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115 lines
4.7 KiB
R
115 lines
4.7 KiB
R
# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Analysis for R #
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# #
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# SOURCE #
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# https://github.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2018-2020 Berends MS, Luz CF et al. #
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# Developed at the University of Groningen, the Netherlands, in #
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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# We created this package for both routine data analysis and academic #
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# research and it was publicly released in the hope that it will be #
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
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# #
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# Visit our website for the full manual and a complete tutorial about #
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# how to conduct AMR analysis: https://msberends.github.io/AMR/ #
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# ==================================================================== #
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library(AMR)
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library(tidyverse)
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# go to https://www.nictiz.nl/standaardisatie/terminologiecentrum/referentielijsten/micro-organismen/ (Ctrl/Cmd + A in table)
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# read the table from clipboard
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snomed <- clipr::read_clip_tbl(skip = 2)
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snomed <- snomed %>%
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dplyr::filter(gsub("(^genus |^familie |^stam |ss.? |subsp.? |subspecies )", "",
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Omschrijving.,
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ignore.case = TRUE) %in% c(microorganisms$fullname,
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microorganisms.old$fullname)) %>%
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dplyr::transmute(fullname = mo_name(Omschrijving.),
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snomed = as.integer(Id)) %>%
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dplyr::filter(!fullname %like% "unknown")
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snomed_trans <- snomed %>%
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group_by(fullname) %>%
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mutate(snomed_list = list(snomed)) %>%
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ungroup() %>%
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select(fullname, snomed = snomed_list) %>%
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distinct(fullname, .keep_all = TRUE)
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microorganisms <- AMR::microorganisms %>%
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left_join(snomed_trans)
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# remove the NULLs, set to NA
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microorganisms$snomed <- lapply(microorganisms$snomed, function(x) if (length(x) == 0) NA else x)
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microorganisms <- dataset_UTF8_to_ASCII(microorganisms)
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usethis::use_data(microorganisms, overwrite = TRUE)
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rm(microorganisms)
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# OLD ---------------------------------------------------------------------
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# baseUrl <- 'https://browser.ihtsdotools.org/snowstorm/snomed-ct'
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# edition <- 'MAIN'
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# version <- '2019-07-31'
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#
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# microorganisms.snomed <- data.frame(conceptid = character(0),
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# mo = character(0),
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# stringsAsFactors = FALSE)
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# microorganisms$snomed <- ""
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#
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# # for (i in 1:50) {
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# for (i in 1:1000) {
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#
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# if (i %% 10 == 0) {
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# cat(paste0(i, " - ", cleaner::percentage(i / nrow(microorganisms)), "\n"))
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# }
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#
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# mo_data <- microorganisms %>%
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# filter(mo == microorganisms$mo[i]) %>%
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# as.list()
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#
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# if (!mo_data$rank %in% c("genus", "species")) {
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# next
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# }
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#
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# searchTerm <- paste0(
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# ifelse(mo_data$rank == "genus", "Genus ", ""),
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# mo_data$fullname,
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# " (organism)")
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#
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# url <- paste0(baseUrl, '/browser/',
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# edition, '/',
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# version,
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# '/descriptions?term=', curl::curl_escape(searchTerm),
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# '&mode=fullText&activeFilter=true&limit=', 250)
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# results <- url %>%
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# httr::GET() %>%
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# httr::content(type = "text", encoding = "UTF-8") %>%
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# jsonlite::fromJSON(flatten = TRUE) %>%
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# .$items
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# if (NROW(results) == 0) {
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# next
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# } else {
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# message("Adding ", crayon::italic(mo_data$fullname))
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# }
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#
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# tryCatch(
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# microorganisms$snomed[i] <- results %>% filter(term == searchTerm) %>% pull(concept.conceptId),
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# error = function(e) invisible()
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# )
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#
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# if (nrow(results) > 1) {
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# microorganisms.snomed <- microorganisms.snomed %>%
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# bind_rows(tibble(conceptid = results %>% filter(term != searchTerm) %>% pull(concept.conceptId) %>% unique(),
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# mo = as.character(mo_data$mo)))
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# }
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# }
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