R/subsetOnDoseUnit.R

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

# 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.

#' Subset a codelist to only those with a particular dose unit.
#'
#' @inheritParams xDoc
#' @inheritParams cdmDoc
#' @inheritParams doseUnitDoc
#' @param negate If FALSE, only concepts with the dose unit specified will be
#' returned. If TRUE, concepts with the dose unit specified will be excluded.
#'
#' @return The codelist with only those concepts associated with the
#' dose unit (if negate = FALSE) or codelist without those concepts associated with the
#' dose unit(if negate = TRUE).
#' @export
#'
#' @examples
#' \donttest{
#' library(CodelistGenerator)
#' cdm <- mockVocabRef()
#' codes <- subsetOnDoseUnit(x = list("codes" = c(20,21)),
#'                           cdm = cdm,
#'                           doseUnit = c("milligram"))
#'
#' codes
#' }
subsetOnDoseUnit <- function(x,
                             cdm,
                             doseUnit,
                             negate = FALSE){

  if(inherits(x, "codelist_with_details")){
    x_original <- x
    withDetails <- TRUE
    x <- codelistFromCodelistWithDetails(x)
  } else {
    withDetails <- FALSE
  }

  omopgenerics::validateCdmArgument(cdm)
  omopgenerics::assertCharacter(doseUnit)
  omopgenerics::assertLogical(negate)
  x <- omopgenerics::newCodelist(x)

  if(isFALSE(inherits(cdm, "cdm_reference"))){
    cli::cli_abort("cdm must be a cdm reference")
  }
  if(isFALSE(is.character(doseUnit))){
    cli::cli_abort("doseUnit must be a character vector")
  }

  tableCodelist <- paste0(omopgenerics::uniqueTableName(),
                          omopgenerics::uniqueId())

  drugStrengthNamed <- cdm$drug_strength |>
    dplyr::left_join(cdm$concept |>
                       dplyr::select("concept_id",
                                     "concept_name"),
                     by= c("amount_unit_concept_id"= "concept_id")) |>
    dplyr::rename("amount_concept_name" = "concept_name") |>
    dplyr::left_join(cdm$concept |>
                        dplyr::select("concept_id",
                                      "concept_name"),
                      by= c("numerator_unit_concept_id"= "concept_id")) |>
    dplyr::rename("numerator_concept_name" = "concept_name")

  for(i in seq_along(x)){
    cdm <- omopgenerics::insertTable(cdm = cdm,
                                     name = tableCodelist,
                                     table = dplyr::tibble(concept_id = x[[i]]),
                                     overwrite = TRUE,
                                     temporary = FALSE)

    x[[i]] <- cdm[[tableCodelist]] |>
      dplyr::inner_join(drugStrengthNamed,
                        by = c("concept_id" = "drug_concept_id")
      ) |>
      dplyr::select("concept_id",
                    "amount_concept_name",
                    "numerator_concept_name") |>
      dplyr::distinct() |>
      dplyr::collect()

    if(isTRUE(negate)){
      x[[i]] <- x[[i]] |>
        dplyr::filter(!(tolower(.data$amount_concept_name) %in% tolower(.env$doseUnit) |
                        tolower(.data$numerator_concept_name) %in% tolower(.env$doseUnit)))
    }else{
      x[[i]] <- x[[i]] |>
        dplyr::filter(tolower(.data$amount_concept_name) %in% tolower(.env$doseUnit) |
                        tolower(.data$numerator_concept_name) %in% tolower(.env$doseUnit))
    }

    x[[i]] <- x[[i]] |>
      dplyr::pull("concept_id")

    x[[i]] <- sort(unique(x[[i]]))

    if(isTRUE(withDetails)){
      x[[i]] <- x_original[[i]] |>
        dplyr::filter(.data$concept_id %in% x[[i]])
    }
  }

  x <- x |>
    vctrs::list_drop_empty()

  CDMConnector::dropTable(cdm = cdm, name = tableCodelist)

  x

}