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| # Copyright 2023 DARWIN EU® | ||
| # | ||
| # This file is part of IncidencePrevalence | ||
| # | ||
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| # 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. | ||
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| #' Get descendant codes for ATC levels | ||
| #' | ||
| #' @param cdm cdm_reference via CDMConnector | ||
| #' @param level ATC level. Can be one or more of "ATC 1st", "ATC 2nd", | ||
| #' "ATC 3rd", "ATC 4th", and "ATC 5th" | ||
| #' @param name ATC name of interest. For example, c("Dermatologicals", | ||
| #' "Nervous System"), would result in a list of length two with the descendant | ||
| #' concepts for these two particular ATC groups. | ||
| #' @param doseForm Only descendants codes with the specified dose form | ||
| #' will be returned. If NULL, descendant codes will be returned regardless | ||
| #' of dose form. | ||
| #' | ||
| #' @return A named list, with each element containing the descendant | ||
| #' concepts for a particular ATC group | ||
| #' @export | ||
| #' | ||
| #' @examples | ||
| #' cdm <- mockVocabRef() | ||
| #' getATCCodes(cdm = cdm, level = "ATC 1st") | ||
| #' DBI::dbDisconnect(attr(cdm, "dbcon"), shutdown = TRUE) | ||
| getATCCodes <- function(cdm, | ||
| level = c("ATC 1st"), | ||
| name = NULL, | ||
| doseForm = NULL) { | ||
| errorMessage <- checkmate::makeAssertCollection() | ||
| checkDbType(cdm = cdm, type = "cdm_reference", messageStore = errorMessage) | ||
| levelCheck <- all(level %in% | ||
| c( | ||
| "ATC 1st", | ||
| "ATC 2nd", | ||
| "ATC 3rd", | ||
| "ATC 4th", | ||
| "ATC 5th" | ||
| )) | ||
| if (!isTRUE(levelCheck)) { | ||
| errorMessage$push( | ||
| "- level can only be from: ATC 1st, ATC 2nd, ATC 3rd, ATC 4th, ATC 5th" | ||
| ) | ||
| } | ||
| checkmate::assertTRUE(levelCheck, add = errorMessage) | ||
| checkmate::assertVector(name, | ||
| add = errorMessage, | ||
| null.ok = TRUE | ||
| ) | ||
| checkmate::reportAssertions(collection = errorMessage) | ||
|
|
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| atc_groups <- cdm$concept %>% | ||
| dplyr::filter(.data$vocabulary_id == "ATC") %>% | ||
| dplyr::filter(.data$concept_class_id %in% .env$level) %>% | ||
| dplyr::collect() | ||
|
|
||
| if (!is.null(name)) { | ||
| atc_groups <- atc_groups %>% | ||
| dplyr::filter(tolower(.data$concept_name) %in% tolower(.env$name)) | ||
| } | ||
|
|
||
| errorMessage <- checkmate::makeAssertCollection() | ||
| atcCheck <- nrow(atc_groups) > 0 | ||
| if (!isTRUE(atcCheck)) { | ||
| errorMessage$push( | ||
| "- No matching ATC codes found" | ||
| ) | ||
| } | ||
| checkmate::assertTRUE(atcCheck, add = errorMessage) | ||
| checkmate::reportAssertions(collection = errorMessage) | ||
|
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||
|
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| atc_descendants <- getDescendants( | ||
| cdm = cdm, | ||
| conceptId = atc_groups$concept_id, | ||
| withAncestor = TRUE, | ||
| doseForm = doseForm | ||
| ) | ||
| if (nrow(atc_descendants) > 0) { | ||
| atc_descendants <- atc_descendants %>% | ||
| dplyr::select(c("concept_id", "ancestor_concept_id")) %>% | ||
| # split different ancestors into multiple cols | ||
| tidyr::separate_wider_delim( | ||
| cols = "ancestor_concept_id", | ||
| delim = ";", | ||
| names_sep = "", | ||
| too_few = "align_start" | ||
| ) | ||
|
|
||
| atc_descendants <- atc_descendants %>% | ||
| # one row per concept + ancestor | ||
| tidyr::pivot_longer(!"concept_id", | ||
| names_to = NULL, | ||
| values_to = "ancestor_concept_id", | ||
| values_drop_na = TRUE | ||
| ) | ||
|
|
||
| # to list | ||
| # one item per concept | ||
| atc_descendants <- split( | ||
| x = atc_descendants, | ||
| f = as.factor(atc_descendants$ancestor_concept_id), | ||
| drop = TRUE | ||
| ) | ||
|
|
||
| # for each item in the list - pull out concepts and name | ||
| for (i in seq_along(atc_descendants)) { | ||
| workingLevel <- atc_groups %>% | ||
| dplyr::filter(.data$concept_id == names(atc_descendants)[i]) %>% | ||
| dplyr::pull("concept_class_id") | ||
| workingName <- atc_groups %>% | ||
| dplyr::filter(.data$concept_id == names(atc_descendants)[i]) %>% | ||
| dplyr::pull("concept_name") | ||
|
|
||
| atc_descendants[[i]] <- atc_descendants[[i]] %>% | ||
| dplyr::select("concept_id") %>% | ||
| dplyr::distinct() %>% | ||
| dplyr::pull() | ||
|
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| names(atc_descendants)[i] <- paste0( | ||
| workingLevel, ": ", workingName, | ||
| " (", names(atc_descendants)[i], ")" | ||
| ) | ||
| } | ||
| } | ||
| return(atc_descendants) | ||
| } | ||
|
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||
| #' Get descendant codes for drug ingredients | ||
| #' | ||
| #' @param cdm cdm_reference via CDMConnector | ||
| #' @param name Names of ingredients of interest. For example, c("acetaminophen", | ||
| #' "codeine"), would result in a list of length two with the descendant | ||
| #' concepts for these two particular drug ingredients. | ||
| #' @param doseForm Only descendants codes with the specified dose form | ||
| #' will be returned. If NULL, descendant codes will be returned regardless | ||
| #' of dose form. | ||
| #' | ||
| #' @return A named list, with each item containing descendant concepts of | ||
| #' an ingredient | ||
| #' @export | ||
| #' | ||
| #' @examples | ||
| #'cdm <- mockVocabRef() | ||
| #'getDrugIngredientCodes(cdm = cdm, name = "Adalimumab") | ||
| #'DBI::dbDisconnect(attr(cdm, "dbcon"), shutdown = TRUE) | ||
| getDrugIngredientCodes <- function(cdm, name = NULL, doseForm = NULL) { | ||
| errorMessage <- checkmate::makeAssertCollection() | ||
| checkDbType(cdm = cdm, type = "cdm_reference", messageStore = errorMessage) | ||
| checkmate::assertVector(name, | ||
| add = errorMessage, | ||
| null.ok = TRUE | ||
| ) | ||
| checkmate::reportAssertions(collection = errorMessage) | ||
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| ingredientConcepts <- cdm$concept %>% | ||
| dplyr::filter(.data$standard_concept == "S") %>% | ||
| dplyr::filter(.data$concept_class_id == "Ingredient") %>% | ||
| dplyr::select("concept_id", "concept_name") %>% | ||
| dplyr::collect() | ||
|
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| if (!is.null(name)) { | ||
| ingredientConcepts <- ingredientConcepts %>% | ||
| dplyr::filter(tolower(.data$concept_name) %in% tolower(.env$name)) | ||
| } | ||
|
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||
| errorMessage <- checkmate::makeAssertCollection() | ||
| ingredientCheck <- nrow(ingredientConcepts) > 0 | ||
| if (!isTRUE(ingredientCheck)) { | ||
| errorMessage$push( | ||
| "- No matching Ingredient codes found" | ||
| ) | ||
| } | ||
| checkmate::assertTRUE(ingredientCheck, add = errorMessage) | ||
| checkmate::reportAssertions(collection = errorMessage) | ||
|
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| # to avoid potential memory problems will batch | ||
| if (nrow(ingredientConcepts) > 0) { | ||
| ingredientCodes <- fetchBatchedDrugIngredientCodes(cdm, | ||
| codes = ingredientConcepts$concept_id, | ||
| batchSize = 500, | ||
| doseForm = doseForm | ||
| ) | ||
| } | ||
|
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| ingredientCodes <- ingredientCodes %>% | ||
| dplyr::select(c("concept_id", "ancestor_concept_id")) %>% | ||
| # split different ancestors into multiple cols | ||
| tidyr::separate_wider_delim( | ||
| cols = "ancestor_concept_id", | ||
| delim = ";", | ||
| names_sep = "", | ||
| too_few = "align_start" | ||
| ) | ||
|
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| ingredientCodes <- ingredientCodes %>% | ||
| # one row per concept + ancestor | ||
| tidyr::pivot_longer(!"concept_id", | ||
| names_to = NULL, | ||
| values_to = "ancestor_concept_id", | ||
| values_drop_na = TRUE | ||
| ) | ||
|
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| # to list | ||
| # one item per concept | ||
| ingredientCodes <- split( | ||
| x = ingredientCodes, | ||
| f = as.factor(ingredientCodes$ancestor_concept_id), | ||
| drop = TRUE | ||
| ) | ||
|
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| # for each item in the list - pull out concepts and name | ||
| for (i in seq_along(ingredientCodes)) { | ||
| workingName <- ingredientConcepts %>% | ||
| dplyr::filter(.data$concept_id == names(ingredientCodes)[[i]]) %>% | ||
| dplyr::pull("concept_name") | ||
|
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| ingredientCodes[[i]] <- ingredientCodes[[i]] %>% | ||
| dplyr::select("concept_id") %>% | ||
| dplyr::distinct() %>% | ||
| dplyr::pull() | ||
|
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| names(ingredientCodes)[[i]] <- paste0( | ||
| "Ingredient", ": ", workingName, | ||
| " (", names(ingredientCodes)[[i]], ")" | ||
| ) | ||
| } | ||
| return(ingredientCodes) | ||
| } | ||
|
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| fetchBatchedDrugIngredientCodes <- function(cdm, codes, batchSize, doseForm) { | ||
| codeBatches <- split( | ||
| codes, | ||
| ceiling(seq_along(codes) / batchSize) | ||
| ) | ||
|
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| descendants <- vector("list", length(codeBatches)) | ||
|
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| cli::cli_progress_bar( | ||
| total = length(descendants), | ||
| format = " -- getting descendants {cli::pb_bar} {cli::pb_current} of {cli::pb_total} ingredient groups" | ||
| ) | ||
| for (i in seq_along(descendants)) { | ||
| cli::cli_progress_update() | ||
| descendants[[i]] <- getDescendants( | ||
| cdm = cdm, | ||
| conceptId = codeBatches[[i]], | ||
| withAncestor = TRUE, | ||
| doseForm = doseForm | ||
| ) | ||
| } | ||
| cli::cli_progress_done() | ||
| descendants <- dplyr::bind_rows(descendants) | ||
|
|
||
| return(descendants) | ||
| } | ||
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