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revise age groups to align with kemr, remove location stratifier
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@citizenrich
citizenrich committed Sep 1, 2023
1 parent d773e64 commit 0bec6e8
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117 changes: 35 additions & 82 deletions input/cql/KenyaEMRStratifiers.cql
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Original file line number Diff line number Diff line change
Expand Up @@ -8,85 +8,33 @@ include FHIRCommon version '4.0.1' called FC
include KenyaEMRConcepts called Cx


// ISO-8601-Derived Periods
// PEPFAR programs are required to report on the following standard age groups:
// <1, 1-4, 5-9, 10-14, 15-19, 20-24, 25-29, 30-34, 35-39, 40-44, 45-49, and 50+.
codesystem "ISO-8601-Derived Periods": 'http://ohie.org/CodeSystem/iso-8601-derived-periods' // { 'P0Y--P1Y', 'P1Y--P5Y', ... }
code "P0Y--P1Y": 'P0Y--P1Y' from "ISO-8601-Derived Periods" display '< 1 year'
code "P1Y--P5Y": 'P1Y--P5Y' from "ISO-8601-Derived Periods" display '1-4 years'
code "P5Y--P10Y": 'P5Y--P10Y' from "ISO-8601-Derived Periods" display '5-9 year'
code "P10Y--P15Y": 'P10Y--P15Y' from "ISO-8601-Derived Periods" display '10-14 year'
code "P15Y--P20Y": 'P15Y--P20Y' from "ISO-8601-Derived Periods" display '15-19 year'
code "P20Y--P25Y": 'P20Y--P25Y' from "ISO-8601-Derived Periods" display '20-24 year'
code "P25Y--P30Y": 'P25Y--P30Y' from "ISO-8601-Derived Periods" display '25-29 year'
code "P30Y--P35Y": 'P30Y--P35Y' from "ISO-8601-Derived Periods" display '30-34 year'
code "P35Y--P40Y": 'P35Y--P40Y' from "ISO-8601-Derived Periods" display '35-39 year'
code "P40Y--P45Y": 'P40Y--P45Y' from "ISO-8601-Derived Periods" display '40-45 year'
code "P45Y--P50Y": 'P45Y--P50Y' from "ISO-8601-Derived Periods" display '45-50 year'
code "P50Y--P9999Y": 'P50Y--P9999Y' from "ISO-8601-Derived Periods" display '50+ years'
// Starting in FY22, the age bands for TX_CURR will be expanded to 50-54, 55-59, 60-64, and 65+
code "P50Y--P55Y": 'P50Y--P55Y' from "ISO-8601-Derived Periods" display '50-55 year'
code "P55Y--P60Y": 'P50Y--P60Y' from "ISO-8601-Derived Periods" display '55-60 year'
code "P60Y--P65Y": 'P50Y--P60Y' from "ISO-8601-Derived Periods" display '60-65 year'
code "P65Y--P9999Y": 'P50Y--P9999Y' from "ISO-8601-Derived Periods" display '65+ years'


parameter "Measurement Period" Interval<DateTime> default Interval[@1990-01-01T00:00:00.0, @2022-08-30T00:00:00.0]

// Not included yet: Key Population Type [Required]
// People who inject drugs (PWID)
// Men who have sex with men (MSM)
// Transgender people (TG)
// Female sex workers (FSW)
// People in prison and other closed settings
codesystem "KEMR Periods": 'http://ohie.org/CodeSystem/kemr-periods'
code "<1": '<1' from "KEMR Periods" display '<1'
code "1-9": '1-9' from "KEMR Periods" display '1-9'
code "10-14": '10-14' from "KEMR Periods" display '10-14'
code "15-19": '15-19' from "KEMR Periods" display '15-19'
code "20-24": '20-24' from "KEMR Periods" display '20-24'
code "25+": '25+' from "KEMR Periods" display '25+'


parameter "Measurement Period" Interval<DateTime> default Interval[@2023-04-01T00:00:00.0, @2023-06-30T00:00:00.0]


context Patient


// unknown and other is included in fhir core patient
// mer guidance requires m, f, unknown, kenya emr uses only mf
define "Sex":
Patient.gender.value


// Age Group
define "Age Group":
case
// age at start of measurement period or end of it?
when AgeInYearsAt(start of "Measurement Period") in Interval[0, 1) then "P0Y--P1Y"
when AgeInYearsAt(start of "Measurement Period") in Interval[1, 5) then "P1Y--P5Y"
when AgeInYearsAt(start of "Measurement Period") in Interval[5, 10) then "P5Y--P10Y"
when AgeInYearsAt(start of "Measurement Period") in Interval[10, 15) then "P10Y--P15Y"
when AgeInYearsAt(start of "Measurement Period") in Interval[15, 20) then "P15Y--P20Y"
when AgeInYearsAt(start of "Measurement Period") in Interval[20, 25) then "P20Y--P25Y"
when AgeInYearsAt(start of "Measurement Period") in Interval[25, 30) then "P25Y--P30Y"
when AgeInYearsAt(start of "Measurement Period") in Interval[30, 35) then "P30Y--P35Y"
when AgeInYearsAt(start of "Measurement Period") in Interval[35, 40) then "P35Y--P40Y"
when AgeInYearsAt(start of "Measurement Period") in Interval[40, 45) then "P40Y--P45Y"
when AgeInYearsAt(start of "Measurement Period") in Interval[45, 50) then "P45Y--P50Y"
when AgeInYearsAt(start of "Measurement Period") in Interval[50, null] then "P50Y--P9999Y"
else null
end


define "Age Group TXCURR":
case
when AgeInYearsAt(start of "Measurement Period") in Interval[0, 1) then "P0Y--P1Y"
when AgeInYearsAt(start of "Measurement Period") in Interval[1, 5) then "P1Y--P5Y"
when AgeInYearsAt(start of "Measurement Period") in Interval[5, 10) then "P5Y--P10Y"
when AgeInYearsAt(start of "Measurement Period") in Interval[10, 15) then "P10Y--P15Y"
when AgeInYearsAt(start of "Measurement Period") in Interval[15, 20) then "P15Y--P20Y"
when AgeInYearsAt(start of "Measurement Period") in Interval[20, 25) then "P20Y--P25Y"
when AgeInYearsAt(start of "Measurement Period") in Interval[25, 30) then "P25Y--P30Y"
when AgeInYearsAt(start of "Measurement Period") in Interval[30, 35) then "P30Y--P35Y"
when AgeInYearsAt(start of "Measurement Period") in Interval[35, 40) then "P35Y--P40Y"
when AgeInYearsAt(start of "Measurement Period") in Interval[40, 45) then "P40Y--P45Y"
when AgeInYearsAt(start of "Measurement Period") in Interval[45, 50) then "P45Y--P50Y"
when AgeInYearsAt(start of "Measurement Period") in Interval[50, 55) then "P50Y--P55Y"
when AgeInYearsAt(start of "Measurement Period") in Interval[55, 60) then "P55Y--P60Y"
when AgeInYearsAt(start of "Measurement Period") in Interval[60, 65) then "P60Y--P65Y"
when AgeInYearsAt(start of "Measurement Period") in Interval[65, null] then "P65Y--P9999Y"
when AgeInYearsAt(start of "Measurement Period") in Interval[0, 1) then "<1"
when AgeInYearsAt(start of "Measurement Period") in Interval[1, 9) then "1-9"
when AgeInYearsAt(start of "Measurement Period") in Interval[10, 14) then "10-14"
when AgeInYearsAt(start of "Measurement Period") in Interval[15, 19) then "15-19"
when AgeInYearsAt(start of "Measurement Period") in Interval[20, 24) then "20-24"
when AgeInYearsAt(start of "Measurement Period") in Interval[25, null] then "25+"
else null
end

Expand All @@ -103,17 +51,18 @@ define "Last Location":
)


// http://fhir.openmrs.org/ext/patient/identifier#location

define "OpenMRS Location":
[Patient] P
// this url is in the ig, but is not correct: 'http://fhir.openmrs.org/core/StructureDefinition/omrs-patient-identifier-location'}
where singleton from {P.identifier.extension[0].url ~ 'http://fhir.openmrs.org/ext/patient/identifier'}
or singleton from {P.identifier.extension[0].url ~ 'http://fhir.openmrs.org/ext/patient/identifier#location'}
or singleton from {P.identifier.extension[1].url ~ 'http://fhir.openmrs.org/ext/patient/identifier'}
or singleton from {P.identifier.extension[1].url ~ 'http://fhir.openmrs.org/ext/patient/identifier#location'}
// or singleton from {P.identifier.extension[1].url ~ 'http://fhir.openmrs.org/ext/patient/identifier'}
// or singleton from {P.identifier.extension[1].url ~ 'http://fhir.openmrs.org/ext/patient/identifier#location'}
return singleton from {P.identifier.extension[0].value.reference.value}



define "Last serviceProvider":
// Some of the Synthea encounters do not have a serviceProvider, so this can return nothing
// Filter out those that are null, then take the last
Expand All @@ -123,32 +72,36 @@ define "Last serviceProvider":


// if..then..else
define "Location":
define "Location Deux":
if "Last Location" is not null then ("Last Location")
// else "Last serviceProvider"
else
if "Last serviceProvider" is not null then "Last serviceProvider"
else
if "OpenMRS Location" is not null then ("OpenMRS Location")
else if "Last serviceProvider" is not null then ("Last serviceProvider")
else if "OpenMRS Location" is not null then ("OpenMRS Location")
else null


// case switch does not work
define "Location Case Switch":
define "Location":
case
// location identifier on patient
when "OpenMRS Location" is not null then ("OpenMRS Location")
// then location of last encounter
when "Last Location" is not null then ("Last Location")
// then organization of last encounter
else "Last serviceProvider"
when "Last serviceProvider" is not null then ("Last serviceProvider")
else null
end


define "Debug location":
Combine({ "Location", "Sex"}, ':')


define "Age Group/Sex/Location":
"Age Group".code + ':' + "Sex" + ':' + "Location"
"Age Group".code & ':' & "Sex" & ':' & "Location"


define "Age Group/Sex/Location TXCURR":
"Age Group TXCURR".code + ':' + "Sex" + ':' + "Location"
"Age Group".code + ':' + "Sex" + ':' + "Location"


define "Age Group/Sex/Location Case Switch":
"Age Group".code + ':' + "Sex" + ':' + "Location"
4 changes: 2 additions & 2 deletions input/cql/KenyaEMRTXCURR.cql
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Original file line number Diff line number Diff line change
Expand Up @@ -262,7 +262,7 @@ define "OpenMRS Location":


define "Stratification":
Stratifiers."Age Group/Sex/Location TXCURR"
Stratifiers."Age Group/Sex"


define "Stratifier": "Stratification"
// define "Stratifier": "Stratification"
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