diff --git a/R/checks.R b/R/checks.R index 9615a141..755f4122 100644 --- a/R/checks.R +++ b/R/checks.R @@ -1,4 +1,4 @@ -# Copyright 2023 DARWIN EU (C) +# Copyright 2024 DARWIN EU (C) # # This file is part of CodelistGenerator # diff --git a/R/codesFromConceptSet.R b/R/codesFromConceptSet.R index 8e25c0b7..092794c5 100644 --- a/R/codesFromConceptSet.R +++ b/R/codesFromConceptSet.R @@ -1,4 +1,4 @@ -# Copyright 2023 DARWIN EU (C) +# Copyright 2024 DARWIN EU (C) # # This file is part of CodelistGenerator # @@ -299,7 +299,13 @@ addDetails <- function(conceptList, cdm){ conceptList <- split( x = conceptList %>% dplyr::select(!"concept_set"), f = as.factor(conceptList$concept_set) - )} + ) + } + + for(i in seq_along(conceptList)){ + conceptList[[i]] <- conceptList[[i]] %>% + dplyr::arrange(.data$concept_name) + } return(conceptList) diff --git a/R/codesInUse.R b/R/codesInUse.R index 0282ed89..83439088 100644 --- a/R/codesInUse.R +++ b/R/codesInUse.R @@ -1,3 +1,19 @@ +# Copyright 2024 DARWIN EU (C) +# +# This file is part of CodelistGenerator +# +# 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. + #' Filter a codelist to keep only the codes used in the database #' #' @param x A codelist diff --git a/R/compareCodelists.R b/R/compareCodelists.R index dcc1717c..f534ae7c 100644 --- a/R/compareCodelists.R +++ b/R/compareCodelists.R @@ -1,4 +1,4 @@ -# Copyright 2023 DARWIN EU® +# Copyright 2024 DARWIN EU® # # This file is part of IncidencePrevalence # diff --git a/R/drugCodes.R b/R/drugCodes.R index 8d4dc159..f2451a54 100644 --- a/R/drugCodes.R +++ b/R/drugCodes.R @@ -1,4 +1,4 @@ -# Copyright 2023 DARWIN EU® +# Copyright 2024 DARWIN EU® # # This file is part of IncidencePrevalence # diff --git a/R/getCandidateCodes.R b/R/getCandidateCodes.R index 6c93c18d..bddad896 100644 --- a/R/getCandidateCodes.R +++ b/R/getCandidateCodes.R @@ -1,4 +1,4 @@ -# Copyright 2023 DARWIN EU® +# Copyright 2024 DARWIN EU (C) # # This file is part of IncidencePrevalence # @@ -14,8 +14,6 @@ # See the License for the specific language governing permissions and # limitations under the License. - - #' Generate candidate codelist for the OMOP CDM #' #' @description diff --git a/R/getICD10StandardCodes.R b/R/getICD10StandardCodes.R index 19165306..1d24bd6c 100644 --- a/R/getICD10StandardCodes.R +++ b/R/getICD10StandardCodes.R @@ -1,3 +1,19 @@ +# Copyright 2024 DARWIN EU (C) +# +# This file is part of IncidencePrevalence +# +# 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. + #' Get corresponding standard codes for ICD-10 chapters and sub-chapters #' #' @param cdm cdm_reference via CDMConnector diff --git a/R/getMappings.R b/R/getMappings.R index a0a55ba0..61ada293 100644 --- a/R/getMappings.R +++ b/R/getMappings.R @@ -1,4 +1,4 @@ -# Copyright 2023 DARWIN EU® +# Copyright 2024 DARWIN EU® # # This file is part of IncidencePrevalence # diff --git a/R/inputValidation.R b/R/inputValidation.R index a7eee75b..97682be5 100644 --- a/R/inputValidation.R +++ b/R/inputValidation.R @@ -1,4 +1,4 @@ -# Copyright 2023 DARWIN EU® +# Copyright 2024 DARWIN EU (C) # # This file is part of IncidencePrevalence # diff --git a/R/mockVocabRef.R b/R/mockVocabRef.R index ccb2575b..8c67e22a 100644 --- a/R/mockVocabRef.R +++ b/R/mockVocabRef.R @@ -1,4 +1,4 @@ -# Copyright 2023 DARWIN EU® +# Copyright 2024 DARWIN EU (C) # # This file is part of IncidencePrevalence # diff --git a/R/runSearch.R b/R/runSearch.R index 46409d64..28abf7e5 100644 --- a/R/runSearch.R +++ b/R/runSearch.R @@ -1,4 +1,4 @@ -# Copyright 2023 DARWIN EU® +# Copyright 2024 DARWIN EU® # # This file is part of IncidencePrevalence # @@ -421,16 +421,9 @@ getMatches <- function(words, for (j in seq_along(workingExclude)) { if (nchar(workingExclude[j]) >= 1) { - if(inherits(workingConcepts, "tbl_sql")){ - workingConcepts <- workingConcepts %>% - dplyr::filter(dplyr::sql(paste0("concept_name LIKE '%", .env$workingExclude[j], "%'"))) - } else { - workingConcepts <- workingConcepts %>% - dplyr::filter(stringr::str_detect( - .data$concept_name, - .env$workingExclude[j] - )) - } + cToSearch <- paste0("%", workingExclude[j], "%") + workingConcepts <- workingConcepts %>% + dplyr::filter(stringr::str_like(.data$concept_name, .env$cToSearch)) } } diff --git a/R/summariseCodeUse.R b/R/summariseCodeUse.R index ff60e77c..c95fdad0 100644 --- a/R/summariseCodeUse.R +++ b/R/summariseCodeUse.R @@ -1,3 +1,19 @@ +# Copyright 2024 DARWIN EU (C) +# +# This file is part of IncidencePrevalence +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + #' Summarise code use in patient-level data #' #' @param x List of concept IDs diff --git a/R/vocabUtilities.R b/R/vocabUtilities.R index 73928ef9..938ccb90 100644 --- a/R/vocabUtilities.R +++ b/R/vocabUtilities.R @@ -1,4 +1,4 @@ -# Copyright 2023 DARWIN EU® +# Copyright 2024 DARWIN EU (C) # # This file is part of IncidencePrevalence # @@ -390,14 +390,20 @@ getDescendantsOnly <- function(cdm, conceptId, ingredientRange, doseForm) { } getDescendantsAndAncestor <- function(cdm, conceptId, ingredientRange, doseForm) { + conceptIdDbTable <- omopgenerics::uniqueTableName() + cdm <- omopgenerics::insertTable(cdm = cdm, + name = conceptIdDbTable, + table = dplyr::tibble(ancestor_concept_id = as.integer(conceptId)), + overwrite = TRUE) descendants <- cdm$concept_ancestor %>% - dplyr::inner_join(dplyr::tibble(ancestor_concept_id = as.integer(conceptId)), - by = "ancestor_concept_id", - copy = TRUE) %>% + dplyr::inner_join(cdm[[conceptIdDbTable]], + by = "ancestor_concept_id") %>% dplyr::rename("concept_id" = "descendant_concept_id") %>% dplyr::left_join(cdm$concept, - by = "concept_id") + by = "concept_id") %>% + dplyr::compute() + CDMConnector::dropTable(cdm, conceptIdDbTable) descendants <- addIngredientCount(cdm = cdm, concepts = descendants) %>% dplyr::filter(.data$ingredient_count >= !!ingredientRange[1], diff --git a/inst/cohorts2/GIBleed_male.json b/inst/cohorts2/GIBleed_male.json new file mode 100644 index 00000000..10faebf7 --- /dev/null +++ b/inst/cohorts2/GIBleed_male.json @@ -0,0 +1,120 @@ +{ + "ConceptSets": [ + { + "id": 0, + "name": "Gastrointestinal hemorrhage", + "expression": { + "items": [ + { + "concept": { + "CONCEPT_CLASS_ID": "Clinical Finding", + "CONCEPT_CODE": "74474003", + "CONCEPT_ID": 192671, + "CONCEPT_NAME": "Gastrointestinal hemorrhage", + "DOMAIN_ID": "Condition", + "INVALID_REASON": "V", + "INVALID_REASON_CAPTION": "Valid", + "STANDARD_CONCEPT": "S", + "STANDARD_CONCEPT_CAPTION": "Standard", + "VOCABULARY_ID": "SNOMED" + }, + "includeDescendants": true + } + ] + } + } + ], + "PrimaryCriteria": { + "CriteriaList": [ + { + "ConditionOccurrence": { + "CodesetId": 0 + } + } + ], + "ObservationWindow": { + "PriorDays": 0, + "PostDays": 0 + }, + "PrimaryCriteriaLimit": { + "Type": "All" + } + }, + "QualifiedLimit": { + "Type": "First" + }, + "ExpressionLimit": { + "Type": "First" + }, + "InclusionRules": [ + { + "name": "Male", + "expression": { + "Type": "ALL", + "CriteriaList": [], + "DemographicCriteriaList": [ + { + "Gender": [ + { + "CONCEPT_CODE": "M", + "CONCEPT_ID": 8507, + "CONCEPT_NAME": "MALE", + "DOMAIN_ID": "Gender", + "INVALID_REASON_CAPTION": "Unknown", + "STANDARD_CONCEPT_CAPTION": "Unknown", + "VOCABULARY_ID": "Gender" + } + ] + } + ], + "Groups": [] + } + }, + { + "name": "30 days prior observation", + "expression": { + "Type": "ALL", + "CriteriaList": [ + { + "Criteria": { + "ObservationPeriod": {} + }, + "StartWindow": { + "Start": { + "Coeff": -1 + }, + "End": { + "Days": 30, + "Coeff": -1 + }, + "UseEventEnd": false + }, + "EndWindow": { + "Start": { + "Days": 0, + "Coeff": 1 + }, + "End": { + "Coeff": 1 + }, + "UseEventEnd": true + }, + "Occurrence": { + "Type": 2, + "Count": 1 + } + } + ], + "DemographicCriteriaList": [], + "Groups": [] + } + } + ], + "CensoringCriteria": [], + "CollapseSettings": { + "CollapseType": "ERA", + "EraPad": 0 + }, + "CensorWindow": {}, + "cdmVersionRange": ">=5.0.0" +} diff --git a/inst/cohorts2/cerebral_venous_sinus_thrombosis_01.json b/inst/cohorts2/cerebral_venous_sinus_thrombosis_01.json new file mode 100644 index 00000000..67431174 --- /dev/null +++ b/inst/cohorts2/cerebral_venous_sinus_thrombosis_01.json @@ -0,0 +1,837 @@ +{ + "cdmVersionRange": ">=5.0.0", + "PrimaryCriteria": { + "CriteriaList": [ + { + "ConditionOccurrence": { + "CodesetId": 0, + "ConditionTypeExclude": false + } + } + ], + "ObservationWindow": { + "PriorDays": 0, + "PostDays": 0 + }, + "PrimaryCriteriaLimit": { + "Type": "All" + } + }, + "AdditionalCriteria": { + "Type": "ALL", + "CriteriaList": [], + "DemographicCriteriaList": [], + "Groups": [] + }, + "ConceptSets": [ + { + "id": 0, + "name": "Cerebral venous sinus thrombosis concept set", + "expression": { + "items": [ + { + "concept": { + "CONCEPT_ID": 4111714, + "CONCEPT_NAME": "Cerebral infarction due to cerebral venous thrombosis, non-pyogenic", + "STANDARD_CONCEPT": "S", + "STANDARD_CONCEPT_CAPTION": "Standard", + "INVALID_REASON": "V", + "INVALID_REASON_CAPTION": "Valid", + "CONCEPT_CODE": "195230003", + "DOMAIN_ID": "Condition", + "VOCABULARY_ID": "SNOMED", + "CONCEPT_CLASS_ID": "Clinical Finding" + }, + "isExcluded": false, + "includeDescendants": false, + "includeMapped": false + }, + { + "concept": { + "CONCEPT_ID": 4102202, + "CONCEPT_NAME": "Cerebral venous sinus thrombosis", + "STANDARD_CONCEPT": "S", + "STANDARD_CONCEPT_CAPTION": "Standard", + "INVALID_REASON": "V", + "INVALID_REASON_CAPTION": "Valid", + "CONCEPT_CODE": "192759008", + "DOMAIN_ID": "Condition", + "VOCABULARY_ID": "SNOMED", + "CONCEPT_CLASS_ID": "Clinical Finding" + }, + "isExcluded": false, + "includeDescendants": false, + "includeMapped": false + }, + { + "concept": { + "CONCEPT_ID": 4046443, + "CONCEPT_NAME": "Cerebral venous thrombosis of cortical vein", + "STANDARD_CONCEPT": "S", + "STANDARD_CONCEPT_CAPTION": "Standard", + "INVALID_REASON": "V", + "INVALID_REASON_CAPTION": "Valid", + "CONCEPT_CODE": "230722002", + "DOMAIN_ID": "Condition", + "VOCABULARY_ID": "SNOMED", + "CONCEPT_CLASS_ID": "Clinical Finding" + }, + "isExcluded": false, + "includeDescendants": false, + "includeMapped": false + }, + { + "concept": { + "CONCEPT_ID": 762938, + "CONCEPT_NAME": "Cerebral venous thrombosis of cortical vein with infarction", + "STANDARD_CONCEPT": "S", + "STANDARD_CONCEPT_CAPTION": "Standard", + "INVALID_REASON": "V", + "INVALID_REASON_CAPTION": "Valid", + "CONCEPT_CODE": "433971000124107", + "DOMAIN_ID": "Condition", + "VOCABULARY_ID": "SNOMED", + "CONCEPT_CLASS_ID": "Clinical Finding" + }, + "isExcluded": false, + "includeDescendants": false, + "includeMapped": false + }, + { + "concept": { + "CONCEPT_ID": 762811, + "CONCEPT_NAME": "Cerebral venous thrombosis of cortical vein without infarction", + "STANDARD_CONCEPT": "S", + "STANDARD_CONCEPT_CAPTION": "Standard", + "INVALID_REASON": "V", + "INVALID_REASON_CAPTION": "Valid", + "CONCEPT_CODE": "432261000124102", + "DOMAIN_ID": "Condition", + "VOCABULARY_ID": "SNOMED", + "CONCEPT_CLASS_ID": "Clinical Finding" + }, + "isExcluded": false, + "includeDescendants": false, + "includeMapped": false + }, + { + "concept": { + "CONCEPT_ID": 4048787, + "CONCEPT_NAME": "Cerebral venous thrombosis of great cerebral vein", + "STANDARD_CONCEPT": "S", + "STANDARD_CONCEPT_CAPTION": "Standard", + "INVALID_REASON": "V", + "INVALID_REASON_CAPTION": "Valid", + "CONCEPT_CODE": "230723007", + "DOMAIN_ID": "Condition", + "VOCABULARY_ID": "SNOMED", + "CONCEPT_CLASS_ID": "Clinical Finding" + }, + "isExcluded": false, + "includeDescendants": false, + "includeMapped": false + }, + { + "concept": { + "CONCEPT_ID": 4048786, + "CONCEPT_NAME": "Cerebral venous thrombosis of sigmoid sinus", + "STANDARD_CONCEPT": "S", + "STANDARD_CONCEPT_CAPTION": "Standard", + "INVALID_REASON": "V", + "INVALID_REASON_CAPTION": "Valid", + "CONCEPT_CODE": "230721009", + "DOMAIN_ID": "Condition", + "VOCABULARY_ID": "SNOMED", + "CONCEPT_CLASS_ID": "Clinical Finding" + }, + "isExcluded": false, + "includeDescendants": false, + "includeMapped": false + }, + { + "concept": { + "CONCEPT_ID": 4043735, + "CONCEPT_NAME": "Cerebral venous thrombosis of straight sinus", + "STANDARD_CONCEPT": "S", + "STANDARD_CONCEPT_CAPTION": "Standard", + "INVALID_REASON": "V", + "INVALID_REASON_CAPTION": "Valid", + "CONCEPT_CODE": "230720005", + "DOMAIN_ID": "Condition", + "VOCABULARY_ID": "SNOMED", + "CONCEPT_CLASS_ID": "Clinical Finding" + }, + "isExcluded": false, + "includeDescendants": false, + "includeMapped": false + }, + { + "concept": { + "CONCEPT_ID": 4120316, + "CONCEPT_NAME": "Intracranial septic thrombophlebitis", + "STANDARD_CONCEPT": "S", + "STANDARD_CONCEPT_CAPTION": "Standard", + "INVALID_REASON": "V", + "INVALID_REASON_CAPTION": "Valid", + "CONCEPT_CODE": "302878004", + "DOMAIN_ID": "Condition", + "VOCABULARY_ID": "SNOMED", + "CONCEPT_CLASS_ID": "Clinical Finding" + }, + "isExcluded": false, + "includeDescendants": false, + "includeMapped": false + }, + { + "concept": { + "CONCEPT_ID": 4194609, + "CONCEPT_NAME": "Intracranial thrombophlebitis", + "STANDARD_CONCEPT": "S", + "STANDARD_CONCEPT_CAPTION": "Standard", + "INVALID_REASON": "V", + "INVALID_REASON_CAPTION": "Valid", + "CONCEPT_CODE": "312586003", + "DOMAIN_ID": "Condition", + "VOCABULARY_ID": "SNOMED", + "CONCEPT_CLASS_ID": "Clinical Finding" + }, + "isExcluded": false, + "includeDescendants": false, + "includeMapped": false + }, + { + "concept": { + "CONCEPT_ID": 4179912, + "CONCEPT_NAME": "Intracranial venous thrombosis", + "STANDARD_CONCEPT": "S", + "STANDARD_CONCEPT_CAPTION": "Standard", + "INVALID_REASON": "V", + "INVALID_REASON_CAPTION": "Valid", + "CONCEPT_CODE": "297157005", + "DOMAIN_ID": "Condition", + "VOCABULARY_ID": "SNOMED", + "CONCEPT_CLASS_ID": "Clinical Finding" + }, + "isExcluded": false, + "includeDescendants": false, + "includeMapped": false + }, + { + "concept": { + "CONCEPT_ID": 4111713, + "CONCEPT_NAME": "Non-pyogenic venous sinus thrombosis", + "STANDARD_CONCEPT": "S", + "STANDARD_CONCEPT_CAPTION": "Standard", + "INVALID_REASON": "V", + "INVALID_REASON_CAPTION": "Valid", + "CONCEPT_CODE": "195229008", + "DOMAIN_ID": "Condition", + "VOCABULARY_ID": "SNOMED", + "CONCEPT_CLASS_ID": "Clinical Finding" + }, + "isExcluded": false, + "includeDescendants": false, + "includeMapped": false + }, + { + "concept": { + "CONCEPT_ID": 314667, + "CONCEPT_NAME": "Nonpyogenic thrombosis of intracranial venous sinus", + "STANDARD_CONCEPT": "S", + "STANDARD_CONCEPT_CAPTION": "Standard", + "INVALID_REASON": "V", + "INVALID_REASON_CAPTION": "Valid", + "CONCEPT_CODE": "42970005", + "DOMAIN_ID": "Condition", + "VOCABULARY_ID": "SNOMED", + "CONCEPT_CLASS_ID": "Clinical Finding" + }, + "isExcluded": false, + "includeDescendants": false, + "includeMapped": false + }, + { + "concept": { + "CONCEPT_ID": 764503, + "CONCEPT_NAME": "Occlusion of cerebral vein by nonpyogenic thrombus", + "STANDARD_CONCEPT": "S", + "STANDARD_CONCEPT_CAPTION": "Standard", + "INVALID_REASON": "V", + "INVALID_REASON_CAPTION": "Valid", + "CONCEPT_CODE": "455901000124101", + "DOMAIN_ID": "Condition", + "VOCABULARY_ID": "SNOMED", + "CONCEPT_CLASS_ID": "Clinical Finding" + }, + "isExcluded": false, + "includeDescendants": false, + "includeMapped": false + }, + { + "concept": { + "CONCEPT_ID": 4116206, + "CONCEPT_NAME": "Septic thrombophlebitis of cavernous sinus", + "STANDARD_CONCEPT": "S", + "STANDARD_CONCEPT_CAPTION": "Standard", + "INVALID_REASON": "V", + "INVALID_REASON_CAPTION": "Valid", + "CONCEPT_CODE": "302879007", + "DOMAIN_ID": "Condition", + "VOCABULARY_ID": "SNOMED", + "CONCEPT_CLASS_ID": "Clinical Finding" + }, + "isExcluded": false, + "includeDescendants": false, + "includeMapped": false + }, + { + "concept": { + "CONCEPT_ID": 4047634, + "CONCEPT_NAME": "Septic thrombophlebitis of cortical vein", + "STANDARD_CONCEPT": "S", + "STANDARD_CONCEPT_CAPTION": "Standard", + "INVALID_REASON": "V", + "INVALID_REASON_CAPTION": "Valid", + "CONCEPT_CODE": "230224002", + "DOMAIN_ID": "Condition", + "VOCABULARY_ID": "SNOMED", + "CONCEPT_CLASS_ID": "Clinical Finding" + }, + "isExcluded": false, + "includeDescendants": false, + "includeMapped": false + }, + { + "concept": { + "CONCEPT_ID": 4043901, + "CONCEPT_NAME": "Septic thrombophlebitis of great cerebral vein", + "STANDARD_CONCEPT": "S", + "STANDARD_CONCEPT_CAPTION": "Standard", + "INVALID_REASON": "V", + "INVALID_REASON_CAPTION": "Valid", + "CONCEPT_CODE": "230225001", + "DOMAIN_ID": "Condition", + "VOCABULARY_ID": "SNOMED", + "CONCEPT_CLASS_ID": "Clinical Finding" + }, + "isExcluded": false, + "includeDescendants": false, + "includeMapped": false + }, + { + "concept": { + "CONCEPT_ID": 4121335, + "CONCEPT_NAME": "Septic thrombophlebitis of lateral sinus", + "STANDARD_CONCEPT": "S", + "STANDARD_CONCEPT_CAPTION": "Standard", + "INVALID_REASON": "V", + "INVALID_REASON_CAPTION": "Valid", + "CONCEPT_CODE": "302881009", + "DOMAIN_ID": "Condition", + "VOCABULARY_ID": "SNOMED", + "CONCEPT_CLASS_ID": "Clinical Finding" + }, + "isExcluded": false, + "includeDescendants": false, + "includeMapped": false + }, + { + "concept": { + "CONCEPT_ID": 4119136, + "CONCEPT_NAME": "Septic thrombophlebitis of sagittal sinus", + "STANDARD_CONCEPT": "S", + "STANDARD_CONCEPT_CAPTION": "Standard", + "INVALID_REASON": "V", + "INVALID_REASON_CAPTION": "Valid", + "CONCEPT_CODE": "302880005", + "DOMAIN_ID": "Condition", + "VOCABULARY_ID": "SNOMED", + "CONCEPT_CLASS_ID": "Clinical Finding" + }, + "isExcluded": false, + "includeDescendants": false, + "includeMapped": false + }, + { + "concept": { + "CONCEPT_ID": 4041680, + "CONCEPT_NAME": "Septic thrombophlebitis of sigmoid sinus", + "STANDARD_CONCEPT": "S", + "STANDARD_CONCEPT_CAPTION": "Standard", + "INVALID_REASON": "V", + "INVALID_REASON_CAPTION": "Valid", + "CONCEPT_CODE": "230223008", + "DOMAIN_ID": "Condition", + "VOCABULARY_ID": "SNOMED", + "CONCEPT_CLASS_ID": "Clinical Finding" + }, + "isExcluded": false, + "includeDescendants": false, + "includeMapped": false + }, + { + "concept": { + "CONCEPT_ID": 4100225, + "CONCEPT_NAME": "Thrombophlebitis lateral venous sinus", + "STANDARD_CONCEPT": "S", + "STANDARD_CONCEPT_CAPTION": "Standard", + "INVALID_REASON": "V", + "INVALID_REASON_CAPTION": "Valid", + "CONCEPT_CODE": "192772009", + "DOMAIN_ID": "Condition", + "VOCABULARY_ID": "SNOMED", + "CONCEPT_CLASS_ID": "Clinical Finding" + }, + "isExcluded": false, + "includeDescendants": false, + "includeMapped": false + }, + { + "concept": { + "CONCEPT_ID": 764716, + "CONCEPT_NAME": "Thrombophlebitis of basal vein of Rosenthal", + "STANDARD_CONCEPT": "S", + "STANDARD_CONCEPT_CAPTION": "Standard", + "INVALID_REASON": "V", + "INVALID_REASON_CAPTION": "Valid", + "CONCEPT_CODE": "5531000124101", + "DOMAIN_ID": "Condition", + "VOCABULARY_ID": "SNOMED", + "CONCEPT_CLASS_ID": "Clinical Finding" + }, + "isExcluded": false, + "includeDescendants": false, + "includeMapped": false + }, + { + "concept": { + "CONCEPT_ID": 4217471, + "CONCEPT_NAME": "Thrombophlebitis of basilar sinus", + "STANDARD_CONCEPT": "S", + "STANDARD_CONCEPT_CAPTION": "Standard", + "INVALID_REASON": "V", + "INVALID_REASON_CAPTION": "Valid", + "CONCEPT_CODE": "8166000", + "DOMAIN_ID": "Condition", + "VOCABULARY_ID": "SNOMED", + "CONCEPT_CLASS_ID": "Clinical Finding" + }, + "isExcluded": false, + "includeDescendants": false, + "includeMapped": false + }, + { + "concept": { + "CONCEPT_ID": 4104695, + "CONCEPT_NAME": "Thrombophlebitis of cavernous sinus", + "STANDARD_CONCEPT": "S", + "STANDARD_CONCEPT_CAPTION": "Standard", + "INVALID_REASON": "V", + "INVALID_REASON_CAPTION": "Valid", + "CONCEPT_CODE": "192770001", + "DOMAIN_ID": "Condition", + "VOCABULARY_ID": "SNOMED", + "CONCEPT_CLASS_ID": "Clinical Finding" + }, + "isExcluded": false, + "includeDescendants": false, + "includeMapped": false + }, + { + "concept": { + "CONCEPT_ID": 4319332, + "CONCEPT_NAME": "Thrombophlebitis of cerebral vein", + "STANDARD_CONCEPT": "S", + "STANDARD_CONCEPT_CAPTION": "Standard", + "INVALID_REASON": "V", + "INVALID_REASON_CAPTION": "Valid", + "CONCEPT_CODE": "95461006", + "DOMAIN_ID": "Condition", + "VOCABULARY_ID": "SNOMED", + "CONCEPT_CLASS_ID": "Clinical Finding" + }, + "isExcluded": false, + "includeDescendants": false, + "includeMapped": false + }, + { + "concept": { + "CONCEPT_ID": 4167985, + "CONCEPT_NAME": "Thrombophlebitis of inferior sagittal sinus", + "STANDARD_CONCEPT": "S", + "STANDARD_CONCEPT_CAPTION": "Standard", + "INVALID_REASON": "V", + "INVALID_REASON_CAPTION": 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"isExcluded": false, + "includeDescendants": false, + "includeMapped": false + }, + { + "concept": { + "CONCEPT_ID": 440750, + "CONCEPT_NAME": "Thrombophlebitis of deep veins of upper extremities", + "STANDARD_CONCEPT": "S", + "STANDARD_CONCEPT_CAPTION": "Standard", + "INVALID_REASON": "V", + "INVALID_REASON_CAPTION": "Valid", + "CONCEPT_CODE": "95452006", + "DOMAIN_ID": "Condition", + "VOCABULARY_ID": "SNOMED", + "CONCEPT_CLASS_ID": "Clinical Finding" + }, + "isExcluded": false, + "includeDescendants": false, + "includeMapped": false + }, + { + "concept": { + "CONCEPT_ID": 4176614, + "CONCEPT_NAME": "Thrombophlebitis of iliac vein", + "STANDARD_CONCEPT": "S", + "STANDARD_CONCEPT_CAPTION": "Standard", + "INVALID_REASON": "V", + "INVALID_REASON_CAPTION": "Valid", + "CONCEPT_CODE": "42861008", + "DOMAIN_ID": "Condition", + "VOCABULARY_ID": "SNOMED", + "CONCEPT_CLASS_ID": "Clinical Finding" + }, + "isExcluded": false, + "includeDescendants": false, + "includeMapped": false + }, + { + "concept": { + "CONCEPT_ID": 761821, + "CONCEPT_NAME": "Thrombophlebitis of left deep femoral vein", + "STANDARD_CONCEPT": "S", + "STANDARD_CONCEPT_CAPTION": "Standard", + "INVALID_REASON": "V", + "INVALID_REASON_CAPTION": "Valid", + "CONCEPT_CODE": "16012151000119109", + "DOMAIN_ID": "Condition", + "VOCABULARY_ID": "SNOMED", + "CONCEPT_CLASS_ID": "Clinical Finding" + }, + "isExcluded": false, + "includeDescendants": false, + "includeMapped": false + }, + { + "concept": { + "CONCEPT_ID": 761819, + "CONCEPT_NAME": "Thrombophlebitis of left femoral vein", + "STANDARD_CONCEPT": "S", + "STANDARD_CONCEPT_CAPTION": "Standard", + "INVALID_REASON": "V", + "INVALID_REASON_CAPTION": "Valid", + "CONCEPT_CODE": "16012071000119101", + "DOMAIN_ID": "Condition", + "VOCABULARY_ID": "SNOMED", + "CONCEPT_CLASS_ID": "Clinical Finding" + }, + "isExcluded": false, + "includeDescendants": false, + "includeMapped": false + }, + { + "concept": { + "CONCEPT_ID": 444097, + "CONCEPT_NAME": "Thrombophlebitis of lower extremities", + "STANDARD_CONCEPT": "S", + "STANDARD_CONCEPT_CAPTION": "Standard", + "INVALID_REASON": "V", + "INVALID_REASON_CAPTION": "Valid", + "CONCEPT_CODE": "46253008", + "DOMAIN_ID": "Condition", + "VOCABULARY_ID": "SNOMED", + "CONCEPT_CLASS_ID": "Clinical Finding" + }, + "isExcluded": false, + "includeDescendants": false, + "includeMapped": false + }, + { + "concept": { + "CONCEPT_ID": 761820, + "CONCEPT_NAME": "Thrombophlebitis of right deep femoral vein", + "STANDARD_CONCEPT": "S", + "STANDARD_CONCEPT_CAPTION": "Standard", + "INVALID_REASON": "V", + "INVALID_REASON_CAPTION": "Valid", + "CONCEPT_CODE": "16012111000119108", + "DOMAIN_ID": "Condition", + "VOCABULARY_ID": "SNOMED", + "CONCEPT_CLASS_ID": "Clinical Finding" + }, + "isExcluded": false, + "includeDescendants": false, + "includeMapped": false + }, + { + "concept": { + "CONCEPT_ID": 761818, + "CONCEPT_NAME": "Thrombophlebitis of right femoral vein", + "STANDARD_CONCEPT": "S", + "STANDARD_CONCEPT_CAPTION": "Standard", + "INVALID_REASON": "V", + "INVALID_REASON_CAPTION": "Valid", + "CONCEPT_CODE": "16011991000119109", + "DOMAIN_ID": "Condition", + "VOCABULARY_ID": "SNOMED", + "CONCEPT_CLASS_ID": "Clinical Finding" + }, + "isExcluded": false, + "includeDescendants": false, + "includeMapped": false + }, + { + "concept": { + "CONCEPT_ID": 4110339, + "CONCEPT_NAME": "Thrombophlebitis of the anterior tibial vein", + "STANDARD_CONCEPT": "S", + "STANDARD_CONCEPT_CAPTION": "Standard", + "INVALID_REASON": "V", + "INVALID_REASON_CAPTION": "Valid", + "CONCEPT_CODE": "195412008", + "DOMAIN_ID": "Condition", + "VOCABULARY_ID": "SNOMED", + "CONCEPT_CLASS_ID": "Clinical Finding" + }, + "isExcluded": false, + "includeDescendants": false, + "includeMapped": false + }, + { + "concept": { + "CONCEPT_ID": 4111868, + "CONCEPT_NAME": "Thrombophlebitis of the common iliac vein", + "STANDARD_CONCEPT": "S", + "STANDARD_CONCEPT_CAPTION": "Standard", + "INVALID_REASON": "V", + "INVALID_REASON_CAPTION": "Valid", + "CONCEPT_CODE": "195425000", + "DOMAIN_ID": "Condition", + "VOCABULARY_ID": "SNOMED", + "CONCEPT_CLASS_ID": "Clinical Finding" + }, + "isExcluded": false, + "includeDescendants": false, + "includeMapped": false + }, + { + "concept": { + "CONCEPT_ID": 4110343, + "CONCEPT_NAME": "Thrombophlebitis of the external iliac vein", + "STANDARD_CONCEPT": "S", + "STANDARD_CONCEPT_CAPTION": "Standard", + "INVALID_REASON": "V", + "INVALID_REASON_CAPTION": "Valid", + "CONCEPT_CODE": "195427008", + "DOMAIN_ID": "Condition", + "VOCABULARY_ID": "SNOMED", + "CONCEPT_CLASS_ID": "Clinical Finding" + }, + "isExcluded": false, + "includeDescendants": false, + "includeMapped": false + }, + { + "concept": { + "CONCEPT_ID": 439314, + "CONCEPT_NAME": "Thrombophlebitis of the femoral vein", + "STANDARD_CONCEPT": "S", + "STANDARD_CONCEPT_CAPTION": "Standard", + "INVALID_REASON": "V", + "INVALID_REASON_CAPTION": "Valid", + "CONCEPT_CODE": "195410000", + "DOMAIN_ID": "Condition", + "VOCABULARY_ID": "SNOMED", + "CONCEPT_CLASS_ID": "Clinical Finding" + }, + "isExcluded": false, + "includeDescendants": false, + "includeMapped": false + }, + { + "concept": { + "CONCEPT_ID": 4109877, + "CONCEPT_NAME": "Thrombophlebitis of the internal iliac vein", + "STANDARD_CONCEPT": "S", + "STANDARD_CONCEPT_CAPTION": "Standard", + "INVALID_REASON": "V", + "INVALID_REASON_CAPTION": "Valid", + "CONCEPT_CODE": "195426004", + "DOMAIN_ID": "Condition", + "VOCABULARY_ID": "SNOMED", + "CONCEPT_CLASS_ID": "Clinical Finding" + }, + "isExcluded": false, + "includeDescendants": false, + "includeMapped": false + }, + { + "concept": { + "CONCEPT_ID": 4112171, + "CONCEPT_NAME": "Thrombophlebitis of the popliteal vein", + "STANDARD_CONCEPT": "S", + "STANDARD_CONCEPT_CAPTION": "Standard", + "INVALID_REASON": "V", + "INVALID_REASON_CAPTION": "Valid", + "CONCEPT_CODE": "195411001", + "DOMAIN_ID": "Condition", + "VOCABULARY_ID": "SNOMED", + "CONCEPT_CLASS_ID": "Clinical Finding" + }, + "isExcluded": false, + "includeDescendants": false, + "includeMapped": false + }, + { + "concept": { + "CONCEPT_ID": 4112172, + "CONCEPT_NAME": "Thrombophlebitis of the posterior tibial vein", + "STANDARD_CONCEPT": "S", + "STANDARD_CONCEPT_CAPTION": "Standard", + "INVALID_REASON": "V", + "INVALID_REASON_CAPTION": "Valid", + "CONCEPT_CODE": "195414009", + "DOMAIN_ID": "Condition", + "VOCABULARY_ID": "SNOMED", + "CONCEPT_CLASS_ID": "Clinical Finding" + }, + "isExcluded": false, + "includeDescendants": false, + "includeMapped": false + }, + { + "concept": { + "CONCEPT_ID": 4250765, + "CONCEPT_NAME": "Thrombophlebitis of tibial vein", + "STANDARD_CONCEPT": "S", + "STANDARD_CONCEPT_CAPTION": "Standard", + "INVALID_REASON": "V", + "INVALID_REASON_CAPTION": "Valid", + "CONCEPT_CODE": "7387004", + "DOMAIN_ID": "Condition", + "VOCABULARY_ID": "SNOMED", + "CONCEPT_CLASS_ID": "Clinical Finding" + }, + "isExcluded": false, + "includeDescendants": false, + "includeMapped": false + }, + { + "concept": { + "CONCEPT_ID": 4317289, + "CONCEPT_NAME": "Thrombosis of mesenteric vein", + "STANDARD_CONCEPT": "S", + "STANDARD_CONCEPT_CAPTION": "Standard", + "INVALID_REASON": "V", + "INVALID_REASON_CAPTION": "Valid", + "CONCEPT_CODE": "95446005", + "DOMAIN_ID": "Condition", + "VOCABULARY_ID": "SNOMED", + "CONCEPT_CLASS_ID": "Clinical Finding" + }, + "isExcluded": false, + "includeDescendants": false, + "includeMapped": false + }, + { + "concept": { + "CONCEPT_ID": 4033521, + "CONCEPT_NAME": "Splenic vein thrombosis", + "STANDARD_CONCEPT": "S", + "STANDARD_CONCEPT_CAPTION": "Standard", + "INVALID_REASON": "V", + "INVALID_REASON_CAPTION": "Valid", + "CONCEPT_CODE": "14534009", + "DOMAIN_ID": "Condition", + "VOCABULARY_ID": "SNOMED", + "CONCEPT_CLASS_ID": "Clinical Finding" + }, + "isExcluded": false, + "includeDescendants": false, + "includeMapped": false + }, + { + "concept": { + "CONCEPT_ID": 36712892, + "CONCEPT_NAME": "Acute thrombosis of splenic vein", + "STANDARD_CONCEPT": "S", + "STANDARD_CONCEPT_CAPTION": "Standard", + "INVALID_REASON": "V", + "INVALID_REASON_CAPTION": "Valid", + "CONCEPT_CODE": "143561000119108", + "DOMAIN_ID": "Condition", + "VOCABULARY_ID": "SNOMED", + "CONCEPT_CLASS_ID": "Clinical Finding" + }, + "isExcluded": false, + "includeDescendants": false, + "includeMapped": false + }, + { + "concept": { + "CONCEPT_ID": 45757410, + "CONCEPT_NAME": "Acute thrombosis of mesenteric vein", + "STANDARD_CONCEPT": "S", + "STANDARD_CONCEPT_CAPTION": "Standard", + "INVALID_REASON": "V", + "INVALID_REASON_CAPTION": "Valid", + "CONCEPT_CODE": "133421000119101", + "DOMAIN_ID": "Condition", + "VOCABULARY_ID": "SNOMED", + "CONCEPT_CLASS_ID": "Clinical Finding" + }, + "isExcluded": false, + "includeDescendants": false, + "includeMapped": false + } + ] + } + }, + { + "id": 16, + "name": "DVT broad- ICD\n", + "expression": { + "items": [ + { + "concept": { + "CONCEPT_ID": 44834756, + "CONCEPT_NAME": "Acute venous embolism and thrombosis of other specified veins", + "STANDARD_CONCEPT": "N", + "STANDARD_CONCEPT_CAPTION": "Non-Standard", + "INVALID_REASON": "V", + "INVALID_REASON_CAPTION": "Valid", + "CONCEPT_CODE": "453.8", + "DOMAIN_ID": "Condition", + "VOCABULARY_ID": "ICD9CM", + "CONCEPT_CLASS_ID": "4-dig nonbill code" + }, + "isExcluded": false, + "includeDescendants": false, + "includeMapped": false + }, + { + "concept": { + "CONCEPT_ID": 45586638, + "CONCEPT_NAME": "Embolism and thrombosis of other specified veins", + "STANDARD_CONCEPT": "N", + "STANDARD_CONCEPT_CAPTION": "Non-Standard", + "INVALID_REASON": "V", + "INVALID_REASON_CAPTION": "Valid", + "CONCEPT_CODE": "I82.8", + "DOMAIN_ID": "Condition", + "VOCABULARY_ID": "ICD10", + "CONCEPT_CLASS_ID": "ICD10 code" + }, + "isExcluded": false, + "includeDescendants": false, + "includeMapped": false + }, + { + "concept": { + "CONCEPT_ID": 45572145, + "CONCEPT_NAME": "Embolism and thrombosis of unspecified vein", + "STANDARD_CONCEPT": "N", + "STANDARD_CONCEPT_CAPTION": "Non-Standard", + "INVALID_REASON": "V", + "INVALID_REASON_CAPTION": "Valid", + "CONCEPT_CODE": "I82.9", + "DOMAIN_ID": "Condition", + "VOCABULARY_ID": "ICD10", + "CONCEPT_CLASS_ID": "ICD10 code" + }, + "isExcluded": false, + "includeDescendants": false, + "includeMapped": false + } + ] + } + } + ], + "QualifiedLimit": { + "Type": "First" + }, + "ExpressionLimit": { + "Type": "All" + }, + "InclusionRules": [], + "EndStrategy": { + "DateOffset": { + "DateField": "StartDate", + "Offset": 0 + } + }, + "CensoringCriteria": [], + "CollapseSettings": { + "CollapseType": "ERA", + "EraPad": 30 + }, + "CensorWindow": {} +} diff --git a/tests/testthat/test-codesFrom.R b/tests/testthat/test-codesFrom.R index 32fe83c1..d6eacc6b 100644 --- a/tests/testthat/test-codesFrom.R +++ b/tests/testthat/test-codesFrom.R @@ -137,5 +137,20 @@ test_that("test inputs - redshift", { ) expect_true("Influenza" %in% x$influenza$concept_name) + # check is sorted alphabetically + x <- codesFromCohort( + cdm = cdm, + path = system.file(package = "CodelistGenerator", + "cohorts2"), + withConceptDetails = TRUE + ) + + expect_equal(sort(x[[1]]$concept_name), x[[1]]$concept_name) + expect_equal(sort(x[[2]]$concept_name), x[[2]]$concept_name) + expect_equal(sort(x[[3]]$concept_name), x[[3]]$concept_name) + CDMConnector::cdmDisconnect(cdm) }) + + + diff --git a/tests/testthat/test-dbms.R b/tests/testthat/test-dbms.R index d6f2bd71..399213bf 100644 --- a/tests/testthat/test-dbms.R +++ b/tests/testthat/test-dbms.R @@ -1,6 +1,5 @@ # Testing against different database platforms - test_that("redshift", { testthat::skip_if(Sys.getenv("CDM5_REDSHIFT_DBNAME") == "") @@ -35,6 +34,9 @@ test_that("redshift", { includeAncestor = TRUE)) expect_true(nrow(asthma) > 0) + # drug ingredients + expect_no_error(getDrugIngredientCodes(cdm, "metformin")) + # achilles cdm$achilles_results <- cdm$condition_occurrence %>% dplyr::group_by(condition_concept_id) %>% @@ -122,3 +124,139 @@ test_that("redshift", { CDMConnector::cdm_disconnect(cdm) }) +test_that("snowflake", { + + testthat::skip_if(Sys.getenv("SNOWFLAKE_SERVER") == "") + + con <- DBI::dbConnect(odbc::odbc(), + SERVER = Sys.getenv("SNOWFLAKE_SERVER"), + UID = Sys.getenv("SNOWFLAKE_USER"), + PWD = Sys.getenv("SNOWFLAKE_PASSWORD"), + DATABASE = Sys.getenv("SNOWFLAKE_DATABASE"), + WAREHOUSE = Sys.getenv("SNOWFLAKE_WAREHOUSE"), + DRIVER = Sys.getenv("SNOWFLAKE_DRIVER")) + + cdm_schema <- strsplit(Sys.getenv("SNOWFLAKE_CDM_SCHEMA"), "\\.")[[1]] + write_schema <- strsplit(Sys.getenv("SNOWFLAKE_SCRATCH_SCHEMA"), "\\.")[[1]] + + cdm <- CDMConnector::cdm_from_con(con = con, + cdm_schema = cdm_schema, + write_schema = write_schema, + cdm_name = "snowflake") + + + # candidate code search + expect_no_error(asthma<-getCandidateCodes(cdm, + keywords = c("asthma", + "irritable airways", + "lung disease", + "respiratory abnormalities", + "sleep apnea", + "chronic obstructive lung disease", + "chronic obstructive lung disease"), + + domains = c("condition", "observation"), + exclude = c("childhood", "juvenile"), + searchInSynonyms = TRUE, + searchNonStandard = TRUE, + includeDescendants = TRUE, + includeAncestor = TRUE)) + expect_true(nrow(asthma) > 0) + + # drug ingredients + expect_no_error(getDrugIngredientCodes(cdm, "metformin")) + + # achilles + cdm$achilles_results <- cdm$condition_occurrence %>% + dplyr::group_by(condition_concept_id) %>% + dplyr::tally(name = "count_value") %>% + dplyr::rename("stratum_1" = "condition_concept_id") %>% + dplyr::mutate(stratum_2 = NA, + stratum_3 = NA, + analysis_id = 401) %>% + dplyr::compute() + + asthma <- list(asthma = c(317009, 257581)) + result_achilles <- summariseAchillesCodeUse(asthma, + cdm = cdm) + result_cdm <- summariseCodeUse(asthma, cdm = cdm) + + expect_equal(result_achilles %>% + dplyr::filter(variable_level == "317009", + variable_name == "record_count") %>% + dplyr::pull("estimate_value"), + result_cdm %>% + dplyr::filter(variable_level == "317009", + variable_name == "record_count ") %>% + dplyr::pull("estimate_value")) + + expect_equal(result_achilles %>% + dplyr::filter(variable_level == "257581", + variable_name == "record_count") %>% + dplyr::pull("estimate_value"), + result_cdm %>% + dplyr::filter(variable_level == "257581", + variable_name == "record_count ") %>% + dplyr::pull("estimate_value")) + + cdm$achilles_results <- cdm$condition_occurrence %>% + dplyr::group_by(person_id, condition_concept_id) %>% + dplyr::tally() %>% + dplyr::ungroup() %>% + dplyr::group_by(condition_concept_id) %>% + dplyr::tally(name = "count_value") %>% + dplyr::rename("stratum_1" = "condition_concept_id") %>% + dplyr::mutate(stratum_2 = NA, + stratum_3 = NA, + analysis_id = 400) %>% + CDMConnector::computeQuery() + + asthma <- list(asthma = c(317009, 257581)) + result_achilles <- summariseAchillesCodeUse(asthma, + cdm = cdm) + result_cdm <- summariseCodeUse(asthma, cdm = cdm) + + expect_equal(result_achilles %>% + dplyr::filter(variable_level == "317009", + variable_name == "record_count") %>% + dplyr::pull("estimate_value"), + result_cdm %>% + dplyr::filter(variable_level == "317009", + variable_name == "record_count ") %>% + dplyr::pull("estimate_value")) + + + + expect_equal(result_achilles %>% + dplyr::filter(group_level == "317009", + variable_name == "person_count") %>% + dplyr::pull("estimate_value"), + result_cdm %>% + dplyr::filter(group_level == "317009", + variable_name == "person_count") %>% + dplyr::pull("estimate_value")) + expect_equal(result_achilles %>% + dplyr::filter(group_level == "257581", + variable_name == "person_count") %>% + dplyr::pull("estimate_value"), + result_cdm %>% + dplyr::filter(group_level == "257581", + variable_name == "person_count") %>% + dplyr::pull("estimate_value")) + + # edge cases + # concept id not in achilles + expect_message(summariseAchillesCodeUse(list(asthma = 123), + cdm = cdm)) + + # expected errors + expect_error(summariseAchillesCodeUse(123, #not a named list + cdm = cdm)) + expect_error(summariseAchillesCodeUse(asthma, + cdm = "cdm")) # not a cdm + expect_error(summariseAchillesCodeUse(asthma, + cdm = cdm, + countBy = "not an option")) + + CDMConnector::cdm_disconnect(cdm) +})