models, perform test and store results in local macro==========*/
qui stcox i.exposure
estat phtest, detail
local univar_completecase_p = round(r(p),0.001)
di `univar_p'
estat phtest, plot(1.exposure) ///
graphregion(fcolor(white)) ///
ylabel(, nogrid labsize(small)) ///
xlabel(, labsize(small)) ///
xtitle("Time", size(small)) ///
ytitle("Scaled Schoenfeld Residuals", size(small)) ///
msize(small) ///
mcolor(gs6) ///
msymbol(circle_hollow) ///
scheme(s1mono) ///
title ("Schoenfeld residuals against time, univariable", position(11) size(medsmall))
graph export "$tabfigdir/`outcome'_schoenplot1_completecase.svg", as(svg) replace
* Close window
graph close
stcox i.exposure i.male age1 age2 age3
estat phtest, detail
local multivar1_completecase_p = round(r(phtest)[2,4],0.001)
estat phtest, plot(1.exposure) ///
graphregion(fcolor(white)) ///
ylabel(, nogrid labsize(small)) ///
xlabel(, labsize(small)) ///
xtitle("Time", size(small)) ///
ytitle("Scaled Schoenfeld Residuals", size(small)) ///
msize(small) ///
mcolor(gs6) ///
msymbol(circle_hollow) ///
scheme(s1mono) ///
title ("Schoenfeld residuals against time, age and sex adjusted", position(11) size(medsmall))
graph export "$tabfigdir/`outcome'_schoenplot2_completecase.svg", as(svg) replace
* Close window
graph close
stcox i.exposure i.male age1 age2 age3 $dagvarlist i.ethnicity
estat phtest, detail
local multivar2_completecase_ethn_p = round(r(phtest)[2,4],0.001)
estat phtest, plot(1.exposure) ///
graphregion(fcolor(white)) ///
ylabel(, nogrid labsize(small)) ///
xlabel(, labsize(small)) ///
xtitle("Time", size(small)) ///
ytitle("Scaled Schoenfeld Residuals", size(small)) ///
msize(small) ///
mcolor(gs6) ///
msymbol(circle_hollow) ///
scheme(s1mono) ///
title ("Schoenfeld residuals against time, DAG adjusted", position(11) size(medsmall))
graph export "$tabfigdir/`outcome'_schoenplot3_completecase_ethn.svg", as(svg) replace
stcox i.exposure i.male age1 age2 age3 $dagvarlist
estat phtest, detail
local multivar2_completecase_p = round(r(phtest)[2,4],0.001)
estat phtest, plot(1.exposure) ///
graphregion(fcolor(white)) ///
ylabel(, nogrid labsize(small)) ///
xlabel(, labsize(small)) ///
xtitle("Time", size(small)) ///
ytitle("Scaled Schoenfeld Residuals", size(small)) ///
msize(small) ///
mcolor(gs6) ///
msymbol(circle_hollow) ///
scheme(s1mono) ///
title ("Schoenfeld residuals against time, DAG adjusted", position(11) size(medsmall))
graph export "$tabfigdir/`outcome'_schoenplot3_completecase.svg", as(svg) replace
stcox i.exposure i.male age1 age2 age3 $fullvarlist i.ethnicity, strata(practice_id)
estat phtest, detail
local multivar3_completecase_ethn_p = round(r(phtest)[2,4],0.001)
estat phtest, plot(1.exposure) ///
graphregion(fcolor(white)) ///
ylabel(, nogrid labsize(small)) ///
xlabel(, labsize(small)) ///
xtitle("Time", size(small)) ///
ytitle("Scaled Schoenfeld Residuals", size(small)) ///
msize(small) ///
mcolor(gs6) ///
msymbol(circle_hollow) ///
scheme(s1mono) ///
title ("Schoenfeld residuals against time, fully adjusted", position(11) size(medsmall))
graph export "$tabfigdir/`outcome'_schoenplot4_completecase_ethn.svg", as(svg) replace
stcox i.exposure i.male age1 age2 age3 $fullvarlist, strata(practice_id)
estat phtest, detail
local multivar3_completecase_p = round(r(phtest)[2,4],0.001)
estat phtest, plot(1.exposure) ///
graphregion(fcolor(white)) ///
ylabel(, nogrid labsize(small)) ///
xlabel(, labsize(small)) ///
xtitle("Time", size(small)) ///
ytitle("Scaled Schoenfeld Residuals", size(small)) ///
msize(small) ///
mcolor(gs6) ///
msymbol(circle_hollow) ///
scheme(s1mono) ///
title ("Schoenfeld residuals against time, fully adjusted", position(11) size(medsmall))
graph export "$tabfigdir/`outcome'_schoenplot4_completecase.svg", as(svg) replace
* Close window
graph close
* Print table of results======================================================*/
cap file close tablecontent
file open tablecontent using $tabfigdir/table6_`outcome'.txt, write text replace
* Column headings
file write tablecontent ("Table 6: Testing the PH assumption - `outcome' - $population Population in complete case cohort") _n
file write tablecontent _tab ("Univariable") _tab ("Age/Sex Adjusted") _tab ///
("DAG Adjusted with ethnicity") _tab ///
("DAG Adjusted without ethnicity") _tab ///
("Fully Adjusted with ethnicity") _tab ///
("Fully Adjusted without ethnicity") _tab _n
file write tablecontent _tab ("p-value") _tab ("p-value") _tab ("p-value") _tab ///
("p-value") _tab ("p-value") _tab ("p-value") _tab _n
* Row heading and content
file write tablecontent ("Treatment Exposure") _tab
file write tablecontent ("`univar_completecase_p'") _tab ("`multivar1_completecase_p'") ///
_tab ("`multivar2_completecase_ethn_p'") _tab ("`multivar2_completecase_p'") ///
_tab ("`multivar3_completecase_ethn_p'") _tab ("`multivar3_completecase_p'")
file write tablecontent _n
file close tablecontent
* Close log file
log close