*! | Version: 1.2 | Last Updated: August 18, 2024
/*----------------------------------------------------------------------------*\
| PELOD-2 Score Calculator - a statistical package designed to calculate |
| the Pediatric Logistic Organ Dysfunction-2 score. |
| |
| For help, please see help pelod2. |
| Additional information available at: |
| https://azamfirei.com/pelod2 |
| |
| Version: 1.2 | Created: November 12, 2023 | Last Updated: August 18, 2024 |
| Author: Razvan Azamfirei - stata@azamfirei.com |
| |
| LICENSE: |
| Copyright 2024 Razvan Azamfirei |
| |
| Licensed under the Apache License, Version 2.0 (the"License"); you may |
| not use this file except in compliance with the License. You may obtain|
| a copy of the License at: |
| http://www.apache.org/licenses/LICENSE-2.0 |
| Unless required by applicable law or agreed to in writing, software |
| distributed under the License is distributed on an "AS IS" BASIS, |
| WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or |
| implied. |
| |
| See the License for the specific language governing permissions and |
| limitations under the License. |
\*----------------------------------------------------------------------------*/
cap program drop pelod2
program pelod2
preserve
*** Check Stata version compatibility
if (c(stata_version) < 17) {
di as txt "Note: this command is written " ///
"and comprehensively tested for Stata release 17.0 or higher."
di as txt "The command was tested on Stata 12.0 with no " ///
"issues. However, a comprehensive validation was not performed."
if (c(stata_version) >= 12) {
di as txt "There are no technical reasons preventing this " ///
"command from working with Stata version " ///
"`c(stata_version)'. However no guarantees are made."
}
else {
di as txt "The command might not work properly with " ///
"Stata version `c(stata_version)'"
}
loc vers = c(stata_version)
}
else loc vers 17
version `vers'
novarabbrev {
qui {
/*----------------------------------------------------------------------------*/
loc cat_vars pupils mv
loc num_vars map lactate gcs wbc plt creatinine pco2
loc num_vars_opt fio2 pao2 pfratio
loc score_vars map_score lactate_score pupils_score ///
gcs_score mv_score pco2_score wbc_score plt_score pfratio_score ///
creatinine_score pelod_score
loc all_vars `cat_vars' `num_vars' `num_vars_opt'
loc options sioption wbcoption plateletoption noimputation ///
rawscoreoption validation trace
loc results pelod_intermediate pelod_final
loc scalars coef_intercept coef_score ///
age0_high age0_low age1_high age1_low age2_high age2_low ///
age3_high age3_low age4_high age4_low age5_low ///
age0_map_high age0_map_low age0_map_medium age0_map_medium2 ///
age1_map_high age1_map_low age1_map_medium age1_map_medium2 ///
age2_map_high age2_map_low age2_map_medium age2_map_medium2 ///
age3_map_high age3_map_low age3_map_medium age3_map_medium2 ///
age4_map_high age4_map_low age4_map_medium age4_map_medium2 ///
age5_map_high age5_map_low age5_map_medium age5_map_medium2 ///
cr0 cr1 cr2 cr3 cr4 cr5 plt0 plt1 wbc0 gcs0 gcs1 lac0 lac1 ///
fio2oor0 fio2oor1 pao2oor0 pao2oor1 pco20 pco21 pfr0 ///
mapoor0 mapoor1
loc help_msg "See help pelod2 for more details."
/*----------------------------------------------------------------------------*/
syntax newvarname(generate) [if] [in], ///
[age(varname num)] [dob(varname)] [doa(varname)] ///
map(varname numeric) ///
lactate(varname numeric) ///
PUPils(varname numeric) ///
GCS(varname numeric) ///
[Fio2(varname numeric) ///
pao2(varname numeric) ///
pfratio(varname numeric)] ///
pco2(varname numeric) ///
mv(varname numeric) ///
WBC(varname numeric) ///
CReatinine(varname numeric) ///
PLT(varname numeric) ///
[WBCUnit(int 1)] [PLTUnit(int 1)] [si] ///
[RAWscore(name)] ///
[noIMPutation] [noVALidation] [TRACE]
marksample touse, nov
/*----------------------------------------------------------------------------*/
tempname `options'
tempvar `results'
tempvar calculated_age age dob doa
sca imputationoption = 1
sca traceoption = 0
sca validationoption = 1
sca rawscoreoption = 0
sca sioption = 0
sca plateletoption = 1
sca wbcoption = 1
/* Get Option State */
if "`trace'" != "" {
set tr on
sca traceoption = 1
}
if "`imputation'" != "" {
sca imputationoption = 0
}
if "`validation'" != "" {
sca validationoption = 0
}
if "`si'" != "" {
sca sioption = 1
}
/* Get Target Variable */
foreach var in `varlist' {
loc pelod2var `var'
}
if "`rawscore'" != "" {
sca rawscoreoption = 1
loc rawscorevar `rawscore'
}
/* Define Variables and Avoid Name Collisions */
foreach score in `score_vars' {
tempvar `score'
}
foreach var in `all_vars' {
tempvar `var'_i
}
foreach var in `cat_vars' `num_vars' {
gen ``var'_i' = ``var''
tempvar `var'
gen ``var'' = ``var'_i'
drop ``var'_i'
}
foreach var in `num_vars_opt' {
capture {
gen``var'_i' = ``var''
tempvar `var'
gen ``var'' = ``var'_i'
drop ``var'_i'
}
}
foreach score in `score_vars' {
if imputationoption == 1 {
gen ``score'' = 0
}
else {
gen ``score'' = .
}
}
/* Set Bounds */
tempname `scalars'
sca coef_intercept = -6.61
sca coef_score = 0.47
/* Age Bounds -- days */
sca age0_low = 0
sca age0_high = 30
sca age1_low = 31
sca age1_high = 365
sca age2_low = 366
sca age2_high = 730
sca age3_low = 731
sca age3_high = 1825
sca age4_low = 1826
sca age4_high = 4380
sca age5_low = 4381
/* MAP Bounds (by age) */
sca age0_map_low = 17
sca age0_map_medium = 30
sca age0_map_medium2 = 31
sca age0_map_high = 45
sca age1_map_low = 25
sca age1_map_medium = 38
sca age1_map_medium2 = 39
sca age1_map_high = 54
sca age2_map_low = 31
sca age2_map_medium = 43
sca age2_map_medium2 = 44
sca age2_map_high = 59
sca age3_map_low = 32
sca age3_map_medium = 44
sca age3_map_medium2 = 45
sca age3_map_high = 61
sca age4_map_low = 36
sca age4_map_medium = 48
sca age4_map_medium2 = 49
sca age4_map_high = 64
sca age5_map_low = 38
sca age5_map_medium = 51
sca age5_map_medium2 = 52
sca age5_map_high = 66
/* GCS Bounds */
sca gcs0 = 5
sca gcs1 = 10
/* Respiratory Bounds */
sca pfr0 = 60
sca pco20 = 59
sca pco21 = 94
/* Heme Bounds (cells/mL) */
sca wbc0 = 2000
sca plt0 = 77000
sca plt1 = 141000
/* Out of Range Bounds */
sca mapoor0 = 0
sca mapoor1 = 200
sca pao2oor0 = 1
sca pao2oor1 = 600
sca fio2oor0 = float(0.21)
sca fio2oor1 = float(1)
sca gcsoor0 = 3
sca gcsoor1 = 15
/* Bounds for Laboratory Values with Multiple Units */
sca cr_conversion_factor = 0.0113
sca lactate_conversion_factor = 0.111
if sioption == 1 {
sca cr0 = float(70)
sca cr1 = float(23)
sca cr2 = float(35)
sca cr3 = float(51)
sca cr4 = float(59)
sca cr5 = float(93)
sca lac0 = float(5.0)
sca lac1 = float(10.9)
}
else {
sca cr0 = float(70 * cr_conversion_factor)
sca cr1 = float(23 * cr_conversion_factor)
sca cr2 = float(35 * cr_conversion_factor)
sca cr3 = float(51 * cr_conversion_factor)
sca cr4 = float(59 * cr_conversion_factor)
sca cr5 = float(93 * cr_conversion_factor)
sca lac0 = float(5.0 * lactate_conversion_factor)
sca lac1 = float(10.9 * lactate_conversion_factor)
}
/* Updates Platelet and WBC Bounds */
if `pltunit' == 1000 {
sca plateletoption = 1000
}
if `wbcunit' == 1000 {
sca wbcoption = 1000
}
if `pltunit' != 1 & `pltunit' != 1000 & !missing(`pltunit') {
di as err "Platelet Unit incorrectly specified."
err 499
}
if `wbcunit' != 1 & `wbcunit' != 1000 & !missing(`wbcunit') {
di as err "WBC Unit incorrectly specified."
err 499
}
forvalues x = 0(1)1 {
sca plt`x' = plt`x' / plateletoption
}
sca wbc0 = wbc0 / wbcoption
/*----------------------------------------------------------------------------*/
/* Age Format Confirmation */
cap conf numeric v `age'
if _rc != 0 {
sca ag1 = 0
}
else {
sca ag1 = 1
}
cap conf numeric v `dob'
if _rc != 0 {
sca ag2 = 0
}
else {
sca ag2 = 1
}
cap conf numeric v `doa'
if _rc != 0 {
sca ag3 = 0
}
else {
sca ag3 = 1
}
sca ag4 = ag2 + ag3
if ag1 == 1 & ag4 == 0 {
sca agecase = 1
}
if ag1 == 1 & inrange(ag4, 1, 2) {
sca agecase = 2
}
if ag1 == 0 & ag4 == 0 {
sca agecase = 3
}
if ag1 == 0 & ag4 == 1 {
sca agecase = 4
}
if ag1 == 0 & ag4 == 2 {
sca agecase = 5
}
if agecase == 2 {
di as err "Both age, DoB and DoA are specified."
di as err "Specify either age or DoB and DoA"
err 103
}
if agecase == 3 {
di as err "Neither age, DoB or DoA are specified."
di as err "Specify either age or DoB and DoA"
err 102
}
if agecase == 4 {
di as err "You must specify both DoB and DoA"
err 102
}
if agecase == 1 {
cou if !inlist(`age', 0, 1, 2, 3, 4, 5, .)
if r(N) != 0 {
di as err "Age is not in the correct format. `help_msg'"
err 498
}
}
if agecase == 5 {
gen `calculated_age' = datediff(`dob', `doa', "d")
cap as `calculated_age' >= 0, fast
if _rc != 0 {
di as err "Calculated age is negative. Observations will " ///
"be ignored."
}
tempvar age
gen `age' = 0 if inrange(`calculated_age', age0_low, age0_high)
replace `age' = 1 if inrange(`calculated_age', age1_low, age1_high)
replace `age' = 2 if inrange(`calculated_age', age2_low, age2_high)
replace `age' = 3 if inrange(`calculated_age', age3_low, age3_high)
replace `age' = 4 if inrange(`calculated_age', age4_low, age4_high)
replace `age' = 5 if inrange(`calculated_age', age5_low, .)
}
/* Binary Format Confirmation */
foreach var in mv pupils {
cou if !inlist(``var'', 0, 1, .)
if r(N) != 0 {
di as err "`var' is not binary. `help_msg'"
err 450
}
if imputationoption == 1 {
cou if ``var'' == .
if r(N) != 0 {
di as err "Some `var' values missing and default values were used. `help_msg'"
}
}
}
qui replace `fio2' = `fio2'/100 if inrange(`fio2', 21, 100)
/* OOB Data Validation */
if validationoption == 1 {
noi {
di "Checking for out-of-range values..."
di as text "The following lists out-of-range values:"
di "GCS"
replace `gcs' = . if !inrange(`gcs', gcsoor0, gcsoor1)
di as text "MAP"
replace `map' = . if !inrange(`map', mapoor0, mapoor1)
capture confirm v `pao2'
if _rc == 0 {
di as text "PaO2"
replace `pao2' = . if !inrange(`pao2', pao2oor0, pao2oor1)
}
capture confirm v `fio2'
if _rc == 0 {
di as text "FiO2"
replace `fio2' = . if ///
!inrange(`fio2', fio2oor0, fio2oor1)
}
}
}
/*----------------------------------------------------------------------------*/
/* Rounding to whole number where appropriate */
replace `pco2' = round(`pco2', 1)
replace `plt' = round(`plt', 1000 / plateletoption)
if sioption == 1 {
replace `creatinine' = round(`creatinine', 1)
}
/* Calculating PF Ratio if not provided */
capture confirm v `pfratio'
if _rc != 0 {
tempname pfratio
gen `pfratio' = .
replace `pfratio' = `pao2'/`fio2' if !missing(`pao2') & ///
!missing(`fio2') & missing(`pfratio')
replace `pfratio' = round(`pfratio', 1)
}
else {
replace `pfratio' = round(`pfratio', 1)
}
/* Score Calculation */
replace `gcs_score' = 4 if `gcs' <= gcs0 & !missing(`gcs')
replace `gcs_score' = 1 if inrange(`gcs', gcs0, gcs1)
replace `gcs_score' = 0 if `gcs' >= gcs1 & !missing(`gcs')
replace `pupils_score' = 5 if `pupils' == 1 & !missing(`pupils')
replace `pupils_score' = 0 if `pupils' == 0 & !missing(`pupils')
replace `pfratio_score' = 2 if `pfratio' <= pfr0 & !missing(`pfratio')
replace `pfratio_score' = 0 if `pfratio' > pfr0 & !missing(`pfratio')
replace `pco2_score' = 3 if `pco2' > pco21 & !missing(`pco2')
replace `pco2_score' = 1 if inrange(`pco2', pco20, pco21)
replace `pco2_score' = 0 if `pco2' < pco20 & !missing(`pco2')
replace `mv_score' = 3 if `mv' == 1
replace `mv_score' = 0 if `mv' == 0
replace `wbc_score' = 2 if `wbc' <= wbc0 & !missing(`wbc')
replace `wbc_score' = 0 if `wbc' > wbc0 & !missing(`wbc')
replace `plt_score' = 2 if `plt' < plt0 & !missing(`plt')
replace `plt_score' = 1 if inrange(`plt', plt0, plt1)
replace `plt_score' = 0 if `plt' > plt1 & !missing(`plt')
replace `lactate_score' = 4 if `lactate' >= lac1 & !missing(`lactate')
replace `lactate_score' = 1 if `lactate' >= lac0 & `lactate' < lac1
replace `lactate_score' = 0 if `lactate' < lac0 & !missing(`lactate')
replace `map_score' = 6 if ( ///
(`age' == 0 & `map' < age0_map_low) | ///
(`age' == 1 & `map' < age1_map_low) | ///
(`age' == 2 & `map' < age2_map_low) | ///
(`age' == 3 & `map' < age3_map_low) | ///
(`age' == 4 & `map' < age4_map_low) | ///
(`age' == 5 & `map' < age5_map_low) ///
) & !missing(`map')
replace `map_score' = 3 if ( ///
(`age' == 0 & inrange(`map', age0_map_low, age0_map_medium)) | ///
(`age' == 1 & inrange(`map', age1_map_low, age1_map_medium)) | ///
(`age' == 2 & inrange(`map', age2_map_low, age2_map_medium)) | ///
(`age' == 3 & inrange(`map', age3_map_low, age3_map_medium)) | ///
(`age' == 4 & inrange(`map', age4_map_low, age4_map_medium)) | ///
(`age' == 5 & inrange(`map', age5_map_low, age5_map_medium)) ///
) & !missing(`map')
replace `map_score' = 2 if ( ///
(`age' == 0 & inrange(`map', age0_map_medium2, age0_map_high)) | ///
(`age' == 1 & inrange(`map', age1_map_medium2, age1_map_high)) | ///
(`age' == 2 & inrange(`map', age2_map_medium2, age2_map_high)) | ///
(`age' == 3 & inrange(`map', age3_map_medium2, age3_map_high)) | ///
(`age' == 4 & inrange(`map', age4_map_medium2, age4_map_high)) | ///
(`age' == 5 & inrange(`map', age5_map_medium2, age5_map_high)) ///
) & !missing(`map')
replace `map_score' = 0 if ( ///
(`age' == 0 & `map' > age0_map_high) | ///
(`age' == 1 & `map' > age1_map_high) | ///
(`age' == 2 & `map' > age2_map_high) | ///
(`age' == 3 & `map' > age3_map_high) | ///
(`age' == 4 & `map' > age4_map_high) | ///
(`age' == 5 & `map' > age5_map_high) ///
) & !missing(`map')
replace `creatinine_score' = 2 if ( ///
(`age' == 0 & `creatinine' >= cr0) | ///
(`age' == 1 & `creatinine' >= cr1) | ///
(`age' == 2 & `creatinine' >= cr2) | ///
(`age' == 3 & `creatinine' >= cr3) | ///
(`age' == 4 & `creatinine' >= cr4) | ///
(`age' == 5 & `creatinine' >= cr5) ///
) & !missing(`creatinine')
replace `creatinine_score' = 0 if ( ///
(`age' == 0 & `creatinine' < cr0) | ///
(`age' == 1 & `creatinine' < cr1) | ///
(`age' == 2 & `creatinine' < cr2) | ///
(`age' == 3 & `creatinine' < cr3) | ///
(`age' == 4 & `creatinine' < cr4) | ///
(`age' == 5 & `creatinine' < cr5) ///
) & !missing(`creatinine')
/*----------------------------------------------------------------------------*/
/* Numeric Score */
tempvar pelod_score
egen `pelod_score' = rowtotal(`map_score' `lactate_score' ///
`pupils_score' `gcs_score' `mv_score' `pco2_score' `wbc_score' ///
`plt_score' `pfratio_score' `creatinine_score')
if imputationoption == 0 {
tempvar missing
egen `missing' = rowmiss(`map_score' `lactate_score' ///
`pupils_score' `gcs_score' `mv_score' `pco2_score' ///
`wbc_score' `plt_score' `pfratio_score' `creatinine_score')
replace `pelod_score' = . if `missing' != 0
}
if rawscoreoption == 1 {
gen `rawscorevar' = `pelod_score'
}
/*----------------------------------------------------------------------------*/
/* Mortality */
gen double `pelod_intermediate' = coef_intercept + ///
(`pelod_score' * coef_score) if `touse'
/* Logistic Transformation and Rounding */
gen double `pelod_final' = ///
round(100 / (1 + exp(-`pelod_intermediate')), 0.1) if `touse'
/* Asign to Permanent Variable */
replace `pelod2var' = `pelod_final' if `touse'
/*----------------------------------------------------------------------------*/
if traceoption == 1 {
set tr off
}
scalar drop `scalars'
}
}
/*----------------------------------------------------------------------------*/
di as text _newline "Calculation completed successfully." _continue
restore, not
end