R/getMappings.R

In oxford-pharmacoepi/CodelistGenerator: Identify Relevant Clinical Codes and Evaluate Their Use

# Copyright 2023 DARWIN EU®
#
# 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.


#' Show mappings from non-standard vocabularies to standard
#'
#' @param candidateCodelist Dataframe
#' @param cdm cdm_reference via CDMConnector::cdm_from_con()
#' @param nonStandardVocabularies Character vector
#'
#' @return tibble
#' @export
#'
#' @examples
#' \dontrun{
#' cdm <- CodelistGenerator::mockVocabRef()
#' codes <- CodelistGenerator::getCandidateCodes(
#'   cdm = cdm,
#'   keywords = "osteoarthritis"
#' )
#' CodelistGenerator::getMappings(
#'   cdm = cdm,
#'   candidateCodelist = codes,
#'   nonStandardVocabularies = "READ"
#')
#'CDMConnector::cdmDisconnect(cdm)
#'}
getMappings <- function(candidateCodelist,
                         cdm = NULL,
                         nonStandardVocabularies = c(
                           "ATC", "ICD10CM", "ICD10PCS",
                           "ICD9CM", "ICD9Proc",
                           "LOINC", "OPCS4", "Read",
                           "RxNorm", "RxNorm Extension",
                           "SNOMED"
                         )) {

  errorMessage <- checkmate::makeAssertCollection()
  checkDbType(cdm = cdm, type = "cdm_reference", messageStore = errorMessage)
  checkmate::assertVector(nonStandardVocabularies, add = errorMessage)
  checkmate::assertDataFrame(candidateCodelist, add = errorMessage)
  checkmate::reportAssertions(collection = errorMessage)

  errorMessage <- checkmate::makeAssertCollection()
  assertTablesExist(cdm, tableName = c("concept",
                                       "concept_relationship",
                                       "concept_ancestor",
                                       "concept_synonym",
                                       "vocabulary"),
                    messageStore = errorMessage)
  checkmate::reportAssertions(collection = errorMessage)

  conceptDb <- cdm$concept
  conceptRelationshipDb <- cdm$concept_relationship

  # lowercase names
  conceptDb <- dplyr::rename_with(conceptDb, tolower)
  conceptRelationshipDb <- dplyr::rename_with(
    conceptRelationshipDb,
    tolower
  )

  # vocabs to upper case
  nonStandardVocabularies <- toupper(nonStandardVocabularies)
  conceptDb <- conceptDb %>%
    dplyr::mutate(vocabulary_id = toupper(.data$vocabulary_id))

  # check nonStandardVocabularies exist
  errorMessage <- checkmate::makeAssertCollection()
  nonStandardVocabulariesInDb <- conceptDb %>%
    dplyr::select("vocabulary_id") %>%
    dplyr::distinct() %>%
    dplyr::collect() %>%
    dplyr::pull()
  for (i in seq_along(nonStandardVocabularies)) {
    nonStandardVocabulariesCheck <- nonStandardVocabularies[i] %in%
      nonStandardVocabulariesInDb
    checkmate::assertTRUE(nonStandardVocabulariesCheck, add = errorMessage)
    if (!isTRUE(nonStandardVocabulariesCheck)) {
      errorMessage$push(
        glue::glue("- Vocabulary {nonStandardVocabularies[i]} not found")
      )
    }
  }
  checkmate::reportAssertions(collection = errorMessage)


  mappedCodes <- conceptDb %>%
    dplyr::inner_join(conceptRelationshipDb %>%
      dplyr::filter(.data$relationship_id == "Mapped from") %>%
      dplyr::filter(.data$concept_id_1 %in% !!candidateCodelist$concept_id) %>%
      dplyr::select("concept_id_1", "concept_id_2") %>%
      dplyr::rename("concept_id" = "concept_id_2"),
    by = c("concept_id")
    ) %>%
    dplyr::filter(.data$vocabulary_id %in% .env$nonStandardVocabularies) %>%
    dplyr::distinct() %>%
    dplyr::collect()

  mappedCodes <- mappedCodes %>%
    dplyr::select(
      "concept_id_1", "concept_id",
      "concept_name", "concept_code",
      "vocabulary_id"
    )

  mappedCodes <- mappedCodes %>%
    dplyr::select("concept_id_1") %>%
    dplyr::rename("concept_id" = "concept_id_1") %>%
    dplyr::left_join(conceptDb %>%
      dplyr::filter(.data$concept_id %in% !!mappedCodes$concept_id_1) %>%
      dplyr::collect(),
    by = c("concept_id")
    ) %>%
    dplyr::select("concept_id", "concept_name", "vocabulary_id") %>%
    dplyr::rename("standard_vocabulary_id" = "vocabulary_id") %>%
    dplyr::rename("concept_id_1" = "concept_id") %>%
    dplyr::rename("standard_concept_name" = "concept_name") %>%
    dplyr::full_join(mappedCodes,
      by = "concept_id_1"
    ) %>%
    dplyr::rename("standard_concept_id" = "concept_id_1") %>%
    dplyr::rename("non_standard_concept_id" = "concept_id") %>%
    dplyr::rename("non_standard_concept_code" = "concept_code") %>%
    dplyr::rename("non_standard_concept_name" = "concept_name") %>%
    dplyr::rename("non_standard_vocabulary_id" = "vocabulary_id")

  mappedCodes <- mappedCodes %>%
    dplyr::distinct() %>%
    dplyr::arrange(.data$standard_concept_id)

  return(mappedCodes)
}