updated definitions

DESCRIPTION

@@ -19,7 +19,7 @@ Suggests:
   testthat,
   knitr
 License: Apache License
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2
 Roxygen: list(markdown = TRUE)
 Encoding: UTF-8
 Language: en-US

extras/UpdatePhenotypes.R

@@ -369,9 +369,9 @@ for (i in (1:nrow(cohortRecord))) {
     "cohorts",
     paste0(cohortRecordUnit$cohortId, ".json")
   ))
-
+debug(CohortDefinitionReviewer::parseCohortDefinitionSpecifications)
   parsed <-
-    CirceComparator::parseCohortDefinitionSpecifications(cohortDefinition = cohortJson |>
+    CohortDefinitionReviewer::parseCohortDefinitionSpecifications(cohortDefinition = cohortJson |>
       RJSONIO::fromJSON(digits = 23))
   if (nrow(parsed) > 0) {
     cohortRecordAugmented[[i]] <- cohortRecordUnit |>

inst/cohorts/1029.json

@@ -176,7 +176,7 @@
 					{
 						"concept" : {
 							"CONCEPT_ID" : 135759,
-							"CONCEPT_NAME" : "Sézary's disease of extranodal AND/OR solid organ site",
+							"CONCEPT_NAME" : "Sézary's disease of extranodal AND/OR solid organ site",
 							"STANDARD_CONCEPT" : "S",
 							"STANDARD_CONCEPT_CAPTION" : "Standard",
 							"INVALID_REASON" : "V",

inst/cohorts/1163.json

@@ -287,7 +287,7 @@
 		},
 		{
 			"id" : 9,
-			"name" : "Kidney transplant conditions",
+			"name" : "Kidney transplant conditions",
 			"expression" : {
 				"items" : [
 					{

inst/cohorts/1215.json

@@ -2509,7 +2509,7 @@
 					{
 						"concept" : {
 							"CONCEPT_ID" : 4261334,
-							"CONCEPT_NAME" : "Pseudolymphoma of lung in Sj�gren's disease",
+							"CONCEPT_NAME" : "Pseudolymphoma of lung in Sjögren's disease",
 							"STANDARD_CONCEPT" : "S",
 							"STANDARD_CONCEPT_CAPTION" : "Standard",
 							"INVALID_REASON" : "V",
@@ -22926,7 +22926,7 @@
 					{
 						"concept" : {
 							"CONCEPT_ID" : 761036,
-							"CONCEPT_NAME" : "Torr�-Muir syndrome co-occurrent with benign sebaceous neoplasm",
+							"CONCEPT_NAME" : "Torré-Muir syndrome co-occurrent with benign sebaceous neoplasm",
 							"STANDARD_CONCEPT" : "S",
 							"STANDARD_CONCEPT_CAPTION" : "Standard",
 							"INVALID_REASON" : "V",

inst/cohorts/1225.json

@@ -7203,7 +7203,7 @@
 	"InclusionRules" : [
 		{
 			"name" : "Evidence of varicella zoster virus infection in the eye",
-			"description" : "a. Positive PCR for varicella zoster virus on aqueous specimen (observations, measurements)\nb. Sectoral iris atrophy in a patient =60 years of age\nc. Concurrent or recent dermatomal Herpes zoster",
+			"description" : "a. Positive PCR for varicella zoster virus on aqueous specimen (observations, measurements)\nb. Sectoral iris atrophy in a patient ≥60 years of age\nc. Concurrent or recent dermatomal Herpes zoster",
 			"expression" : {
 				"Type" : "ANY",
 				"CriteriaList" : [

inst/cohorts/1226.json

@@ -7203,7 +7203,7 @@
 	"InclusionRules" : [
 		{
 			"name" : "Evidence of varicella zoster virus infection in the eye",
-			"description" : "a. Positive PCR for varicella zoster virus on aqueous specimen (observations, measurements)\nb. Sectoral iris atrophy in a patient =60 years of age\nc. Concurrent or recent dermatomal Herpes zoster",
+			"description" : "a. Positive PCR for varicella zoster virus on aqueous specimen (observations, measurements)\nb. Sectoral iris atrophy in a patient ≥60 years of age\nc. Concurrent or recent dermatomal Herpes zoster",
 			"expression" : {
 				"Type" : "ANY",
 				"CriteriaList" : [

inst/cohorts/1227.json

@@ -7369,7 +7369,7 @@
 	"InclusionRules" : [
 		{
 			"name" : "Evidence of herpes simplex infection in the eye",
-			"description" : "a. Positive PCR for herpes simplex on aqueous specimen (observations, measurements)\nb. Sectoral iris atrophy in a patient =50 years of age\nc. Herpes simplex keratitis",
+			"description" : "a. Positive PCR for herpes simplex on aqueous specimen (observations, measurements)\nb. Sectoral iris atrophy in a patient ≤50 years of age\nc. Herpes simplex keratitis",
 			"expression" : {
 				"Type" : "ANY",
 				"CriteriaList" : [

inst/cohorts/1228.json

@@ -7369,7 +7369,7 @@
 	"InclusionRules" : [
 		{
 			"name" : "Evidence of herpes simplex infection in the eye",
-			"description" : "a. Positive PCR for herpes simplex on aqueous specimen (observations, measurements)\nb. Sectoral iris atrophy in a patient =50 years of age\nc. Herpes simplex keratitis",
+			"description" : "a. Positive PCR for herpes simplex on aqueous specimen (observations, measurements)\nb. Sectoral iris atrophy in a patient ≤50 years of age\nc. Herpes simplex keratitis",
 			"expression" : {
 				"Type" : "ANY",
 				"CriteriaList" : [

inst/cohorts/1229.json

@@ -862,7 +862,7 @@
 					{
 						"concept" : {
 							"CONCEPT_ID" : 3655585,
-							"CONCEPT_NAME" : "Mucocutaneous Behçet disease",
+							"CONCEPT_NAME" : "Mucocutaneous Behçet disease",
 							"STANDARD_CONCEPT" : "S",
 							"STANDARD_CONCEPT_CAPTION" : "Standard",
 							"INVALID_REASON" : "V",
@@ -5940,7 +5940,7 @@
 					{
 						"concept" : {
 							"CONCEPT_ID" : 3655585,
-							"CONCEPT_NAME" : "Mucocutaneous Behçet disease",
+							"CONCEPT_NAME" : "Mucocutaneous Behçet disease",
 							"STANDARD_CONCEPT" : "S",
 							"STANDARD_CONCEPT_CAPTION" : "Standard",
 							"INVALID_REASON" : "V",
@@ -5957,7 +5957,7 @@
 					{
 						"concept" : {
 							"CONCEPT_ID" : 4293711,
-							"CONCEPT_NAME" : "Behçet's disease affecting oral mucosa",
+							"CONCEPT_NAME" : "Behçet's disease affecting oral mucosa",
 							"STANDARD_CONCEPT" : "S",
 							"STANDARD_CONCEPT_CAPTION" : "Standard",
 							"INVALID_REASON" : "V",
@@ -6042,7 +6042,7 @@
 					{
 						"concept" : {
 							"CONCEPT_ID" : 4295174,
-							"CONCEPT_NAME" : "Penile ulceration due to Behçet's disease",
+							"CONCEPT_NAME" : "Penile ulceration due to Behçet's disease",
 							"STANDARD_CONCEPT" : "S",
 							"STANDARD_CONCEPT_CAPTION" : "Standard",
 							"INVALID_REASON" : "V",