Update indicator CQL and related resources (#32)

* Added updated template CQL

* Updated measures and libraries

* Publishing from develop branch

* Sanitized  measure descriptions

.github/workflows/deploy.yml

@@ -7,9 +7,8 @@ name: Deploy to Github Pages
 
 # Controls when the action will run. 
 on:
-  # Triggers the workflow on push or pull request events but only for the main branch
   push:
-    branches: [ main ]
+    branches: [ develop ]
 
   # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:

input/cql/HIVB2DT.cql → input/cql/HIVB2DTLogic.cql

@@ -1,12 +1,18 @@
-/*
- * Library: HIV.B2.DT
- * Check for signs of serious illness
- * Consolidated guidelines on HIV prevention, testing, treatment, service delivery and monitoring: recommendations for a public health approach (2021) Chapter 5: Advanced HIV Disease. Figure 5.1: Algorithm for providing a package of care for people with advanced HIV disease.  
- * Should this just be for anyone with HIV? 
- * Wouldn't other  disease domains also code for general exam?
- */
-
-library HIVB2DT
+/**
+Library: HIV.B2.DT Logic
+
+@DecisionID: HIV.B2.DT
+@BusinessRule:
+@Trigger: 
+@Description: 
+
+Check for signs of serious illness
+Consolidated guidelines on HIV prevention, testing, treatment, service delivery and monitoring: recommendations for a public health approach (2021) Chapter 5: Advanced HIV Disease. Figure 5.1: Algorithm for providing a package of care for people with advanced HIV disease.  
+Should this just be for anyone with HIV? 
+Wouldn't other  disease domains also code for general exam?
+*/
+
+library HIVB2DTLogic
 
  using FHIR version '4.0.1'
 

input/cql/HIVB7DT.cql → input/cql/HIVB7DTLogic.cql

@@ -1,10 +1,18 @@
-/*
- * Library: HIV.B7.DT Test Using Algorithm
- * WHO standard testing strategy for HIV-1 diagnosis (among people ≥18 months of age)
- * HIV.B7 Test for HIV using testing algorithm, HIV.C4 Test for HIV using testing algorithm, HIV.D.11 Retest using HIV strategy
- */
+/**
+Library: HIV.B7.DT Logic
+
+@DecisionID: HIV.B7.DT
+@BusinessRule:
+@Trigger: 
+@Description: 
+
+Test Using Algorithm
+
+WHO standard testing strategy for HIV-1 diagnosis (among people ≥18 months of age)
+HIV.B7 Test for HIV using testing algorithm, HIV.C4 Test for HIV using testing algorithm, HIV.D.11 Retest using HIV strategy
+*/
 
-library HIVB7DT
+library HIVB7DTLogic
 
 using FHIR version '4.0.1'
 

input/cql/HIVConceptsCustom.cql

@@ -1,4 +1,4 @@
-library HIVConcepts_custom
+library HIVConceptsCustom
 
 codesystem "ConditionCategoryCodes": 'http://terminology.hl7.org/CodeSystem/condition-category'
 codesystem "ConditionClinicalStatusCodes": 'http://terminology.hl7.org/CodeSystem/condition-clinical'

input/cql/HIVIND11Logic.cql

@@ -1,4 +1,4 @@
-/*
+/**
  * Library: HIV.IND.11 Logic
  * Ref No: PRV.11
  * Short Name: OAMT coverage
@@ -14,40 +14,41 @@
  * Denominator Exclusions: 
  *
  * Disaggregations:
- * • Gender (female, male, other*)
- * • Age (<25, 25+ years)
- * • Provider type (key population-led or community-led organization, public sector provider, other entities such as private for-profit and not-for-profit organizations, including faith-based, international, nongovernmental)
- * • Setting: facility-based service (including hospitals, health clinics, general practice offices, etc.) or community-based service (including drop-in centres, community service delivery points, mobile clinics or vans, outreach teams, community support groups, etc.)
- * • Cities and other administrative regions of epidemiologic importance
- * 
+ * • Gender (female, male, other*) 
+ *  • Age (<25, 25+ years) 
+ *  • Provider type (key population-led or community-led organization, public sector provider, other entities such as private for-profit and not-for-profit organizations, including faith-based, international, nongovernmental) 
+ *  • Setting: facility-based service (including hospitals, health clinics, general practice offices, etc.) or community-based service (including drop-in centres, community service delivery points, mobile clinics or vans, outreach teams, community support groups, etc.) 
+ *  • Cities and other administrative regions of epidemiologic importance
+ *
  * Disaggregation Elements: Gender | Age (<25, 25+ years)
  *
  * Numerator and Denominator Elements:
- * Currently on OAMT | Key population member type | Reporting date
+ * Currently on OAMT 
+ *  Key population member type 
+ *  Reporting date
  *
  * Reference: Consolidated guidelines on person-centred HIV strategic information: strengthening routine data for impact. Geneva: World Health Organization; 2022
  * 
  * Data Concepts:
- *  
- * HIV.A.DE17: Age | Calculated age (number of years) of the client based on date of birth 
- * HIV.A.DE18: Gender* | Gender of the client* 
- * HIV.A.DE19: Female | Client identifies as female 
- * HIV.A.DE20: Male | Client identifies as male 
- * HIV.A.DE21: Transgender male | Client identifies as transgender male 
- * HIV.A.DE22: Transgender female | Client identifies as transgender female 
- * HIV.A.DE23: Other | Additional category 
- * HIV.B.DE50: Key population member type* | The type of key population that the client is included in 
- * HIV.B.DE51: Sex worker | Client is a sex worker 
- * HIV.B.DE52: Men who have sex with men | Client is a man who has sex with men 
- * HIV.B.DE53: Trans and gender-diverse people | Client identifies as trans and gender-diverse 
- * HIV.B.DE54: People who inject drugs | Client is a person who injects drugs 
- * HIV.B.DE55: People living in prisons and other closed settings | Client lives in a prison or another closed setting 
- * HIV.E.DE114: Key population member type* | The type of key population that the infant's mother is included in 
- * HIV.E.DE115: Sex worker | Infant's mother is a sex worker 
- * HIV.E.DE116: People who inject drugs | Infant's mother is a person who injects drugs 
- * HIV.E.DE117: Trans and gender-diverse people | Infant's mother identifies as trans and gender-diverse 
- * HIV.E.DE118: People living in prisons and other closed setting | Infant's mother is in a prison or closed setting 
- * HIV.PRV.DE20: Currently on OAMT | Client is currently on opioid agonist maintenance treatment (OAMT) at reporting date, defined according to country/program to account for medication dispensed and LTFU criterion 
+ * HIV.A.DE17: Age | Calculated age (number of years) of the client based on date of birth
+ * HIV.A.DE18: Gender* | Gender of the client*
+ * HIV.A.DE19: Female | Client identifies as female
+ * HIV.A.DE20: Male | Client identifies as male
+ * HIV.A.DE21: Transgender male | Client identifies as transgender male
+ * HIV.A.DE22: Transgender female | Client identifies as transgender female
+ * HIV.A.DE23: Other | Additional category
+ * HIV.B.DE50: Key population member type* | The type of key population that the client is included in
+ * HIV.B.DE51: Sex worker | Client is a sex worker
+ * HIV.B.DE52: Men who have sex with men | Client is a man who has sex with men
+ * HIV.B.DE53: Trans and gender-diverse people | Client identifies as trans and gender-diverse
+ * HIV.B.DE54: People who inject drugs | Client is a person who injects drugs
+ * HIV.B.DE55: People living in prisons and other closed settings | Client lives in a prison or another closed setting
+ * HIV.E.DE114: Key population member type* | The type of key population that the infant's mother is included in
+ * HIV.E.DE115: Sex worker | Infant's mother is a sex worker
+ * HIV.E.DE116: People who inject drugs | Infant's mother is a person who injects drugs
+ * HIV.E.DE117: Trans and gender-diverse people | Infant's mother identifies as trans and gender-diverse
+ * HIV.E.DE118: People living in prisons and other closed setting | Infant's mother is in a prison or closed setting
+ * HIV.PRV.DE20: Currently on OAMT | Client is currently on opioid agonist maintenance treatment (OAMT) at reporting date, defined according to country/program to account for medication dispensed and LTFU criterion
  * HIV.Config.DE22: Reporting date | Reporting date, for surveys performed on a specific date
  *
  * Additional Context
@@ -65,7 +66,43 @@ using FHIR version '4.0.1'
 
 include HIVCommon version '0.0.1' called HIC
 include FHIRHelpers version '4.0.1'
-include WHOCommon called WCom
 include FHIRCommon called FC
+include WHOCommon called WCom
 
 // Indicator Definition
+parameter "Measurement Period" Interval<Date> default Interval[@2023-01-01, @2023-01-30]
+
+context Patient
+/* Populations */
+
+/*
+ *Initial Population
+ */
+
+define "Initial Population":
+  true
+
+/**
+ * Numerator
+ * 
+ * Definition: Number of people on OAMT at specified census date
+ * Calculation: Number of clients with "Key population member type"='People who inject drugs' AND "Currently on OAMT"=True for a specific "Reporting date"
+ */
+
+define "Numerator":
+  true
+
+
+/**
+ * Denominator
+ *
+ * Definition: a) Programme/service provider level: number of opioid dependent people accessing service | b) Population level: population size estimate of opioid dependent people in relevant geographic area
+ * Calculation: Programme/service provider level: | COUNT of opioid dependent people accessing service |  | Population level:  | *Estimated population size of opioid dependent people in relevant geographic area
+ */
+
+define "Denominator":
+  true
+
+
+/* end Populations */
+

input/cql/HIVIND12Logic.cql

@@ -1,4 +1,4 @@
-/*
+/**
  * Library: HIV.IND.12 Logic
  * Ref No: PRV.12
  * Short Name: Total person-years on OAMT
@@ -14,36 +14,39 @@
  * Denominator Exclusions: 
  *
  * Disaggregations:
- * • Gender (female, male, other*)
- * • Age (15–19, 20–24, 25–49, 50+ years)
- * • Provider type (key population-led or community-led organization, public sector provider, other entities such as private for-profit and not-for-profit organizations, including faith-based, international, nongovernmental)
- * • Setting: facility-based service (including hospitals, health clinics, general practice offices, etc.) or community-based service (including drop-in centres, community service delivery points, mobile clinics or vans, outreach teams, community support groups, etc.)
- * • Cities and other administrative regions of epidemiologic importance
- * 
+ * • Gender (female, male, other*) 
+ *  • Age (15–19, 20–24, 25–49, 50+ years) 
+ *  • Provider type (key population-led or community-led organization, public sector provider, other entities such as private for-profit and not-for-profit organizations, including faith-based, international, nongovernmental) 
+ *  • Setting: facility-based service (including hospitals, health clinics, general practice offices, etc.) or community-based service (including drop-in centres, community service delivery points, mobile clinics or vans, outreach teams, community support groups, etc.) 
+ *  • Cities and other administrative regions of epidemiologic importance
+ *
  * Disaggregation Elements: Gender | Age
  *
  * Numerator and Denominator Elements:
- * Date OAMT initiated | Date of loss to follow-up or OAMT stopped | Medications prescribed | Reporting period end date | Reporting period start date
+ * Date OAMT initiated 
+ *  Date of loss to follow-up or OAMT stopped 
+ *  Medications prescribed 
+ *  Reporting period end date 
+ *  Reporting period start date
  *
  * Reference: Consolidated guidelines on person-centred HIV strategic information: strengthening routine data for impact. Geneva: World Health Organization; 2022
  * 
  * Data Concepts:
- *  
- * HIV.A.DE17: Age | Calculated age (number of years) of the client based on date of birth 
- * HIV.A.DE18: Gender* | Gender of the client* 
- * HIV.A.DE19: Female | Client identifies as female 
- * HIV.A.DE20: Male | Client identifies as male 
- * HIV.A.DE21: Transgender male | Client identifies as transgender male 
- * HIV.A.DE22: Transgender female | Client identifies as transgender female 
- * HIV.A.DE23: Other | Additional category 
- * HIV.C.DE75: Medications prescribed | Medications the client was prescribed 
- * HIV.C.DE76: PrEP for HIV prevention | Client was prescribed pre-exposure prophylaxis (PrEP) for HIV prevention 
- * HIV.C.DE77: PEP for HIV prevention | Client was prescribed post-exposure prophylaxis (PEP) for HIV prevention 
- * HIV.C.DE78: Other | Client was prescribed other medications 
- * HIV.D.DE457: Medications prescribed | Name or regimen code of all other medications prescribed during the visit 
- * HIV.PRV.DE17: Date OAMT initiated | Date client initiated opioid agonist maintenance treatment (OAMT) 
- * HIV.PRV.DE25: Date of loss to follow-up or OAMT stopped | Date of loss to follow-up or opioid agonist maintenance treatment (OAMT) stopped 
- * HIV.Config.DE20: Reporting period end date | End date of the reporting period 
+ * HIV.A.DE17: Age | Calculated age (number of years) of the client based on date of birth
+ * HIV.A.DE18: Gender* | Gender of the client*
+ * HIV.A.DE19: Female | Client identifies as female
+ * HIV.A.DE20: Male | Client identifies as male
+ * HIV.A.DE21: Transgender male | Client identifies as transgender male
+ * HIV.A.DE22: Transgender female | Client identifies as transgender female
+ * HIV.A.DE23: Other | Additional category
+ * HIV.C.DE75: Medications prescribed | Medications the client was prescribed
+ * HIV.C.DE76: PrEP for HIV prevention | Client was prescribed pre-exposure prophylaxis (PrEP) for HIV prevention
+ * HIV.C.DE77: PEP for HIV prevention | Client was prescribed post-exposure prophylaxis (PEP) for HIV prevention
+ * HIV.C.DE78: Other | Client was prescribed other medications
+ * HIV.D.DE457: Medications prescribed | Name or regimen code of all other medications prescribed during the visit
+ * HIV.PRV.DE17: Date OAMT initiated | Date client initiated opioid agonist maintenance treatment (OAMT)
+ * HIV.PRV.DE25: Date of loss to follow-up or OAMT stopped | Date of loss to follow-up or opioid agonist maintenance treatment (OAMT) stopped
+ * HIV.Config.DE20: Reporting period end date | End date of the reporting period
  * HIV.Config.DE21: Reporting period start date | Start date of the reporting period
  *
  * Additional Context
@@ -61,7 +64,43 @@ using FHIR version '4.0.1'
 
 include HIVCommon version '0.0.1' called HIC
 include FHIRHelpers version '4.0.1'
-include WHOCommon called WCom
 include FHIRCommon called FC
+include WHOCommon called WCom
 
 // Indicator Definition
+parameter "Measurement Period" Interval<Date> default Interval[@2023-01-01, @2023-01-30]
+
+context Patient
+/* Populations */
+
+/*
+ *Initial Population
+ */
+
+define "Initial Population":
+  true
+
+/**
+ * Numerator
+ * 
+ * Definition: Total PYFU on OAMT during defined reporting period. | Calculated from the sum of the time on OAMT of each OAMT recipient during the reporting period.
+ * Calculation: SUM of [DIFFERENCE in MIN("Date OAMT initiated", "Reporting period start date") and MAX("Date of loss to follow-up or OAMT stopped", "Reporting period end date")] for all clients with "Medications prescribed" IN 'Methadone', 'Buprenorphine'
+ */
+
+define "Numerator":
+  true
+
+
+/**
+ * Denominator
+ *
+ * Definition: a) Programme/service provider level: estimated PYFU for all opioid dependent people accessing service during defined reporting period | b) Population level: estimated PYFU for total population of opioid dependent people in relevant geographic area during defined reporting period
+ * Calculation: Service level: Not calculated in DAK |  | Population denominator:  | *Estimated PYFU for all opioid-dependent people accessing service during defined reporting period |  | Note: Can be reported only as numerator; by population or service level if these denominator estimates available.
+ */
+
+define "Denominator":
+  true
+
+
+/* end Populations */
+