mirror of https://github.com/msberends/AMR.git
75 lines
3.7 KiB
R
75 lines
3.7 KiB
R
# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Data 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) 2018-2022 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 data 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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# we will use Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS)
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# as a source, which copies directly from the latest US SNOMED CT version
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# - go to https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009
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# - check that current online version is higher than SNOMED_VERSION$current_version
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# - if so, click on 'Download Value Set', choose 'TXT'
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snomed <- read_tsv("data-raw/SNOMED_PHVS_Microorganism_CDC_V12.txt", skip = 3) %>%
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select(1:2) %>%
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set_names(c("snomed", "mo"))
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# save all valid genera, species and subspecies
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vctr <- unique(unlist(strsplit(c(microorganisms$fullname, microorganisms.old$fullname), " ")))
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vctr <- tolower(vctr[vctr %like% "^[a-z]+$"])
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# remove all parts of the name that are no valid values in genera, species or subspecies
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# this takes ~20 seconds
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snomed <- snomed %>%
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mutate(fullname = vapply(FUN.VALUE = character(1),
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# split on space and/or comma
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strsplit(tolower(mo), "[ ,]"),
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function(x) trimws(paste0(x[x %in% vctr], collapse = " "))),
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# remove " group"
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fullname = gsub(" group", "", fullname, fixed = TRUE))
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snomed_keep <- snomed %>%
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filter(fullname %in% tolower(c(microorganisms$fullname, microorganisms.old$fullname))) %>%
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group_by(fullname_lower = fullname) %>%
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summarise(snomed = list(snomed))
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message(nrow(snomed_keep), " MO's will get a SNOMED code.")
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# save to microorganisms data set
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microorganisms <- microorganisms %>%
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# remove old snomed
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select(-snomed) %>%
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# create dummy var for joining
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mutate(fullname_lower = tolower(fullname)) %>%
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# join new snomed
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left_join(snomed_keep) %>%
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# remove dummy var
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select(-fullname_lower) %>%
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AMR:::dataset_UTF8_to_ASCII()
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# don't forget to update the version number in SNOMED_VERSION in ./R/globals.R!
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# usethis::use_data(microorganisms, overwrite = TRUE, version = 2, compress = "xz")
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