Now Lets Get Down to Technical Stuff

Now Lets Get Down to Technical Stuff#

Let’s start by reproducing some old results

Old results#

Source population#

Extract vector-matrix#

Hide code cell source 
qui {
capture log close 
log using jamascript.log, replace 
global repo https://github.com/muzaale/forum/raw/main/ 
/*--Edit this Line --*/
global dir ~/documents/liveserver/age/
// cls; some commands don't work outside Stata!!
/*noi di "What is your work directory?" _request(workdir)
if "$workdir" == "" {
	di as err "Please provide your work directory"
	exit
}
else {
	cd $workdir
	noi di "jamascript is running ..."
}
*/
use ${repo}esrdRisk_t02tT, clear
tab donor rSMGJcEdF_d
g entry = rSMGJcEdF_t0
//linkage for donors after 2011 is untrustworthy
replace rSMGJcEdF_d=0 if rSMGJcEdF_tT > d(31dec2011)
replace rSMGJcEdF_tT = d(31dec2011) if rSMGJcEdF_tT > d(31dec2011)
//linkage before 1994 is untrustworthy
#delimit ;
replace entry = d(01jan1994) if  
    entry < d(01jan1994) &  
	rSMGJcEdF_tT > d(01jan1994); 
stset rSMGJcEdF_tT,  
    origin(rSMGJcEdF_t0)  
	entry(`entry')  
	fail(rSMGJcEdF_d==2)  
	scale(365.25); 
#delimit cr 
sts list, fail by(donor) at(5 12 15) saving(km, replace ) 
preserve  
    use km, clear  
	replace failure=failure*100
    sum failure if donor==1 & time==5
	local don5y: di %3.2f r(mean)
    sum failure if donor==1 & time==12
	local don12y: di %3.2f r(mean)
	sum failure if donor==1 & time==15
	local don15y: di %3.2f r(mean)
	//
    sum failure if donor==2 & time==5
	local hnd5y: di %3.2f r(mean)
    sum failure if donor==2 & time==12
	local hnd12y: di %3.2f r(mean)
	sum failure if donor==2 & time==15
	local hnd15y: di %3.2f r(mean)
	//
    sum failure if donor==3 & time==5
	local gpop5y: di %3.2f r(mean)
    sum failure if donor==3 & time==12
	local gpop12y: di %3.2f r(mean)
	sum failure if donor==3 & time==15
	local gpop15y: di %3.2f r(mean)
restore 
#delimit ;
sts graph, 
    by(donor)  
    fail 
	per(100)  
	xlab(0(3)15) 
	ylab(0(10)40,  
	    format(%2.0f))  
	tmax(15)  
	risktable(, color(stc1) group (1)  
	    order(3 " " 2 " " 1 " ")  
		ti("#")  
	) 
	risktable(, color(stc2) group(2))  
	risktable(, color(stc3) group(3))  
	legend(on 
	ring(0)  
	    pos(11)  
	   order(3 2 1)  
	   lab(3 "General population")  
	   lab(2 "Healthy nondonor")  
	   lab(1 "Living donor")  
	)  
	ti("Morte")  
	text(`don5y' 5 "`don5y'%", col(stc1))  
	text(`don12y' 12 "`don12y'%", col(stc1))  
	text(`don15y' 15 "`don15y'%", col(stc1))  
	text(`hnd5y' 5 "`hnd5y'%", col(stc2))  
	text(`hnd12y' 12 "`hnd12y'%", col(stc2)) 
	text(`hnd15y' 15 "`hnd15y'%", col(stc2))  
	text(`gpop5y' 5 "`gpop5y'%", col(stc3))  
	text(`gpop12y' 12 "`gpop12y'%", col(stc3))  
	text(`gpop15y' 15 "`gpop15y'%", col(stc3));
#delimit cr

graph export ${dir}jamascript.png, replace 
keep _* entry age_t0 female race donor
rename age_t0 age
//dataset
save ${dir}jamascript.dta, replace 
noi stcox i.donor, basesurv(s0)
noi list s0 _t donor in 1/10
matrix define b=e(b)
keep s0 _t 
//s0
sort _t s0
list in 1/10
save ${dir}s0.dta, replace 
export delimited using ${dir}s0.csv, replace 
matrix beta = e(b)
svmat beta 
keep beta*
drop if missing(beta1)
//betas
list 
save b.dta, replace 
export delimited using ${dir}b.csv, replace 
log close 
//noi ls
}
Hide code cell output 
  Cell In[1], line 7
    // cls; some commands don't work outside Stata!!
                             ^
SyntaxError: unterminated string literal (detected at line 7)

logfile

#

Hide code cell source 
qui {
use ${repo}esrdRisk_t02tT, clear
tab donor rSMGJcEdF_d
g entry = rSMGJcEdF_t0
//linkage for donors after 2011 is untrustworthy
replace rSMGJcEdF_d=0 if rSMGJcEdF_tT > d(31dec2011)
replace rSMGJcEdF_tT = d(31dec2011) if rSMGJcEdF_tT > d(31dec2011)
//linkage before 1994 is untrustworthy
#delimit ;
replace entry = d(01jan1994) if  
    entry < d(01jan1994) &  
	rSMGJcEdF_tT > d(01jan1994); 
stset rSMGJcEdF_tT,  
    origin(rSMGJcEdF_t0)  
	entry(`entry')  
	fail(rSMGJcEdF_d==2)  
	scale(365.25); 

#delimit cr

stcox i.donor don_age don_female i.don_race i.don_educat don_hyperten don_smoke don_bmi don_bp_preop_syst  don_egfr if inlist(donor,1,2), basesurv(s0_v1)

export delimited _t s0_v1 using "~/documents/liveserver/age/s0_v1.csv", replace

tab donor if !missing(s0_v1)

matrix define m=e(b)
matrix list m
di exp(m[1,2])
svmat m
list m*
keep m*
drop if missing(m1)
export delimited using "don_nondon_v1.csv", replace
}

To create a CSV of the coefficient vector in Stata, you’ll need to extract the matrix and then export it to a CSV file. Here’s how you can do it:

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