*! TMPM2: v2.0 2020.05.20 Osler and Cook. //
*! Calculates Trauma Mortality Prediction Model values //
*! for each observation using AIS, ICD-9-CM and ICD-10-CM Codes. //
*! Journal page 19. 2020.05.23
*! Requires marc2_table
// Scalar definitions:
// TMO indicator for 1p1v
// ADC a subsequent scalar for 1p1v
*! 2021.11.22
program tmpm2, rclass
version 11.0
syntax [varlist] [, i(varname) inj(string) ais icd9 icd10 ]
quietly {
local directory "`c(pwd)'/"
*- identify the user's original file
scalar userfile = c(filename)
capture save "usrtemp1x.dta", replace
sort `i'
// Userfile WIDE OR LONG ? // // ok 2020.07.19
quietly findfile "usrtemp1x.dta"
use `"`r(fn)'"'
renpfix `inj' dxx
keep `i' dxx*
capture confirm string variable `i'
if !_rc {
}
else {
capture tostring `i', replace u
}
foreach v of varlist dxx* {
confirm string variable `v'
if !_rc {
}
else {
capture tostring dxx*, replace u
}
}
tempvar filelong ord
quietly ds dxx*
local ndx : word count `r(varlist)'
gen `filelong'=(`ndx'==1)
if `filelong'==0 { // 0 = WIDE
reshape long dxx, i(`i') j(ord) // RESHAPE LONG
drop if dxx==""
drop ord `filelong'
}
compress
sort dxx
drop if dxx==""
capture save "usrtemp2.dta", replace
// IDENTIFY LEXICON IN USER'S DATA THEN PREP marc2_table.dta // // ok 2020.07.19
quietly findfile "usrtemp2.dta"
use `"`r(fn)'"'
////////////////
// ICD-10-CM //
////////////////
if "`icd10'"!="" { // The data are ICD-10 lex2==1
preserve
findfile "marc2_table.dta"
use `"`r(fn)'"', clear
keep if lex2==1
capture save "marc2_table2.dta", replace
clear
restore
scalar lex2=1
}
else { // The data are NOT ICD-10
}
////////////////
// ICD-9-CM //
////////////////
if "`icd9'"!="" { // The data are ICD-9 lex2==2
gen trauma1 = (dxx>"799.99" & dxx<"960")
keep if trauma1==1
drop trauma1
preserve
findfile "marc2_table.dta"
use `"`r(fn)'"', clear
keep if lex2==2
capture save "marc2_table2.dta", replace
clear
restore
scalar lex2=2
}
else { // The data are NOT ICD-10 or ICD-9
}
////////////////
// AIS //
////////////////
if "`ais'"!="" { // The data are AIS lex2==3
preserve
findfile "marc2_table.dta"
use `"`r(fn)'"', clear
keep if lex2==3
capture save "marc2_table2.dta", replace
clear
restore
scalar lex2=3
}
else {
}
clear
*- Load User's data -* // MERGE WITH MARC TABLE ok 2020.07.19
quietly findfile "usrtemp2.dta"
use `"`r(fn)'"'
quietly findfile "marc2_table2.dta"
merge m:1 dxx using `"`r(fn)'"' // MERGE
keep if _merge==3
drop _merge
drop if marc2==. | `i'==""
capture save "temp1.dta", replace //temp1
//
quietly {
*Deal with "same region"
use "temp1.dta", clear
gsort `i' -marc2
by `i', sort: gen n=_n
gen sr=(rs==rs[_n+1] & (`i'==`i'[_n+1] & n==1))
replace sr=1 if (`i'==`i'[_n-1] & sr[_n-1]==1)
sort `i'
drop if n>5
keep `i' sr marc2
capture save "temp2.dta", replace
clear
use "temp2.dta", clear
by `i', sort: gen N=_N // `i'
by `i', sort: gen orig=_n
expand 5 if N<5, gen(new)
sort `i' new orig, stable
replace marc2=0 if new==1
bys `i': drop if _n>5 & new==1
keep `i' marc2 sr
bys `i': gen ord=_n
reshape wide marc2, i(`i') j(ord)
if lex2==1 { // Data are ICD-10
foreach v of varlist marc21- marc25 {
replace `v'=0 if `v'==.
}
gen Imarc=marc21*marc22 // generate the interaction term
replace Imarc=0 if Imarc==.
gen xBeta=(0.48840329*marc21) + ///
(0.50077127*marc22) + ///
(0.33604308*marc23) + ///
(0.30354563*marc24) + ///
(0.41945388*marc25) + ///
(-0.06767112*Imarc) + ///
(-0.04381364*sr) + ///
(-2.2846757)
foreach v of varlist marc2* {
replace `v'=0 if `v'==.
}
capture save "XBeta_checktemp.dta", replace
gen pDeath=normal(xBeta)
format pDeath %08.6f
lab var pDeath "Prob Death ICD-10"
keep `i' pDeath
sort `i'
compress
capture save "id_pdeath.dta", replace
clear
}
else {
if lex2==2 { // Data are ICD-9
foreach v of varlist marc2* {
replace `v'=0 if `v'==.
}
gen Imarc=marc21*marc22 // generate the interaction term
replace Imarc=0 if Imarc==.
gen xBeta = (1.406958*marc21) + ///
(1.409992*marc22) + ///
(0.5205343*marc23) + ///
(0.4150946*marc24) + ///
(0.8883929*marc25) + ///
(-0.0890527*sr) + ///
(-0.7782696*Imarc) + ///
(-2.217565)
foreach v of varlist marc2* {
replace `v'=0 if `v'==.
}
gen pDeath=normal(xBeta)
format pDeath %08.6f
lab var pDeath "Prob Death ICD-9"
order `i' pDeath
keep `i' pDeath
sort `i'
compress
capture save "id_pdeath.dta", replace
clear
}
else {
if lex2==3 { // Data are AIS
foreach v of varlist marc2* {
replace `v'=0 if `v'==.
}
gen Imarc=marc21*marc22 // generate the interaction term
replace Imarc=0 if Imarc==.
gen xBeta=(1.3142935*marc21) + ///
(1.2505921*marc22) + ///
(0.62937847*marc23) + ///
(0.61438086*marc24) + ///
(0.97266839*marc25) + ///
(-0.06138731*sr) + ///
(-0.46506898*Imarc) + ///
(-2.5658983)
foreach v of varlist marc2* {
replace `v'=0 if `v'==.
}
gen pDeath =normal(xBeta)
format pDeath %08.6f
lab var pDeath "Prob Death AIS"
order `i' pDeath
keep `i' pDeath
sort `i'
capture save "id_pdeath.dta", replace
clear
}
}
}
quietly findfile "usrtemp1x.dta"
use `"`r(fn)'"', clear
sort `i'
merge m:1 `i' using "id_pdeath.dta", nogenerate norep
scalar drop lex2
erase "usrtemp1x.dta"
erase "usrtemp2.dta"
erase "marc2_table2.dta"
erase "id_pdeath.dta"
erase "temp1.dta"
erase "temp2.dta"
}
}
end
exit