mirror of https://github.com/msberends/AMR.git
1687 lines
72 KiB
R
1687 lines
72 KiB
R
# ==================================================================== #
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# TITLE: #
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# AMR: An R Package for Working with Antimicrobial Resistance Data #
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# #
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# SOURCE CODE: #
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# https://github.com/msberends/AMR #
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# #
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# PLEASE CITE THIS SOFTWARE AS: #
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# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
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# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
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# Data. Journal of Statistical Software, 104(3), 1-31. #
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# https://doi.org/10.18637/jss.v104.i03 #
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# #
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# Developed at the University of Groningen and the University Medical #
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# Center Groningen in The Netherlands, in collaboration with many #
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# colleagues from around the world, see our website. #
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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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# THIS SCRIPT REQUIRES AT LEAST 16 GB RAM
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# (at least 10 GB will be used by the R session for the size of the files)
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# 1. Go to https://doi.org/10.15468/39omei and find the download link for the
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# latest GBIF backbone taxonony under "Endpoints" and unpack Taxon.tsv from it (~2.2 GB)
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# ALSO BE SURE to get the date of release and update R/aa_globals.R later!
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# 2. Go to https://lpsn.dsmz.de/downloads (register first) and download the latest
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# CSV file (~12,5 MB) as "taxonomy.csv". Their API unfortunately does
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# not include the full taxonomy and is currently (2022) pretty worthless.
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# 3. For data about human pathogens, we use Bartlett et al. (2022),
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# https://doi.org/10.1099/mic.0.001269. Their latest supplementary material
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# can be found here: https://github.com/padpadpadpad/bartlett_et_al_2022_human_pathogens.
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# . Download their latest xlsx file in the `data` folder and save it to our
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# . `data-raw` folder.
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# 4. Set this folder_location to the path where these two files are:
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folder_location <- "~/Downloads/backbone/"
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file_gbif <- paste0(folder_location, "Taxon.tsv")
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file_lpsn <- paste0(folder_location, "taxonomy.csv")
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file_bartlett <- "data-raw/bartlett_et_al_2022_human_pathogens.xlsx"
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# 4. Run the rest of this script line by line and check everything :)
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if (!file.exists(file_gbif)) stop("GBIF file not found")
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if (!file.exists(file_lpsn)) stop("LPSN file not found")
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if (!file.exists(file_bartlett)) stop("Bartlett et al. Excel file not found")
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library(dplyr)
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library(vroom) # to import files
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library(rvest) # to scape LPSN website
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library(progress) # to show progress bars
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library(readxl) # for reading the Bartlett Excel file
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devtools::load_all(".") # load AMR package
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# Helper functions --------------------------------------------------------
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get_author_year <- function(ref) {
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# Only keep first author, e.g. transform 'Smith, Jones, 2011' to 'Smith et al., 2011'
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authors2 <- iconv(ref, from = "UTF-8", to = "ASCII//TRANSLIT")
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authors2 <- gsub(" ?\\(Approved Lists [0-9]+\\) ?", " () ", authors2)
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authors2 <- gsub(" [)(]+ $", "", authors2)
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# remove leading and trailing brackets
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authors2 <- trimws(gsub("^[(](.*)[)]$", "\\1", authors2))
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# only take part after brackets if there's a name
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authors2 <- ifelse(grepl(".*[)] [a-zA-Z]+.*", authors2),
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gsub(".*[)] (.*)", "\\1", authors2),
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authors2
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)
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# replace parentheses with emend. to get the latest authors
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authors2 <- gsub("(", " emend. ", authors2, fixed = TRUE)
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authors2 <- gsub(")", "", authors2, fixed = TRUE)
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authors2 <- gsub(" +", " ", authors2)
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authors2 <- trimws(authors2)
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# get year from last 4 digits
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lastyear <- as.integer(gsub(".*([0-9]{4})$", "\\1", authors2))
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# can never be later than now
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lastyear <- ifelse(lastyear > as.integer(format(Sys.Date(), "%Y")),
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NA,
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lastyear
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)
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# get authors without last year
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authors <- gsub("(.*)[0-9]{4}$", "\\1", authors2)
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# not sure what this is
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authors <- gsub("(Saito)", "", authors, fixed = TRUE)
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authors <- gsub("(Oudem.)", "", authors, fixed = TRUE)
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# remove nonsense characters from names
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authors <- gsub("[^a-zA-Z,'&. -]", "", authors)
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# no initials, only surname
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authors <- gsub("[A-Z][.]", "", authors, ignore.case = FALSE)
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# remove trailing and leading spaces
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authors <- trimws(authors)
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# keep only the part after last 'emend.' to get the latest authors
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authors <- gsub(".*emend[.] ?", "", authors)
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# only keep first author and replace all others by 'et al'
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authors <- gsub("(,| and| et| &| ex| emend\\.?) .*", " et al.", authors)
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# et al. always with ending dot
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authors <- gsub(" et al\\.?", " et al.", authors)
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authors <- gsub(" ?,$", "", authors)
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# don't start with 'sensu' or 'ehrenb'
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authors <- gsub("^(sensu|Ehrenb.?|corrig.?) ", "", authors, ignore.case = TRUE)
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# no initials, only surname
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authors <- trimws(authors)
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authors <- gsub("^([A-Z][.])+( & ?)?", "", authors, ignore.case = FALSE)
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authors <- gsub("^([A-Z]+ )+", "", authors, ignore.case = FALSE)
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# remove dots
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authors <- gsub(".", "", authors, fixed = TRUE)
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authors <- gsub("et al", "et al.", authors, fixed = TRUE)
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authors[nchar(authors) <= 3] <- ""
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# combine author and year if year is available
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ref <- ifelse(!is.na(lastyear),
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paste0(authors, ", ", lastyear),
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authors
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)
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# fix beginning and ending
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ref <- gsub(", $", "", ref)
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ref <- gsub("^, ", "", ref)
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ref <- gsub("^(emend|et al.,?)", "", ref)
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ref <- trimws(ref)
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ref <- gsub("'", "", ref)
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# a lot start with a lowercase character - fix that
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ref[!grepl("^d[A-Z]", ref)] <- gsub("^([a-z])", "\\U\\1", ref[!grepl("^d[A-Z]", ref)], perl = TRUE)
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# specific one for the French that are named dOrbigny
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ref[grepl("^d[A-Z]", ref)] <- gsub("^d", "d'", ref[grepl("^d[A-Z]", ref)])
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ref <- gsub(" +", " ", ref)
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ref[ref == ""] <- NA_character_
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ref
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}
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df_remove_nonASCII <- function(df) {
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# Remove non-ASCII characters (these are not allowed by CRAN)
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df %>%
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mutate_if(is.character, iconv, from = "UTF-8", to = "ASCII//TRANSLIT") %>%
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# also remove invalid characters
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mutate_if(is.character, ~ gsub("[\"'`]+", "", .)) %>%
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AMR:::dataset_UTF8_to_ASCII()
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}
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# to retrieve LPSN and authors from LPSN website
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get_lpsn_and_author <- function(rank, name) {
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name <- gsub("^Candidatus ", "", name)
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url <- paste0("https://lpsn.dsmz.de/", tolower(rank), "/", tolower(name))
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page_txt <- tryCatch(read_html(url), error = function(e) NULL)
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if (is.null(page_txt)) {
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warning("No LPSN found for ", tolower(rank), " '", name, "'")
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lpsn <- NA_character_
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ref <- NA_character_
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status <- "unknown"
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} else {
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page_txt <- page_txt %>%
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html_element("#detail-page") %>%
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html_text()
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lpsn <- gsub(".*Record number:[\r\n\t ]*([0-9]+).*", "\\1", page_txt, perl = FALSE)
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ref <- page_txt %>%
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gsub(".*?Name: (.*[0-9]{4}?).*", "\\1", ., perl = FALSE) %>%
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gsub(name, "", ., fixed = TRUE) %>%
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gsub("^\"?Candidatus ?\"?", "", .) %>%
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trimws()
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status <- trimws(gsub(".*Nomenclatural status:[\r\n\t ]*([a-zA-Z, ]+)[\r\n\t].*", "\\1", page_txt, perl = FALSE))
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if ((status %like% "validly published" & status %unlike% "not valid") | status %like% "[\r\n\t]") {
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# we used to take "accepted" for every LPSN record, also candidates. Now only for missing values and explicit accepted ones.
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status <- "accepted"
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} else {
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status <- "not validly published"
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}
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}
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c("lpsn" = lpsn, "ref" = ref, "status" = status)
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}
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# this will e.g. take the family from the root genus record, and gives all species that family
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get_top_lvl <- function(current, rank, rank_target) {
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if (!rank_target %in% rank) {
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current[1]
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} else {
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out <- current[rank == rank_target][1]
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if (out %in% c("", NA)) {
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out <- names(sort(table(current[which(!current %in% c("", NA))]), decreasing = TRUE)[1])
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if (is.null(out)) {
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out <- ""
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}
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}
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out
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}
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}
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# MB/ August 2022: useless, does not contain full taxonomy, e.g. LPSN::request(cred, category = "family") is empty.
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# get_from_lpsn <- function (user, pw) {
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# if (!"LPSN" %in% rownames(utils::installed.packages())) {
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# stop("Install the official LPSN package for R using: install.packages('LPSN', repos = 'https://r-forge.r-project.org')")
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# }
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# cred <- LPSN::open_lpsn(user, pw)
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#
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# lpsn_genus <- LPSN::request(cred, category = "genus")
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# message("Downloading genus data (n = ", lpsn_genus$count, ") from LPSN API...")
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# lpsn_genus <- as.data.frame(LPSN::retrieve(cred, category = "genus"))
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#
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# lpsn_species <- LPSN::request(cred, category = "species")
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# message("Downloading species data (n = ", lpsn_species$count, ") from LPSN API...")
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# lpsn_species <- as.data.frame(LPSN::retrieve(cred, category = "species"))
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#
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# lpsn_subspecies <- LPSN::request(cred, category = "subspecies")
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# message("Downloading subspecies data (n = ", lpsn_subspecies$count, ") from LPSN API...")
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# lpsn_subspecies <- as.data.frame(LPSN::retrieve(cred, category = "subspecies"))
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#
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# message("Binding rows...")
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# lpsn_total <- bind_rows(lpsn_genus, lpsn_species, lpsn_subspecies)
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# message("Done.")
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# lpsn_total
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# }
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# Read GBIF data ----------------------------------------------------------
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taxonomy_gbif.bak <- vroom(file_gbif)
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include_fungal_orders <- c(
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"Eurotiales", "Microascales", "Mucorales", "Saccharomycetales",
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"Schizosaccharomycetales", "Tremellales", "Onygenales", "Pneumocystales"
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)
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# get latest taxonomic names of these fungal orders
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include_fungal_orders_ids <- taxonomy_gbif.bak %>%
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filter(order %in% include_fungal_orders)
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include_fungal_orders <- taxonomy_gbif.bak %>%
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filter(taxonID %in% c(include_fungal_orders_ids$taxonID, include_fungal_orders_ids$acceptedNameUsageID)) %>%
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distinct(order) %>%
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pull(order) |>
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sort()
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# check some columns to validate below filters
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taxonomy_gbif.bak$taxonomicStatus |> table() |> sort() |> as.data.frame()
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taxonomy_gbif.bak$taxonRank |> table() |> sort() |> as.data.frame()
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taxonomy_gbif <- taxonomy_gbif.bak %>%
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# immediately filter rows we really never want
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filter(
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# never doubtful status, only accepted and all synonyms, and only ranked items
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taxonomicStatus != "doubtful",
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taxonRank != "unranked",
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# include these kingdoms (no Chromista)
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kingdom %in% c("Archaea", "Bacteria", "Protozoa") |
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# include all of these fungal orders
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order %in% include_fungal_orders |
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# and all of these important genera (see "data-raw/_pre_commit_checks.R")
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# (they also contain bacteria and protozoa, but these will get prevalence = 2 later on)
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genus %in% AMR:::MO_PREVALENT_GENERA
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) %>%
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select(
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kingdom,
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phylum,
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class,
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order,
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family,
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genus,
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species = specificEpithet,
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subspecies = infraspecificEpithet,
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rank = taxonRank,
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status = taxonomicStatus,
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ref = scientificNameAuthorship,
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gbif = taxonID,
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gbif_parent = parentNameUsageID,
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gbif_renamed_to = acceptedNameUsageID
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) %>%
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mutate(
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# do this mutate after the original selection/filtering, as it decreases computing time tremendously
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status = ifelse(status == "accepted", "accepted", "synonym"),
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# checked taxonRank - the "form" and "variety" always have a subspecies, so:
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rank = ifelse(rank %in% c("form", "variety"), "subspecies", rank),
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source = "GBIF"
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) %>%
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filter(
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# their data is messy - keep only these:
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rank == "kingdom" & !is.na(kingdom) |
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rank == "phylum" & !is.na(phylum) |
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rank == "class" & !is.na(class) |
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rank == "order" & !is.na(order) |
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rank == "family" & !is.na(family) |
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rank == "genus" & !is.na(genus) |
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rank == "species" & !is.na(species) |
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rank == "subspecies" & !is.na(subspecies)
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) %>%
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# some items end with _A or _B... why??
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mutate_all(~ gsub("_[A-Z]$", "", .x, perl = TRUE)) %>%
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# now we have duplicates, remove these, but prioritise "accepted" status and highest taxon ID
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arrange(status, gbif) %>%
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distinct(kingdom, phylum, class, order, family, genus, species, subspecies, .keep_all = TRUE) %>%
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filter(
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kingdom %unlike% "[0-9]",
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phylum %unlike% "[0-9]",
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class %unlike% "[0-9]",
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order %unlike% "[0-9]",
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family %unlike% "[0-9]",
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genus %unlike% "[0-9]"
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)
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# integrity tests
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sort(table(taxonomy_gbif$rank))
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sort(table(taxonomy_gbif$status))
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taxonomy_gbif
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# Read LPSN data ----------------------------------------------------------
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taxonomy_lpsn.bak <- vroom(file_lpsn)
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taxonomy_lpsn <- taxonomy_lpsn.bak %>%
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transmute(
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genus = genus_name,
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species = sp_epithet,
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subspecies = subsp_epithet,
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rank = case_when(
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!is.na(subsp_epithet) ~ "subspecies",
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!is.na(sp_epithet) ~ "species",
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TRUE ~ "genus"
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),
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status = ifelse(is.na(record_lnk), "accepted", "synonym"),
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ref = authors,
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lpsn = as.character(record_no),
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lpsn_parent = NA_character_,
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lpsn_renamed_to = as.character(record_lnk)
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) %>%
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mutate(source = "LPSN")
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# integrity tests
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sort(table(taxonomy_lpsn$rank))
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sort(table(taxonomy_lpsn$status))
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taxonomy_lpsn
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# download additional taxonomy to the domain/kingdom level (their API is not sufficient...)
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taxonomy_lpsn_missing <- tibble(
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kingdom = character(0),
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phylum = character(0),
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class = character(0),
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order = character(0),
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family = character(0),
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genus = character(0)
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)
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for (page in LETTERS) {
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# this will not alter `taxonomy_lpsn` yet
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message("Downloading page ", page, "...", appendLF = TRUE)
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url <- paste0("https://lpsn.dsmz.de/genus?page=", page)
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x <- tryCatch(read_html(url),
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error = function(e) {
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message("Waiting 10 seconds because of error: ", e$message)
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Sys.sleep(10)
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read_html(url)
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})
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x <- x %>%
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# class "main-list" is the main table
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html_element(".main-list") %>%
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# get every list element with a set <id> attribute
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html_elements("li[id]")
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pb <- progress_bar$new(total = length(x), format = "[:bar] :current/:total :eta")
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for (i in seq_len(length(x))) {
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pb$tick()
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elements <- x[[i]] %>% html_elements("a")
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hrefs <- elements %>% html_attr("href")
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ranks <- hrefs %>% gsub(".*/(.*?)/.*", "\\1", .)
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names <- elements %>%
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html_text() %>%
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gsub('"', "", ., fixed = TRUE)
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# no species, this must be until genus level
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hrefs <- hrefs[ranks != "species"]
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names <- names[ranks != "species"]
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ranks <- ranks[ranks != "species"]
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ranks[ranks == "domain"] <- "kingdom"
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suppressMessages(
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df <- names %>%
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tibble() %>%
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t() %>%
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as_tibble(.name_repair = "unique") %>%
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setNames(ranks) %>%
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# no candidates please
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filter(genus %unlike% "^(Candidatus|\\[)")
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)
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taxonomy_lpsn_missing <- taxonomy_lpsn_missing %>%
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bind_rows(df)
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}
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message(" => ", length(x), " entries incl. candidates (cleaned total: ", nrow(taxonomy_lpsn_missing), ")")
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}
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taxonomy_lpsn_missing <- taxonomy_lpsn_missing |> distinct()
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# had to pick the right genus/family combination here:
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taxonomy_lpsn_missing <- taxonomy_lpsn_missing |> filter(!(genus == "Pusillimonas" & family == "Oscillospiraceae"))
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taxonomy_lpsn.bak2 <- taxonomy_lpsn.bak
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taxonomy_lpsn <- taxonomy_lpsn %>%
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left_join(taxonomy_lpsn_missing, by = "genus") %>%
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select(kingdom:family, everything()) %>%
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# remove entries like "[Bacteria, no family]" and "[Bacteria, no class]"
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mutate_all(function(x) ifelse(x %like_case% " no ", NA_character_, x))
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taxonomy_lpsn.bak2 <- taxonomy_lpsn
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# download family directly from LPSN website using scraping, by using get_lpsn_and_author()
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# try it first:
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# get_lpsn_and_author("genus", "Escherichia")
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pb <- progress_bar$new(total = length(unique(taxonomy_lpsn$family)), format = "[:bar] :current/:total :eta")
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for (f in unique(taxonomy_lpsn$family)) {
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pb$tick()
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if (is.na(f)) next
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tax_info <- get_lpsn_and_author("Family", f)
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taxonomy_lpsn <- taxonomy_lpsn %>%
|
|
bind_rows(tibble(
|
|
kingdom = taxonomy_lpsn$kingdom[which(taxonomy_lpsn$family == f)[1]],
|
|
phylum = taxonomy_lpsn$phylum[which(taxonomy_lpsn$family == f)[1]],
|
|
class = taxonomy_lpsn$class[which(taxonomy_lpsn$family == f)[1]],
|
|
order = taxonomy_lpsn$order[which(taxonomy_lpsn$family == f)[1]],
|
|
family = f,
|
|
rank = "family",
|
|
status = unname(tax_info["status"]),
|
|
source = "LPSN",
|
|
lpsn = unname(tax_info["lpsn"]),
|
|
ref = unname(tax_info["ref"])
|
|
))
|
|
}
|
|
# download order directly from LPSN website using scraping
|
|
pb <- progress_bar$new(total = length(unique(taxonomy_lpsn$order)), format = "[:bar] :current/:total :eta")
|
|
for (o in unique(taxonomy_lpsn$order)) {
|
|
pb$tick()
|
|
if (is.na(o)) next
|
|
tax_info <- get_lpsn_and_author("Order", o)
|
|
taxonomy_lpsn <- taxonomy_lpsn %>%
|
|
bind_rows(tibble(
|
|
kingdom = taxonomy_lpsn$kingdom[which(taxonomy_lpsn$order == o)[1]],
|
|
phylum = taxonomy_lpsn$phylum[which(taxonomy_lpsn$order == o)[1]],
|
|
class = taxonomy_lpsn$class[which(taxonomy_lpsn$order == o)[1]],
|
|
order = o,
|
|
rank = "order",
|
|
status = unname(tax_info["status"]),
|
|
source = "LPSN",
|
|
lpsn = unname(tax_info["lpsn"]),
|
|
ref = unname(tax_info["ref"])
|
|
))
|
|
}
|
|
# download class directly from LPSN website using scraping
|
|
pb <- progress_bar$new(total = length(unique(taxonomy_lpsn$class)), format = "[:bar] :current/:total :eta")
|
|
for (cc in unique(taxonomy_lpsn$class)) {
|
|
pb$tick()
|
|
if (is.na(cc)) next
|
|
tax_info <- get_lpsn_and_author("Class", cc)
|
|
taxonomy_lpsn <- taxonomy_lpsn %>%
|
|
bind_rows(tibble(
|
|
kingdom = taxonomy_lpsn$kingdom[which(taxonomy_lpsn$class == cc)[1]],
|
|
phylum = taxonomy_lpsn$phylum[which(taxonomy_lpsn$class == cc)[1]],
|
|
class = cc,
|
|
rank = "class",
|
|
status = unname(tax_info["status"]),
|
|
source = "LPSN",
|
|
lpsn = unname(tax_info["lpsn"]),
|
|
ref = unname(tax_info["ref"])
|
|
))
|
|
}
|
|
# download phylum directly from LPSN website using scraping
|
|
pb <- progress_bar$new(total = length(unique(taxonomy_lpsn$phylum)), format = "[:bar] :current/:total :eta")
|
|
for (p in unique(taxonomy_lpsn$phylum)) {
|
|
pb$tick()
|
|
if (is.na(p)) next
|
|
tax_info <- get_lpsn_and_author("Phylum", p)
|
|
taxonomy_lpsn <- taxonomy_lpsn %>%
|
|
bind_rows(tibble(
|
|
kingdom = taxonomy_lpsn$kingdom[which(taxonomy_lpsn$phylum == p)[1]],
|
|
phylum = p,
|
|
rank = "phylum",
|
|
status = unname(tax_info["status"]),
|
|
source = "LPSN",
|
|
lpsn = unname(tax_info["lpsn"]),
|
|
ref = unname(tax_info["ref"])
|
|
))
|
|
}
|
|
# download kingdom directly from LPSN website using scraping
|
|
pb <- progress_bar$new(total = length(unique(taxonomy_lpsn$kingdom)), format = "[:bar] :current/:total :eta")
|
|
for (k in unique(taxonomy_lpsn$kingdom)) {
|
|
pb$tick()
|
|
if (is.na(k)) next
|
|
tax_info <- get_lpsn_and_author("Domain", k)
|
|
taxonomy_lpsn <- taxonomy_lpsn %>%
|
|
bind_rows(tibble(
|
|
kingdom = k,
|
|
rank = "kingdom",
|
|
status = unname(tax_info["status"]),
|
|
source = "LPSN",
|
|
lpsn = unname(tax_info["lpsn"]),
|
|
ref = unname(tax_info["ref"])
|
|
))
|
|
}
|
|
|
|
# integrity tests
|
|
sort(table(taxonomy_lpsn$rank))
|
|
sort(table(taxonomy_lpsn$status))
|
|
|
|
|
|
# Save intermediate results -----------------------------------------------
|
|
|
|
saveRDS(taxonomy_gbif, "data-raw/taxonomy_gbif.rds", version = 2)
|
|
saveRDS(taxonomy_lpsn, "data-raw/taxonomy_lpsn.rds", version = 2)
|
|
# this allows to always get back to this point by simply loading the files from data-raw/.
|
|
|
|
|
|
# Add full names ----------------------------------------------------------
|
|
|
|
taxonomy_gbif <- taxonomy_gbif %>%
|
|
# clean NAs and add fullname
|
|
mutate(across(kingdom:subspecies, function(x) ifelse(is.na(x), "", x)),
|
|
fullname = trimws(case_when(
|
|
rank == "family" ~ family,
|
|
rank == "order" ~ order,
|
|
rank == "class" ~ class,
|
|
rank == "phylum" ~ phylum,
|
|
rank == "kingdom" ~ kingdom,
|
|
TRUE ~ paste(genus, species, subspecies)
|
|
)), .before = 1
|
|
) %>%
|
|
# keep only one GBIF taxon ID per full name
|
|
arrange(fullname, gbif) %>%
|
|
distinct(kingdom, rank, fullname, .keep_all = TRUE)
|
|
|
|
taxonomy_lpsn <- taxonomy_lpsn %>%
|
|
# clean NAs and add fullname
|
|
mutate(across(kingdom:subspecies, function(x) ifelse(is.na(x), "", x)),
|
|
fullname = trimws(case_when(
|
|
rank == "family" ~ family,
|
|
rank == "order" ~ order,
|
|
rank == "class" ~ class,
|
|
rank == "phylum" ~ phylum,
|
|
rank == "kingdom" ~ kingdom,
|
|
TRUE ~ paste(genus, species, subspecies)
|
|
)), .before = 1
|
|
) %>%
|
|
# keep only one LPSN record ID per full name
|
|
arrange(fullname, lpsn) %>%
|
|
distinct(kingdom, rank, fullname, .keep_all = TRUE)
|
|
|
|
# set parent LPSN IDs, requires full name
|
|
taxonomy_lpsn$lpsn_parent[taxonomy_lpsn$rank == "phylum"] <- taxonomy_lpsn$lpsn[match(taxonomy_lpsn$kingdom[taxonomy_lpsn$rank == "phylum"], taxonomy_lpsn$fullname)]
|
|
taxonomy_lpsn$lpsn_parent[taxonomy_lpsn$rank == "class"] <- taxonomy_lpsn$lpsn[match(taxonomy_lpsn$phylum[taxonomy_lpsn$rank == "class"], taxonomy_lpsn$fullname)]
|
|
taxonomy_lpsn$lpsn_parent[taxonomy_lpsn$rank == "order"] <- taxonomy_lpsn$lpsn[match(taxonomy_lpsn$class[taxonomy_lpsn$rank == "order"], taxonomy_lpsn$fullname)]
|
|
taxonomy_lpsn$lpsn_parent[taxonomy_lpsn$rank == "family"] <- taxonomy_lpsn$lpsn[match(taxonomy_lpsn$order[taxonomy_lpsn$rank == "family"], taxonomy_lpsn$fullname)]
|
|
taxonomy_lpsn$lpsn_parent[taxonomy_lpsn$rank == "genus"] <- taxonomy_lpsn$lpsn[match(taxonomy_lpsn$family[taxonomy_lpsn$rank == "genus"], taxonomy_lpsn$fullname)]
|
|
taxonomy_lpsn$lpsn_parent[taxonomy_lpsn$rank == "species"] <- taxonomy_lpsn$lpsn[match(taxonomy_lpsn$genus[taxonomy_lpsn$rank == "species"], taxonomy_lpsn$fullname)]
|
|
taxonomy_lpsn$lpsn_parent[taxonomy_lpsn$rank == "subspecies"] <- taxonomy_lpsn$lpsn[match(paste(taxonomy_lpsn$genus[taxonomy_lpsn$rank == "subspecies"], taxonomy_lpsn$species[taxonomy_lpsn$rank == "subspecies"]), taxonomy_lpsn$fullname)]
|
|
|
|
|
|
# Combine the datasets ----------------------------------------------------
|
|
|
|
taxonomy <- taxonomy_lpsn |>
|
|
# start by adding GBIF to the bottom
|
|
bind_rows(taxonomy_gbif) |>
|
|
# group on unique species
|
|
group_by(kingdom, fullname) |>
|
|
# fill the NAs in LPSN/GBIF fields and ref with the other source (so LPSN: 123 and GBIF: NA will become LPSN: 123 and GBIF: 123)
|
|
mutate(across(matches("^(lpsn|gbif|ref)"), function(x) rep(x[!is.na(x)][1], length(x)))) |>
|
|
# ungroup again
|
|
ungroup() |>
|
|
# only keep unique species per kingdom
|
|
distinct(kingdom, fullname, .keep_all = TRUE) |>
|
|
arrange(fullname)
|
|
|
|
# get missing entries from existing microorganisms data set
|
|
taxonomy.old <- AMR::microorganisms %>%
|
|
select(all_of(colnames(taxonomy))) %>%
|
|
filter(
|
|
!paste(kingdom, fullname) %in% paste(taxonomy$kingdom, taxonomy$fullname),
|
|
# these will be added later:
|
|
source != "manually added")
|
|
taxonomy <- taxonomy %>%
|
|
bind_rows(taxonomy.old) %>%
|
|
arrange(fullname) %>%
|
|
filter(fullname != "")
|
|
|
|
# fix rank
|
|
table(taxonomy$rank, useNA = "always")
|
|
taxonomy <- taxonomy %>%
|
|
mutate(rank = case_when(
|
|
subspecies != "" ~ "subspecies",
|
|
species != "" ~ "species",
|
|
genus != "" ~ "genus",
|
|
family != "" ~ "family",
|
|
order != "" ~ "order",
|
|
class != "" ~ "class",
|
|
phylum != "" ~ "phylum",
|
|
kingdom != "" ~ "kingdom",
|
|
TRUE ~ NA_character_
|
|
))
|
|
table(taxonomy$rank, useNA = "always")
|
|
|
|
# at this point, it happens that some genera within kingdoms have multiple families / orders, etc., see here:
|
|
taxonomy |> filter(genus != "") |> group_by(kingdom, genus) |> filter(n_distinct(family) > 1) |> View()
|
|
# so make this universal
|
|
taxonomy <- taxonomy |>
|
|
group_by(kingdom, genus) |>
|
|
mutate(family = get_top_lvl(family, rank, "genus")) |>
|
|
group_by(kingdom, family) |>
|
|
mutate(order = get_top_lvl(order, rank, "family")) |>
|
|
group_by(kingdom, order) |>
|
|
mutate(class = get_top_lvl(class, rank, "order")) |>
|
|
group_by(kingdom, class) |>
|
|
mutate(phylum = get_top_lvl(phylum, rank, "class")) |>
|
|
ungroup()
|
|
# and remove the taxonomy where it must remain empty
|
|
taxonomy <- taxonomy |>
|
|
mutate(phylum = ifelse(rank %in% c("kingdom"), "", phylum),
|
|
class = ifelse(rank %in% c("kingdom", "phylum"), "", class),
|
|
order = ifelse(rank %in% c("kingdom", "phylum", "class"), "", order),
|
|
family = ifelse(rank %in% c("kingdom", "phylum", "class", "order"), "", family),
|
|
genus = ifelse(rank %in% c("kingdom", "phylum", "class", "order", "family"), "", genus),
|
|
species = ifelse(rank %in% c("kingdom", "phylum", "class", "order", "family", "genus"), "", species),
|
|
subspecies = ifelse(rank %in% c("kingdom", "phylum", "class", "order", "family", "genus", "species"), "", subspecies))
|
|
|
|
|
|
# Save intermediate results (0) -------------------------------------------
|
|
|
|
saveRDS(taxonomy, "data-raw/taxonomy0.rds")
|
|
|
|
|
|
# Add missing and fix old taxonomic entries -------------------------------
|
|
|
|
# this part will make sure that the whole taxonomy of every included species exists, so no missing genera, classes, etc.
|
|
|
|
current_gbif <- taxonomy_gbif.bak %>%
|
|
filter(is.na(acceptedNameUsageID)) %>%
|
|
mutate(
|
|
taxonID = as.character(taxonID),
|
|
parentNameUsageID = as.character(parentNameUsageID)
|
|
)
|
|
|
|
# add missing kingdoms
|
|
taxonomy_all_missing <- taxonomy %>%
|
|
filter(kingdom != "") %>%
|
|
distinct(kingdom) %>%
|
|
mutate(
|
|
fullname = kingdom,
|
|
rank = "kingdom"
|
|
) %>%
|
|
filter(!paste(kingdom, rank) %in% paste(taxonomy$kingdom, taxonomy$rank)) %>%
|
|
left_join(
|
|
current_gbif %>%
|
|
select(kingdom, rank = taxonRank, ref = scientificNameAuthorship, gbif = taxonID, gbif_parent = parentNameUsageID),
|
|
by = c("kingdom", "rank")
|
|
) %>%
|
|
mutate(source = ifelse(!is.na(gbif), "GBIF", "manually added"),
|
|
status = ifelse(!is.na(gbif), "accepted", "unknown"))
|
|
|
|
# 2 = phylum ... 6 = genus
|
|
for (i in 2:6) {
|
|
i_name <- colnames(taxonomy)[i + 1]
|
|
message("Adding missing: ", i_name, "... ", appendLF = FALSE)
|
|
to_add <- taxonomy %>%
|
|
filter(.[[i + 1]] != "") %>%
|
|
distinct(kingdom, .[[i + 1]], .keep_all = TRUE) %>%
|
|
select(kingdom:(i + 1)) %>%
|
|
mutate(
|
|
fullname = .[[ncol(.)]],
|
|
rank = i_name
|
|
) %>%
|
|
filter(!paste(kingdom, .[[ncol(.) - 2]], rank) %in% paste(taxonomy$kingdom, taxonomy[[i + 1]], taxonomy$rank)) %>%
|
|
# get GBIF identifier where available
|
|
left_join(
|
|
current_gbif %>%
|
|
select(kingdom, all_of(i_name), rank = taxonRank, ref = scientificNameAuthorship, gbif = taxonID, gbif_parent = parentNameUsageID),
|
|
by = c("kingdom", "rank", i_name)
|
|
) %>%
|
|
mutate(source = ifelse(!is.na(gbif), "GBIF", "manually added"),
|
|
status = ifelse(!is.na(gbif), "accepted", "unknown"))
|
|
message("n = ", nrow(to_add))
|
|
taxonomy_all_missing <- taxonomy_all_missing %>%
|
|
bind_rows(to_add)
|
|
}
|
|
taxonomy_all_missing %>% View()
|
|
|
|
taxonomy <- taxonomy %>%
|
|
bind_rows(taxonomy_all_missing)
|
|
|
|
# fix for duplicate fullnames within a kingdom (such as Nitrospira which is the name of the genus AND its class)
|
|
taxonomy <- taxonomy %>%
|
|
mutate(
|
|
rank_index = case_when(
|
|
rank == "subspecies" ~ 1,
|
|
rank == "species" ~ 2,
|
|
rank == "genus" ~ 3,
|
|
rank == "family" ~ 4,
|
|
rank == "order" ~ 5,
|
|
rank == "class" ~ 6,
|
|
TRUE ~ 7
|
|
),
|
|
fullname_rank = paste0(fullname, " {", rank, "}")
|
|
) %>%
|
|
arrange(kingdom, fullname, rank_index) %>%
|
|
group_by(kingdom, fullname) %>%
|
|
mutate(fullname = if_else(row_number() > 1, fullname_rank, fullname)) %>%
|
|
ungroup() %>%
|
|
select(-fullname_rank, -rank_index) %>%
|
|
arrange(fullname)
|
|
|
|
# now also add missing species that have subspecies (requires combination with genus)
|
|
taxonomy <- taxonomy %>%
|
|
bind_rows(
|
|
taxonomy %>%
|
|
filter(species != "") %>%
|
|
distinct(kingdom, genus, species, .keep_all = TRUE) %>%
|
|
select(kingdom:species) %>%
|
|
mutate(
|
|
fullname = paste(genus, species),
|
|
rank = "species"
|
|
) %>%
|
|
filter(!paste(kingdom, genus, species, rank) %in% paste(taxonomy$kingdom, taxonomy$genus, taxonomy$species, taxonomy$rank)) %>%
|
|
# get GBIF identifier where available
|
|
left_join(
|
|
current_gbif %>%
|
|
select(kingdom, genus, species = specificEpithet, rank = taxonRank, ref = scientificNameAuthorship, gbif = taxonID, gbif_parent = parentNameUsageID),
|
|
by = c("kingdom", "rank", "genus", "species")
|
|
) %>%
|
|
mutate(source = ifelse(!is.na(gbif), "GBIF", "manually added"),
|
|
status = ifelse(!is.na(gbif), "accepted", "unknown"))
|
|
)
|
|
|
|
|
|
# remove NAs from taxonomy again, and keep unique full names
|
|
taxonomy <- taxonomy %>%
|
|
mutate(across(kingdom:subspecies, function(x) ifelse(is.na(x), "", x))) %>%
|
|
arrange(kingdom, fullname, ref) |>
|
|
distinct(kingdom, fullname, .keep_all = TRUE) %>%
|
|
filter(kingdom != "")
|
|
|
|
|
|
# Save intermediate results (1) -------------------------------------------
|
|
|
|
saveRDS(taxonomy, "data-raw/taxonomy1.rds")
|
|
|
|
|
|
# Get previously manually added entries -----------------------------------
|
|
|
|
manually_added <- AMR::microorganisms %>%
|
|
filter(source == "manually added",
|
|
!paste(kingdom, fullname) %in% paste(taxonomy$kingdom, taxonomy$fullname),
|
|
!rank %in% c("kingdom", "phylum", "class", "order", "family")) %>%
|
|
select(fullname:subspecies, ref, source, rank)
|
|
|
|
# get latest taxonomy for those entries
|
|
for (g in unique(manually_added$genus[manually_added$genus != "" & manually_added$genus %in% taxonomy$genus])) {
|
|
manually_added$family[which(manually_added$genus == g)] <- taxonomy$family[which(taxonomy$genus == g & is.na(taxonomy$lpsn))][1]
|
|
}
|
|
for (f in unique(manually_added$family[manually_added$family != "" & manually_added$family %in% taxonomy$family])) {
|
|
manually_added$order[which(manually_added$family == f)] <- taxonomy$order[which(taxonomy$family == f & is.na(taxonomy$lpsn))][1]
|
|
}
|
|
for (o in unique(manually_added$order[manually_added$order != "" & manually_added$order %in% taxonomy$order])) {
|
|
manually_added$class[which(manually_added$order == o)] <- taxonomy$class[which(taxonomy$order == o & is.na(taxonomy$lpsn))][1]
|
|
}
|
|
for (cc in unique(manually_added$class[manually_added$class != "" & manually_added$class %in% taxonomy$class])) {
|
|
manually_added$phylum[which(manually_added$class == cc)] <- taxonomy$phylum[which(taxonomy$class == cc & is.na(taxonomy$lpsn))][1]
|
|
}
|
|
for (p in unique(manually_added$phylum[manually_added$phylum != "" & manually_added$phylum %in% taxonomy$phylum])) {
|
|
manually_added$kingdom[which(manually_added$phylum == p)] <- taxonomy$kingdom[which(taxonomy$phylum == p & is.na(taxonomy$lpsn))][1]
|
|
}
|
|
|
|
manually_added <- manually_added %>%
|
|
mutate(
|
|
status = "unknown",
|
|
rank = ifelse(fullname %like% "unknown", "(unknown rank)", rank)
|
|
)
|
|
manually_added
|
|
|
|
# these are now included in the new taxonomy, check them
|
|
manually_added |> filter(fullname %in% taxonomy$fullname)
|
|
|
|
taxonomy <- taxonomy %>%
|
|
# here also the 'unknowns' are added, such as "(unknown fungus)"
|
|
bind_rows(manually_added) %>%
|
|
arrange(fullname)
|
|
|
|
table(taxonomy$rank, useNA = "always")
|
|
|
|
# Get LPSN data for records missing from `taxonomy_lpsn` ------------------
|
|
|
|
# Weirdly enough, some LPSN records were lacking from `taxonomy_lpsn`,
|
|
# such as family Thiotrichaceae and its order Thiotrichales. When running
|
|
# get_lpsn_and_author("family", "Thiotrichaceae") you do get a result.
|
|
# So check every non-LPSN records from the kingdom of Bacteria and add it
|
|
gbif_bacteria <- which(taxonomy$kingdom == "Bacteria" & taxonomy$source == "GBIF" & taxonomy$rank %in% c("phylum", "class", "order", "family"))
|
|
added <- 0
|
|
pb <- progress_bar$new(total = length(gbif_bacteria), format = "[:bar] :current/:total :eta")
|
|
for (record in gbif_bacteria) {
|
|
pb$tick()
|
|
lpsn <- get_lpsn_and_author(rank = taxonomy$rank[record],
|
|
name = taxonomy$fullname[record])
|
|
if (is.na(lpsn["lpsn"])) {
|
|
next
|
|
} else {
|
|
added <- added + 1
|
|
taxonomy$source[record] <- "LPSN"
|
|
taxonomy$lpsn[record] <- unname(lpsn["lpsn"])
|
|
taxonomy$ref[record] <- unname(lpsn["ref"])
|
|
taxonomy$status[record] <- unname(lpsn["status"])
|
|
}
|
|
}
|
|
message(added, " GBIF records altered to latest LPSN")
|
|
taxbak <- taxonomy
|
|
|
|
# Clean scientific reference ----------------------------------------------
|
|
|
|
taxonomy <- taxonomy %>%
|
|
mutate(ref = get_author_year(ref))
|
|
|
|
|
|
# Get the latest upper taxonomy from LPSN for non-LPSN data ---------------
|
|
|
|
# (e.g., phylum above class "Bacilli" was still "Firmicutes" in 2023, should be "Bacillota")
|
|
for (k in unique(taxonomy$kingdom[taxonomy$kingdom != ""])) {
|
|
message("Fixing GBIF taxonomy for kingdom ", k, ".", appendLF = FALSE)
|
|
i <- 0
|
|
for (g in unique(taxonomy$genus[taxonomy$genus != "" & taxonomy$kingdom == k & taxonomy$source == "LPSN"])) {
|
|
i <- i + 1
|
|
if (i %% 50 == 0) message(".", appendLF = FALSE)
|
|
taxonomy$family[which(taxonomy$genus == g & taxonomy$kingdom == k)] <- taxonomy$family[which(taxonomy$genus == g & taxonomy$kingdom == k & taxonomy$source == "LPSN")][1]
|
|
}
|
|
for (f in unique(taxonomy$family[taxonomy$family != "" & taxonomy$kingdom == k & taxonomy$source == "LPSN"])) {
|
|
i <- i + 1
|
|
if (i %% 50 == 0) message(".", appendLF = FALSE)
|
|
taxonomy$order[which(taxonomy$family == f & taxonomy$kingdom == k)] <- taxonomy$order[which(taxonomy$family == f & taxonomy$kingdom == k & taxonomy$source == "LPSN")][1]
|
|
}
|
|
for (o in unique(taxonomy$order[taxonomy$order != "" & taxonomy$kingdom == k & taxonomy$source == "LPSN"])) {
|
|
i <- i + 1
|
|
if (i %% 50 == 0) message(".", appendLF = FALSE)
|
|
taxonomy$class[which(taxonomy$order == o & taxonomy$kingdom == k)] <- taxonomy$class[which(taxonomy$order == o & taxonomy$kingdom == k & taxonomy$source == "LPSN")][1]
|
|
}
|
|
for (cc in unique(taxonomy$class[taxonomy$class != "" & taxonomy$kingdom == k & taxonomy$source == "LPSN"])) {
|
|
i <- i + 1
|
|
if (i %% 50 == 0) message(".", appendLF = FALSE)
|
|
taxonomy$phylum[which(taxonomy$class == cc & taxonomy$kingdom == k)] <- taxonomy$phylum[which(taxonomy$class == cc & taxonomy$kingdom == k & taxonomy$source == "LPSN")][1]
|
|
}
|
|
message("OK.")
|
|
}
|
|
|
|
# we need to fix parent GBIF identifiers
|
|
taxonomy$gbif_parent[taxonomy$rank == "phylum"] <- taxonomy$gbif[match(taxonomy$kingdom[taxonomy$rank == "phylum"], taxonomy$fullname)]
|
|
taxonomy$gbif_parent[taxonomy$rank == "class"] <- taxonomy$gbif[match(taxonomy$phylum[taxonomy$rank == "class"], taxonomy$fullname)]
|
|
taxonomy$gbif_parent[taxonomy$rank == "order"] <- taxonomy$gbif[match(taxonomy$class[taxonomy$rank == "order"], taxonomy$fullname)]
|
|
taxonomy$gbif_parent[taxonomy$rank == "family"] <- taxonomy$gbif[match(taxonomy$order[taxonomy$rank == "family"], taxonomy$fullname)]
|
|
taxonomy$gbif_parent[taxonomy$rank == "genus"] <- taxonomy$gbif[match(taxonomy$family[taxonomy$rank == "genus"], taxonomy$fullname)]
|
|
taxonomy$gbif_parent[taxonomy$rank == "species"] <- taxonomy$gbif[match(taxonomy$genus[taxonomy$rank == "species"], taxonomy$fullname)]
|
|
taxonomy$gbif_parent[taxonomy$rank == "subspecies"] <- taxonomy$gbif[match(paste(taxonomy$genus[taxonomy$rank == "subspecies"], taxonomy$species[taxonomy$rank == "subspecies"]), taxonomy$fullname)]
|
|
# and LPSN parents
|
|
taxonomy$lpsn_parent[taxonomy$rank == "phylum"] <- taxonomy$lpsn[match(taxonomy$kingdom[taxonomy$rank == "phylum"], taxonomy$fullname)]
|
|
taxonomy$lpsn_parent[taxonomy$rank == "class"] <- taxonomy$lpsn[match(taxonomy$phylum[taxonomy$rank == "class"], taxonomy$fullname)]
|
|
taxonomy$lpsn_parent[taxonomy$rank == "order"] <- taxonomy$lpsn[match(taxonomy$class[taxonomy$rank == "order"], taxonomy$fullname)]
|
|
taxonomy$lpsn_parent[taxonomy$rank == "family"] <- taxonomy$lpsn[match(taxonomy$order[taxonomy$rank == "family"], taxonomy$fullname)]
|
|
taxonomy$lpsn_parent[taxonomy$rank == "genus"] <- taxonomy$lpsn[match(taxonomy$family[taxonomy$rank == "genus"], taxonomy$fullname)]
|
|
taxonomy$lpsn_parent[taxonomy$rank == "species"] <- taxonomy$lpsn[match(taxonomy$genus[taxonomy$rank == "species"], taxonomy$fullname)]
|
|
taxonomy$lpsn_parent[taxonomy$rank == "subspecies"] <- taxonomy$lpsn[match(paste(taxonomy$genus[taxonomy$rank == "subspecies"], taxonomy$species[taxonomy$rank == "subspecies"]), taxonomy$fullname)]
|
|
|
|
# these still have no record in our data set:
|
|
which(!taxonomy$lpsn_parent %in% taxonomy$lpsn)
|
|
which(!taxonomy$gbif_parent %in% taxonomy$gbif)
|
|
|
|
# fix rank
|
|
taxonomy <- taxonomy %>%
|
|
mutate(rank = case_when(
|
|
subspecies != "" ~ "subspecies",
|
|
species != "" ~ "species",
|
|
genus != "" ~ "genus",
|
|
family != "" ~ "family",
|
|
order != "" ~ "order",
|
|
class != "" ~ "class",
|
|
phylum != "" ~ "phylum",
|
|
kingdom != "" ~ "kingdom",
|
|
TRUE ~ NA_character_
|
|
))
|
|
|
|
|
|
# Add prevalence ----------------------------------------------------------
|
|
|
|
taxonomy_lpsn.bak3 <- taxonomy
|
|
pathogens <- read_excel(file_bartlett, sheet = "Tab 6 Full List")
|
|
|
|
# get all established, both old and current taxonomic names
|
|
established <- pathogens %>%
|
|
filter(status == "established") %>%
|
|
mutate(fullname = paste(genus, species)) %>%
|
|
pull(fullname) %>%
|
|
c(
|
|
unlist(mo_current(.)),
|
|
unlist(mo_synonyms(., keep_synonyms = FALSE))
|
|
) %>%
|
|
strsplit(" ", fixed = TRUE) %>%
|
|
sapply(function(x) ifelse(length(x) == 1, x, paste(x[1], x[2]))) %>%
|
|
sort() %>%
|
|
unique()
|
|
|
|
# get all putative, both old and current taxonomic names
|
|
putative <- pathogens %>%
|
|
filter(status == "putative") %>%
|
|
mutate(fullname = paste(genus, species)) %>%
|
|
pull(fullname) %>%
|
|
c(
|
|
unlist(mo_current(.)),
|
|
unlist(mo_synonyms(., keep_synonyms = FALSE))
|
|
) %>%
|
|
strsplit(" ", fixed = TRUE) %>%
|
|
sapply(function(x) ifelse(length(x) == 1, x, paste(x[1], x[2]))) %>%
|
|
sort() %>%
|
|
unique()
|
|
|
|
established <- established[established %unlike% "unknown"]
|
|
putative <- putative[putative %unlike% "unknown"]
|
|
|
|
established_genera <- established %>%
|
|
strsplit(" ", fixed = TRUE) %>%
|
|
sapply(function(x) x[1]) %>%
|
|
sort() %>%
|
|
unique()
|
|
|
|
putative_genera <- putative %>%
|
|
strsplit(" ", fixed = TRUE) %>%
|
|
sapply(function(x) x[1]) %>%
|
|
sort() %>%
|
|
unique()
|
|
|
|
nonbacterial_genera <- AMR:::MO_PREVALENT_GENERA %>%
|
|
c(
|
|
unlist(mo_current(.)),
|
|
unlist(mo_synonyms(., keep_synonyms = FALSE))
|
|
) %>%
|
|
strsplit(" ", fixed = TRUE) %>%
|
|
sapply(function(x) x[1]) %>%
|
|
sort() %>%
|
|
unique()
|
|
nonbacterial_genera <- nonbacterial_genera[nonbacterial_genera %unlike% "unknown"]
|
|
|
|
# update prevalence based on taxonomy (following the recent and thorough work of Bartlett et al., 2022)
|
|
# see https://doi.org/10.1099/mic.0.001269
|
|
taxonomy <- taxonomy %>%
|
|
mutate(prevalence = case_when(
|
|
# 'established' means 'have infected at least three persons in three or more references'
|
|
paste(genus, species) %in% established & rank %in% c("species", "subspecies") ~ 1.0,
|
|
# other genera in the 'established' group
|
|
genus %in% established_genera & rank == "genus" ~ 1.0,
|
|
|
|
# 'putative' means 'fewer than three known cases'
|
|
paste(genus, species) %in% putative & rank %in% c("species", "subspecies") ~ 1.25,
|
|
# other genera in the 'putative' group
|
|
genus %in% putative_genera & rank == "genus" ~ 1.25,
|
|
|
|
# species and subspecies in 'established' and 'putative' groups
|
|
genus %in% c(established_genera, putative_genera) & rank %in% c("species", "subspecies") ~ 1.5,
|
|
# other species from a genus in either group
|
|
genus %in% nonbacterial_genera & rank %in% c("genus", "species", "subspecies") ~ 1.5,
|
|
# we keep track of prevalent genera too of non-bacterial species
|
|
genus %in% AMR:::MO_PREVALENT_GENERA & kingdom != "Bacteria" & rank %in% c("genus", "species", "subspecies") ~ 1.25,
|
|
|
|
# all others
|
|
TRUE ~ 2.0
|
|
))
|
|
|
|
table(taxonomy$prevalence, useNA = "always")
|
|
# (a lot will be removed further below)
|
|
|
|
|
|
# Save intermediate results (2) -------------------------------------------
|
|
|
|
saveRDS(taxonomy, "data-raw/taxonomy2.rds")
|
|
|
|
|
|
# Add microbial IDs -------------------------------------------------------
|
|
|
|
# MO codes in the AMR package have the form KINGDOM_GENUS_SPECIES_SUBSPECIES where all are abbreviated.
|
|
|
|
# Kingdom is abbreviated with 1 character, with exceptions for Animalia and Plantae
|
|
mo_kingdom <- taxonomy %>%
|
|
filter(rank == "kingdom") %>%
|
|
select(kingdom) %>%
|
|
mutate(mo_kingdom = case_when(
|
|
kingdom == "Animalia" ~ "AN",
|
|
kingdom == "Archaea" ~ "A",
|
|
kingdom == "Bacteria" ~ "B",
|
|
kingdom == "Chromista" ~ "C",
|
|
kingdom == "Fungi" ~ "F",
|
|
kingdom == "Plantae" ~ "PL",
|
|
kingdom == "Protozoa" ~ "P",
|
|
TRUE ~ ""
|
|
))
|
|
|
|
# phylum until family are abbreviated with 8 characters and prefixed with their rank
|
|
|
|
# Phylum - keep old and fill up for new ones
|
|
mo_phylum <- taxonomy %>%
|
|
filter(rank == "phylum") %>%
|
|
distinct(kingdom, phylum) %>%
|
|
left_join(
|
|
AMR::microorganisms %>%
|
|
filter(rank == "phylum") %>%
|
|
transmute(kingdom,
|
|
phylum = fullname,
|
|
mo_old = gsub("[A-Z]{1,2}_", "", as.character(mo))
|
|
),
|
|
by = c("kingdom", "phylum")
|
|
) %>%
|
|
group_by(kingdom) %>%
|
|
mutate(
|
|
mo_phylum8 = AMR:::abbreviate_mo(phylum, minlength = 8, prefix = "[PHL]_"),
|
|
mo_phylum9 = AMR:::abbreviate_mo(phylum, minlength = 9, prefix = "[PHL]_"),
|
|
mo_phylum = ifelse(!is.na(mo_old), mo_old, mo_phylum8),
|
|
mo_duplicated = duplicated(mo_phylum),
|
|
mo_phylum = ifelse(mo_duplicated, mo_phylum9, mo_phylum),
|
|
mo_duplicated = duplicated(mo_phylum)
|
|
) %>%
|
|
ungroup()
|
|
if (any(mo_phylum$mo_duplicated, na.rm = TRUE)) stop("Duplicate MO codes for phylum!")
|
|
mo_phylum <- mo_phylum %>%
|
|
select(kingdom, phylum, mo_phylum)
|
|
|
|
# Class - keep old and fill up for new ones
|
|
mo_class <- taxonomy %>%
|
|
filter(rank == "class") %>%
|
|
distinct(kingdom, class) %>%
|
|
left_join(
|
|
AMR::microorganisms %>%
|
|
filter(rank == "class") %>%
|
|
transmute(kingdom,
|
|
class = fullname,
|
|
mo_old = gsub("[A-Z]{1,2}_", "", as.character(mo))
|
|
),
|
|
by = c("kingdom", "class")
|
|
) %>%
|
|
group_by(kingdom) %>%
|
|
mutate(
|
|
mo_class8 = AMR:::abbreviate_mo(class, minlength = 8, prefix = "[CLS]_"),
|
|
mo_class9 = AMR:::abbreviate_mo(class, minlength = 9, prefix = "[CLS]_"),
|
|
mo_class = ifelse(!is.na(mo_old), mo_old, mo_class8),
|
|
mo_duplicated = duplicated(mo_class),
|
|
mo_class = ifelse(mo_duplicated, mo_class9, mo_class),
|
|
mo_duplicated = duplicated(mo_class)
|
|
) %>%
|
|
ungroup()
|
|
if (any(mo_class$mo_duplicated, na.rm = TRUE)) stop("Duplicate MO codes for class!")
|
|
mo_class <- mo_class %>%
|
|
select(kingdom, class, mo_class)
|
|
|
|
# Order - keep old and fill up for new ones
|
|
mo_order <- taxonomy %>%
|
|
filter(rank == "order") %>%
|
|
distinct(kingdom, order) %>%
|
|
left_join(
|
|
AMR::microorganisms %>%
|
|
filter(rank == "order") %>%
|
|
transmute(kingdom,
|
|
order = fullname,
|
|
mo_old = gsub("[A-Z]{1,2}_", "", as.character(mo))
|
|
),
|
|
by = c("kingdom", "order")
|
|
) %>%
|
|
group_by(kingdom) %>%
|
|
mutate(
|
|
mo_order8 = AMR:::abbreviate_mo(order, minlength = 8, prefix = "[ORD]_"),
|
|
mo_order9 = AMR:::abbreviate_mo(order, minlength = 9, prefix = "[ORD]_"),
|
|
mo_order = ifelse(!is.na(mo_old), mo_old, mo_order8),
|
|
mo_duplicated = duplicated(mo_order),
|
|
mo_order = ifelse(mo_duplicated, mo_order9, mo_order),
|
|
mo_duplicated = duplicated(mo_order)
|
|
) %>%
|
|
ungroup()
|
|
if (any(mo_order$mo_duplicated, na.rm = TRUE)) stop("Duplicate MO codes for order!")
|
|
mo_order <- mo_order %>%
|
|
select(kingdom, order, mo_order)
|
|
|
|
# Family - keep old and fill up for new ones
|
|
mo_family <- taxonomy %>%
|
|
filter(rank == "family") %>%
|
|
distinct(kingdom, family) %>%
|
|
left_join(
|
|
AMR::microorganisms %>%
|
|
filter(rank == "family") %>%
|
|
transmute(kingdom,
|
|
family = fullname,
|
|
mo_old = gsub("[A-Z]{1,2}_", "", as.character(mo))
|
|
),
|
|
by = c("kingdom", "family")
|
|
) %>%
|
|
group_by(kingdom) %>%
|
|
mutate(
|
|
mo_family8 = AMR:::abbreviate_mo(family, minlength = 8, prefix = "[FAM]_"),
|
|
mo_family9 = AMR:::abbreviate_mo(family, minlength = 9, prefix = "[FAM]_"),
|
|
mo_family = ifelse(!is.na(mo_old), mo_old, mo_family8),
|
|
mo_duplicated = duplicated(mo_family),
|
|
mo_family = ifelse(mo_duplicated, mo_family9, mo_family),
|
|
mo_duplicated = duplicated(mo_family)
|
|
) %>%
|
|
ungroup()
|
|
if (any(mo_family$mo_duplicated, na.rm = TRUE)) stop("Duplicate MO codes for family!")
|
|
mo_family <- mo_family %>%
|
|
select(kingdom, family, mo_family)
|
|
|
|
# construct code part for genus - keep old code where available and generate new ones where needed
|
|
mo_genus <- taxonomy %>%
|
|
filter(rank == "genus") %>%
|
|
distinct(kingdom, genus) %>%
|
|
# get available old MO codes
|
|
left_join(
|
|
AMR::microorganisms %>%
|
|
filter(rank == "genus") %>%
|
|
transmute(mo_genus_old = gsub("^[A-Z]+_", "", as.character(mo)), kingdom, genus) %>%
|
|
distinct(kingdom, genus, .keep_all = TRUE),
|
|
by = c("kingdom", "genus")
|
|
) %>%
|
|
distinct(kingdom, genus, .keep_all = TRUE) %>%
|
|
# since kingdom is part of the code, genus abbreviations may be duplicated between kingdoms
|
|
group_by(kingdom) %>%
|
|
# generate new MO codes for genus and set the right one
|
|
mutate(
|
|
mo_genus_new5 = AMR:::abbreviate_mo(genus, 5),
|
|
mo_genus_new5b = paste0(AMR:::abbreviate_mo(genus, 5), 1),
|
|
mo_genus_new6 = AMR:::abbreviate_mo(genus, 6),
|
|
mo_genus_new7 = AMR:::abbreviate_mo(genus, 7),
|
|
mo_genus_new8 = AMR:::abbreviate_mo(genus, 8),
|
|
mo_genus_new = case_when(
|
|
!is.na(mo_genus_old) ~ mo_genus_old,
|
|
!mo_genus_new5 %in% mo_genus_old ~ mo_genus_new5,
|
|
!mo_genus_new6 %in% mo_genus_old ~ mo_genus_new6,
|
|
!mo_genus_new7 %in% mo_genus_old ~ mo_genus_new7,
|
|
!mo_genus_new8 %in% mo_genus_old ~ mo_genus_new8,
|
|
!mo_genus_new5b %in% mo_genus_old ~ mo_genus_new5b,
|
|
TRUE ~ mo_genus_old
|
|
),
|
|
mo_duplicated = duplicated(mo_genus_new),
|
|
mo_genus_new = case_when(
|
|
!mo_duplicated ~ mo_genus_new,
|
|
mo_duplicated & mo_genus_new == mo_genus_new5 ~ mo_genus_new6,
|
|
mo_duplicated & mo_genus_new == mo_genus_new6 ~ mo_genus_new7,
|
|
mo_duplicated & mo_genus_new == mo_genus_new7 ~ mo_genus_new8,
|
|
mo_duplicated & mo_genus_new == mo_genus_new8 ~ mo_genus_new5b,
|
|
TRUE ~ NA_character_
|
|
),
|
|
mo_duplicated = duplicated(mo_genus_new)
|
|
) %>%
|
|
ungroup()
|
|
if (any(mo_genus$mo_duplicated, na.rm = TRUE) | anyNA(mo_genus$mo_genus_new)) stop("Duplicate MO codes for genus!")
|
|
# no duplicates *within kingdoms*, so keep the right columns for left joining later
|
|
mo_genus <- mo_genus %>%
|
|
select(kingdom, genus, mo_genus = mo_genus_new)
|
|
|
|
# same for species - keep old where available and create new per kingdom-genus where needed:
|
|
mo_species <- taxonomy %>%
|
|
filter(rank == "species") %>%
|
|
distinct(kingdom, genus, species) %>%
|
|
left_join(
|
|
AMR::microorganisms %>%
|
|
filter(rank == "species") %>%
|
|
transmute(mo_species_old = gsub("^[A-Z]+_[A-Z]+_", "", as.character(mo)), kingdom, genus, species) %>%
|
|
filter(mo_species_old %unlike% "-") %>%
|
|
distinct(kingdom, genus, species, .keep_all = TRUE),
|
|
by = c("kingdom", "genus", "species")
|
|
) %>%
|
|
distinct(kingdom, genus, species, .keep_all = TRUE) %>%
|
|
group_by(kingdom, genus) %>%
|
|
mutate(
|
|
mo_species_new4 = AMR:::abbreviate_mo(species, 4, hyphen_as_space = TRUE),
|
|
mo_species_new5 = AMR:::abbreviate_mo(species, 5, hyphen_as_space = TRUE),
|
|
mo_species_new5b = paste0(AMR:::abbreviate_mo(species, 5, hyphen_as_space = TRUE), 1),
|
|
mo_species_new6 = AMR:::abbreviate_mo(species, 6, hyphen_as_space = TRUE),
|
|
mo_species_new7 = AMR:::abbreviate_mo(species, 7, hyphen_as_space = TRUE),
|
|
mo_species_new8 = AMR:::abbreviate_mo(species, 8, hyphen_as_space = TRUE),
|
|
mo_species_new = case_when(
|
|
!is.na(mo_species_old) ~ mo_species_old,
|
|
!mo_species_new4 %in% mo_species_old ~ mo_species_new4,
|
|
!mo_species_new5 %in% mo_species_old ~ mo_species_new5,
|
|
!mo_species_new6 %in% mo_species_old ~ mo_species_new6,
|
|
!mo_species_new7 %in% mo_species_old ~ mo_species_new7,
|
|
!mo_species_new8 %in% mo_species_old ~ mo_species_new8,
|
|
!mo_species_new5b %in% mo_species_old ~ mo_species_new5b,
|
|
TRUE ~ mo_species_old
|
|
),
|
|
mo_duplicated = duplicated(mo_species_new),
|
|
mo_species_new = case_when(
|
|
!mo_duplicated ~ mo_species_new,
|
|
mo_duplicated & mo_species_new == mo_species_new4 ~ mo_species_new5,
|
|
mo_duplicated & mo_species_new == mo_species_new5 ~ mo_species_new6,
|
|
mo_duplicated & mo_species_new == mo_species_new6 ~ mo_species_new7,
|
|
mo_duplicated & mo_species_new == mo_species_new7 ~ mo_species_new8,
|
|
mo_duplicated & mo_species_new == mo_species_new8 ~ mo_species_new5b,
|
|
TRUE ~ NA_character_
|
|
),
|
|
mo_duplicated = duplicated(mo_species_new)
|
|
) %>%
|
|
ungroup()
|
|
if (any(mo_species$mo_duplicated, na.rm = TRUE) | anyNA(mo_species$mo_species_new)) stop("Duplicate MO codes for species!")
|
|
# no duplicates *within kingdoms*, so keep the right columns for left joining later
|
|
mo_species <- mo_species %>%
|
|
select(kingdom, genus, species, mo_species = mo_species_new)
|
|
|
|
# same for subspecies - keep old where available and create new per kingdom-genus-species where needed:
|
|
mo_subspecies <- taxonomy %>%
|
|
filter(rank == "subspecies") %>%
|
|
distinct(kingdom, genus, species, subspecies) %>%
|
|
left_join(
|
|
AMR::microorganisms %>%
|
|
filter(rank %in% c("subspecies", "subsp.", "infraspecies")) %>%
|
|
transmute(mo_subspecies_old = gsub("^[A-Z]+_[A-Z]+_[A-Z]+_", "", as.character(mo)), kingdom, genus, species, subspecies) %>%
|
|
filter(mo_subspecies_old %unlike% "-") %>%
|
|
distinct(kingdom, genus, species, subspecies, .keep_all = TRUE),
|
|
by = c("kingdom", "genus", "species", "subspecies")
|
|
) %>%
|
|
distinct(kingdom, genus, species, subspecies, .keep_all = TRUE) %>%
|
|
group_by(kingdom, genus, species) %>%
|
|
mutate(
|
|
mo_subspecies_new4 = AMR:::abbreviate_mo(subspecies, 4, hyphen_as_space = TRUE),
|
|
mo_subspecies_new5 = AMR:::abbreviate_mo(subspecies, 5, hyphen_as_space = TRUE),
|
|
mo_subspecies_new5b = paste0(AMR:::abbreviate_mo(subspecies, 5, hyphen_as_space = TRUE), 1),
|
|
mo_subspecies_new6 = AMR:::abbreviate_mo(subspecies, 6, hyphen_as_space = TRUE),
|
|
mo_subspecies_new7 = AMR:::abbreviate_mo(subspecies, 7, hyphen_as_space = TRUE),
|
|
mo_subspecies_new8 = AMR:::abbreviate_mo(subspecies, 8, hyphen_as_space = TRUE),
|
|
mo_subspecies_new = case_when(
|
|
!is.na(mo_subspecies_old) ~ mo_subspecies_old,
|
|
!mo_subspecies_new4 %in% mo_subspecies_old ~ mo_subspecies_new4,
|
|
!mo_subspecies_new5 %in% mo_subspecies_old ~ mo_subspecies_new5,
|
|
!mo_subspecies_new6 %in% mo_subspecies_old ~ mo_subspecies_new6,
|
|
!mo_subspecies_new7 %in% mo_subspecies_old ~ mo_subspecies_new7,
|
|
!mo_subspecies_new8 %in% mo_subspecies_old ~ mo_subspecies_new8,
|
|
!mo_subspecies_new5b %in% mo_subspecies_old ~ mo_subspecies_new5b,
|
|
TRUE ~ mo_subspecies_old
|
|
),
|
|
mo_duplicated = duplicated(mo_subspecies_new),
|
|
mo_subspecies_new = case_when(
|
|
!mo_duplicated ~ mo_subspecies_new,
|
|
mo_duplicated & mo_subspecies_new == mo_subspecies_new4 ~ mo_subspecies_new5,
|
|
mo_duplicated & mo_subspecies_new == mo_subspecies_new5 ~ mo_subspecies_new6,
|
|
mo_duplicated & mo_subspecies_new == mo_subspecies_new6 ~ mo_subspecies_new7,
|
|
mo_duplicated & mo_subspecies_new == mo_subspecies_new7 ~ mo_subspecies_new8,
|
|
mo_duplicated & mo_subspecies_new == mo_subspecies_new8 ~ mo_subspecies_new5b,
|
|
TRUE ~ NA_character_
|
|
),
|
|
mo_duplicated = duplicated(mo_subspecies_new)
|
|
) %>%
|
|
ungroup()
|
|
if (any(mo_subspecies$mo_duplicated, na.rm = TRUE) | anyNA(mo_subspecies$mo_subspecies_new)) stop("Duplicate MO codes for subspecies!")
|
|
# no duplicates *within kingdoms*, so keep the right columns for left joining later
|
|
mo_subspecies <- mo_subspecies %>%
|
|
select(kingdom, genus, species, subspecies, mo_subspecies = mo_subspecies_new)
|
|
|
|
# unknowns - manually added
|
|
mo_unknown <- AMR::microorganisms %>%
|
|
filter(fullname %like% "unknown") %>%
|
|
transmute(fullname, mo_unknown = as.character(mo))
|
|
|
|
# apply the new codes!
|
|
taxonomy <- taxonomy %>%
|
|
left_join(mo_kingdom, by = "kingdom") %>%
|
|
left_join(mo_phylum, by = c("kingdom", "phylum")) %>%
|
|
left_join(mo_class, by = c("kingdom", "class")) %>%
|
|
left_join(mo_order, by = c("kingdom", "order")) %>%
|
|
left_join(mo_family, by = c("kingdom", "family")) %>%
|
|
left_join(mo_genus, by = c("kingdom", "genus")) %>%
|
|
left_join(mo_species, by = c("kingdom", "genus", "species")) %>%
|
|
left_join(mo_subspecies, by = c("kingdom", "genus", "species", "subspecies")) %>%
|
|
left_join(mo_unknown, by = "fullname") %>%
|
|
mutate(across(starts_with("mo_"), function(x) ifelse(is.na(x), "", x))) %>%
|
|
mutate(
|
|
mo = case_when(
|
|
fullname %like% "unknown" ~ mo_unknown,
|
|
# add special cases for taxons higher than genus
|
|
rank == "kingdom" ~ paste(mo_kingdom, "[KNG]", toupper(kingdom), sep = "_"),
|
|
rank == "phylum" ~ paste(mo_kingdom, mo_phylum, sep = "_"),
|
|
rank == "class" ~ paste(mo_kingdom, mo_class, sep = "_"),
|
|
rank == "order" ~ paste(mo_kingdom, mo_order, sep = "_"),
|
|
rank == "family" ~ paste(mo_kingdom, mo_family, sep = "_"),
|
|
TRUE ~ paste(mo_kingdom, mo_genus, mo_species, mo_subspecies, sep = "_")
|
|
),
|
|
mo = trimws(gsub("_+$", "", mo)),
|
|
.before = 1
|
|
) %>%
|
|
select(!starts_with("mo_")) %>%
|
|
arrange(fullname)
|
|
|
|
# now check these - e.g. Nitrospira is the name of a genus AND its class
|
|
taxonomy %>%
|
|
filter(fullname %in% .[duplicated(fullname), "fullname", drop = TRUE]) %>%
|
|
View()
|
|
|
|
# fullnames must be unique, we'll keep the most relevant ones only
|
|
taxonomy <- taxonomy %>%
|
|
mutate(rank_index = case_when(
|
|
kingdom == "Bacteria" ~ 1,
|
|
kingdom == "Fungi" ~ 2,
|
|
kingdom == "Protozoa" ~ 3,
|
|
kingdom == "Archaea" ~ 4,
|
|
kingdom == "Animalia" ~ 5,
|
|
TRUE ~ 6
|
|
)) %>%
|
|
arrange(fullname, rank_index) %>%
|
|
distinct(fullname, .keep_all = TRUE) %>%
|
|
select(-rank_index) %>%
|
|
filter(mo != "")
|
|
|
|
# keep the codes from manually added ones
|
|
manual_mos <- as.character(AMR::microorganisms$mo)[match(taxonomy$fullname[taxonomy$source == "manually added"], AMR::microorganisms$fullname)]
|
|
taxonomy$mo[taxonomy$source == "manually added"][!is.na(manual_mos)] <- manual_mos[!is.na(manual_mos)]
|
|
|
|
# this must not exist:
|
|
taxonomy %>%
|
|
filter(mo %like% "__") %>%
|
|
View()
|
|
taxonomy <- taxonomy %>% filter(mo %unlike% "__")
|
|
taxonomy_lpsn.bak4 <- taxonomy
|
|
|
|
|
|
# Some integrity checks ---------------------------------------------------
|
|
|
|
# are mo codes unique?
|
|
taxonomy %>% filter(mo %in% .[duplicated(mo), "mo", drop = TRUE]) |> arrange(mo) |> View()
|
|
# no, there are not, so sort on MO and keep the first
|
|
taxonomy <- taxonomy %>% arrange(mo) |> distinct(mo, .keep_all = TRUE)
|
|
|
|
taxonomy <- taxonomy |>
|
|
mutate(fullname = case_match(rank,
|
|
"phylum" ~ phylum,
|
|
"class" ~ class,
|
|
"order" ~ order,
|
|
"family" ~ family,
|
|
.default = fullname))
|
|
# are fullnames unique?
|
|
taxonomy %>% filter(fullname %in% .[duplicated(fullname), "fullname", drop = TRUE])
|
|
|
|
# are all GBIFs available?
|
|
taxonomy %>%
|
|
filter((!gbif_parent %in% gbif) | (!lpsn_parent %in% lpsn)) %>%
|
|
count(source = ifelse(!gbif_parent %in% gbif, "GBIF", "LPSN"),
|
|
rank)
|
|
|
|
# so fix again all parent GBIF identifiers
|
|
taxonomy$gbif_parent[taxonomy$rank == "phylum"] <- taxonomy$gbif[match(taxonomy$kingdom[taxonomy$rank == "phylum"], taxonomy$fullname)]
|
|
taxonomy$gbif_parent[taxonomy$rank == "class"] <- taxonomy$gbif[match(taxonomy$phylum[taxonomy$rank == "class"], taxonomy$fullname)]
|
|
taxonomy$gbif_parent[taxonomy$rank == "order"] <- taxonomy$gbif[match(taxonomy$class[taxonomy$rank == "order"], taxonomy$fullname)]
|
|
taxonomy$gbif_parent[taxonomy$rank == "family"] <- taxonomy$gbif[match(taxonomy$order[taxonomy$rank == "family"], taxonomy$fullname)]
|
|
taxonomy$gbif_parent[taxonomy$rank == "genus"] <- taxonomy$gbif[match(taxonomy$family[taxonomy$rank == "genus"], taxonomy$fullname)]
|
|
taxonomy$gbif_parent[taxonomy$rank == "species"] <- taxonomy$gbif[match(taxonomy$genus[taxonomy$rank == "species"], taxonomy$fullname)]
|
|
taxonomy$gbif_parent[taxonomy$rank == "subspecies"] <- taxonomy$gbif[match(paste(taxonomy$genus[taxonomy$rank == "subspecies"], taxonomy$species[taxonomy$rank == "subspecies"]), taxonomy$fullname)]
|
|
# and LPSN identifiers
|
|
taxonomy$lpsn_parent[taxonomy$rank == "phylum"] <- taxonomy$lpsn[match(taxonomy$kingdom[taxonomy$rank == "phylum"], taxonomy$fullname)]
|
|
taxonomy$lpsn_parent[taxonomy$rank == "class"] <- taxonomy$lpsn[match(taxonomy$phylum[taxonomy$rank == "class"], taxonomy$fullname)]
|
|
taxonomy$lpsn_parent[taxonomy$rank == "order"] <- taxonomy$lpsn[match(taxonomy$class[taxonomy$rank == "order"], taxonomy$fullname)]
|
|
taxonomy$lpsn_parent[taxonomy$rank == "family"] <- taxonomy$lpsn[match(taxonomy$order[taxonomy$rank == "family"], taxonomy$fullname)]
|
|
taxonomy$lpsn_parent[taxonomy$rank == "genus"] <- taxonomy$lpsn[match(taxonomy$family[taxonomy$rank == "genus"], taxonomy$fullname)]
|
|
taxonomy$lpsn_parent[taxonomy$rank == "species"] <- taxonomy$lpsn[match(taxonomy$genus[taxonomy$rank == "species"], taxonomy$fullname)]
|
|
taxonomy$lpsn_parent[taxonomy$rank == "subspecies"] <- taxonomy$lpsn[match(paste(taxonomy$genus[taxonomy$rank == "subspecies"], taxonomy$species[taxonomy$rank == "subspecies"]), taxonomy$fullname)]
|
|
|
|
# check again
|
|
taxonomy %>%
|
|
filter((!gbif_parent %in% gbif) | (!lpsn_parent %in% lpsn)) %>%
|
|
count(source = ifelse(!gbif_parent %in% gbif, "GBIF", "LPSN"),
|
|
rank)
|
|
|
|
|
|
|
|
# Save intermediate results (3) -------------------------------------------
|
|
|
|
saveRDS(taxonomy, "data-raw/taxonomy3.rds")
|
|
|
|
|
|
# Redo LPSN missings and parents ------------------------------------------
|
|
|
|
gbif_bacteria_second_run <- which(taxonomy$kingdom == "Bacteria" & taxonomy$source == "GBIF" & taxonomy$rank %in% c("phylum", "class", "order", "family"))
|
|
gbif_bacteria_second_run <- gbif_bacteria_second_run[!gbif_bacteria_second_run %in% gbif_bacteria]
|
|
added <- 0
|
|
pb <- progress_bar$new(total = length(gbif_bacteria_second_run), format = "[:bar] :current/:total :eta")
|
|
for (record in gbif_bacteria_second_run) {
|
|
pb$tick()
|
|
lpsn <- get_lpsn_and_author(rank = taxonomy$rank[record],
|
|
name = taxonomy$fullname[record])
|
|
if (is.na(lpsn["lpsn"])) {
|
|
next
|
|
} else {
|
|
added <- added + 1
|
|
taxonomy$source[record] <- "LPSN"
|
|
taxonomy$lpsn[record] <- unname(lpsn["lpsn"])
|
|
taxonomy$ref[record] <- unname(lpsn["ref"])
|
|
taxonomy$status[record] <- unname(lpsn["status"])
|
|
}
|
|
}
|
|
message(added, " GBIF records altered to latest LPSN")
|
|
taxbak <- taxonomy
|
|
taxonomy$lpsn_parent[taxonomy$rank == "phylum"] <- taxonomy$lpsn[match(taxonomy$kingdom[taxonomy$rank == "phylum"], taxonomy$fullname)]
|
|
taxonomy$lpsn_parent[taxonomy$rank == "class"] <- taxonomy$lpsn[match(taxonomy$phylum[taxonomy$rank == "class"], taxonomy$fullname)]
|
|
taxonomy$lpsn_parent[taxonomy$rank == "order"] <- taxonomy$lpsn[match(taxonomy$class[taxonomy$rank == "order"], taxonomy$fullname)]
|
|
taxonomy$lpsn_parent[taxonomy$rank == "family"] <- taxonomy$lpsn[match(taxonomy$order[taxonomy$rank == "family"], taxonomy$fullname)]
|
|
taxonomy$lpsn_parent[taxonomy$rank == "genus"] <- taxonomy$lpsn[match(taxonomy$family[taxonomy$rank == "genus"], taxonomy$fullname)]
|
|
taxonomy$lpsn_parent[taxonomy$rank == "species"] <- taxonomy$lpsn[match(taxonomy$genus[taxonomy$rank == "species"], taxonomy$fullname)]
|
|
taxonomy$lpsn_parent[taxonomy$rank == "subspecies"] <- taxonomy$lpsn[match(paste(taxonomy$genus[taxonomy$rank == "subspecies"], taxonomy$species[taxonomy$rank == "subspecies"]), taxonomy$fullname)]
|
|
|
|
# TODO: there is no order Eggerthellales anymore
|
|
|
|
|
|
# Remove unwanted taxonomic entries from Protoza/Fungi --------------------
|
|
|
|
# this must be done after the microbial ID generation, since it will otherwise generate a lot of different IDs
|
|
taxonomy <- taxonomy %>%
|
|
filter(
|
|
# Protozoa:
|
|
!(phylum %in% c("Choanozoa", "Mycetozoa") & prevalence == 3),
|
|
# Fungi:
|
|
!(phylum %in% c("Ascomycota", "Zygomycota", "Basidiomycota") & prevalence == 3 & rank %in% c("genus", "species", "subspecies")),
|
|
!(genus %in% c("Phoma", "Leptosphaeria", "Physarum") & rank %in% c("species", "subspecies")), # only genus of this rare fungus, with resp. 1300 and 800 species
|
|
# (leave Alternaria in there, part of human mycobiome and opportunistic pathogen)
|
|
# Animalia:
|
|
!genus %in% c("Lucilia", "Lumbricus"),
|
|
!(class == "Insecta" & rank %in% c("species", "subspecies")), # keep only genus of insects, not all of their (sub)species
|
|
!(genus == "Amoeba" & kingdom == "Animalia"),
|
|
!(genus %in% c("Aedes", "Anopheles") & rank %in% c("species", "subspecies")), # only genus of the many hundreds of mosquitoes species
|
|
kingdom != "Plantae"
|
|
) # this kingdom only contained Curvularia and Hymenolepis, which have coincidental twin names with Fungi
|
|
|
|
# no ghost families, orders classes, phyla
|
|
taxonomy <- taxonomy %>%
|
|
group_by(kingdom, family) %>%
|
|
# (but keep the ghost families of bacteria)
|
|
filter(n() > 1 | fullname %like% "unknown" | rank == "kingdom" | kingdom == "Bacteria") %>%
|
|
group_by(kingdom, order) %>%
|
|
filter(n() > 1 | fullname %like% "unknown" | rank == "kingdom") %>%
|
|
group_by(kingdom, class) %>%
|
|
filter(n() > 1 | fullname %like% "unknown" | rank == "kingdom") %>%
|
|
group_by(kingdom, phylum) %>%
|
|
filter(n() > 1 | fullname %like% "unknown" | rank == "kingdom") %>%
|
|
ungroup()
|
|
|
|
|
|
for (i in which(colnames(taxonomy) %in% c("phylum", "class", "order", "family")) - 1) {
|
|
i_name <- colnames(taxonomy)[i + 1]
|
|
message("Adding missing: ", i_name, "... ", appendLF = FALSE)
|
|
to_add <- taxonomy %>%
|
|
filter(.[[i + 1]] != "") %>%
|
|
distinct(kingdom, .[[i + 1]], .keep_all = TRUE) %>%
|
|
select(kingdom:(i + 1)) %>%
|
|
mutate(
|
|
fullname = .[[ncol(.)]],
|
|
rank = i_name
|
|
) %>%
|
|
filter(!paste(kingdom, .[[ncol(.) - 2]], rank) %in% paste(taxonomy$kingdom, taxonomy[[i + 1]], taxonomy$rank)) %>%
|
|
# get GBIF identifier where available
|
|
left_join(
|
|
current_gbif %>%
|
|
select(kingdom, all_of(i_name), rank = taxonRank, ref = scientificNameAuthorship, gbif = taxonID, gbif_parent = parentNameUsageID),
|
|
by = c("kingdom", "rank", i_name)
|
|
) %>%
|
|
mutate(source = ifelse(!is.na(gbif), "GBIF", "manually added"),
|
|
status = ifelse(!is.na(gbif), "accepted", "unknown"))
|
|
message("n = ", nrow(to_add))
|
|
# taxonomy_all_missing <- taxonomy_all_missing %>%
|
|
# bind_rows(to_add)
|
|
}
|
|
|
|
|
|
|
|
|
|
message(
|
|
"\nCongratulations! The new taxonomic table will contain ", format(nrow(taxonomy), big.mark = " "), " rows.\n",
|
|
"This was ", format(nrow(AMR::microorganisms), big.mark = " "), " rows.\n"
|
|
)
|
|
|
|
# these are the new ones:
|
|
taxonomy %>%
|
|
filter(!paste(kingdom, fullname) %in% paste(AMR::microorganisms$kingdom, AMR::microorganisms$fullname)) %>%
|
|
View()
|
|
# these were removed:
|
|
AMR::microorganisms %>%
|
|
filter(!paste(kingdom, fullname) %in% paste(taxonomy$kingdom, taxonomy$fullname)) %>%
|
|
View()
|
|
AMR::microorganisms %>%
|
|
filter(!fullname %in% taxonomy$fullname) %>%
|
|
View()
|
|
|
|
|
|
# Some manual fixes -------------------------------------------------------
|
|
|
|
# Candida haemulonis and C. duobushaemulonis should be Candida haemulonii and C. duobushaemulonii
|
|
# not sure how this can be, but GBIF contained spelling errors?
|
|
# see https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3486233/
|
|
taxonomy$species[which(taxonomy$fullname %like% "^Candida .*haemulonis")] <- gsub("nis$", "nii", taxonomy$species[which(taxonomy$fullname %like% "^Candida .*haemulonis")])
|
|
taxonomy$fullname[which(taxonomy$fullname %like% "^Candida .*haemulonis")] <- gsub("nis$", "nii", taxonomy$fullname[which(taxonomy$fullname %like% "^Candida .*haemulonis")])
|
|
|
|
|
|
# Add SNOMED CT -----------------------------------------------------------
|
|
|
|
# we will use Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS)
|
|
# as a source, which copies directly from the latest US SNOMED CT version
|
|
# - go to https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009
|
|
# - check that current online version is higher than TAXONOMY_VERSION$SNOMED
|
|
# - if so, click on 'Download Value Set', choose 'TXT'
|
|
snomed <- vroom("data-raw/SNOMED_PHVS_Microorganism_CDC_V12.txt", skip = 3) %>%
|
|
select(1:2) %>%
|
|
setNames(c("snomed", "mo")) %>%
|
|
mutate(snomed = as.character(snomed))
|
|
|
|
# try to get name of MO
|
|
snomed <- snomed %>%
|
|
mutate(mo = gsub("ss. ", "", mo, fixed = TRUE)) %>%
|
|
mutate(fullname = case_when(
|
|
mo %like_case% "[A-Z][a-z]+ [a-z]+ [a-z]{4,} " ~ gsub("(^|.*)([A-Z][a-z]+ [a-z]+ [a-z]{4,}) .*", "\\2", mo),
|
|
mo %like_case% "[A-Z][a-z]+ [a-z]{4,} " ~ gsub("(^|.*)([A-Z][a-z]+ [a-z]{4,}) .*", "\\2", mo),
|
|
mo %like_case% "[A-Z][a-z]+" ~ gsub("(^|.*)([A-Z][a-z]+) .*", "\\2", mo),
|
|
TRUE ~ NA_character_
|
|
)) %>%
|
|
filter(fullname %in% taxonomy$fullname)
|
|
|
|
message(nrow(snomed), " SNOMED codes will be added to ", n_distinct(snomed$fullname), " microorganisms")
|
|
|
|
snomed <- snomed %>%
|
|
group_by(fullname) %>%
|
|
summarise(snomed = list(snomed))
|
|
|
|
taxonomy <- taxonomy %>%
|
|
left_join(snomed, by = "fullname")
|
|
|
|
|
|
# Add oxygen tolerance (aerobe/anaerobe) ----------------------------------
|
|
|
|
# We will use the BacDive data base for this:
|
|
# - go to https://bacdive.dsmz.de/advsearch and filter 'Oxygen tolerance' on "*"
|
|
# - click on the 'Download tabel as CSV' button
|
|
#
|
|
bacdive <- vroom::vroom("data-raw/bacdive.csv", skip = 2) %>%
|
|
select(species, oxygen = `Oxygen tolerance`)
|
|
bacdive <- bacdive %>%
|
|
# fill in missing species from previous rows
|
|
mutate(species = ifelse(is.na(species), lag(species), species)) %>%
|
|
filter(!is.na(species), !is.na(oxygen), oxygen %unlike% "tolerant", species %unlike% "unclassified") %>%
|
|
mutate(mo = as.mo(species, keep_synonyms = FALSE))
|
|
bacdive <- bacdive %>%
|
|
# now determine type per species
|
|
group_by(mo) %>%
|
|
summarise(species = first(species),
|
|
oxygen_tolerance = case_when(any(oxygen %like% "facultative") ~ "facultative anaerobe",
|
|
all(oxygen == "microaerophile") ~ "microaerophile",
|
|
all(oxygen %in% c("anaerobe", "obligate anaerobe")) ~ "anaerobe",
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|
all(oxygen %in% c("anaerobe", "obligate anaerobe", "microaerophile")) ~ "anaerobe/microaerophile",
|
|
all(oxygen %in% c("aerobe", "obligate aerobe")) ~ "aerobe",
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|
all(!oxygen %in% c("anaerobe", "obligate anaerobe")) ~ "aerobe",
|
|
all(c("aerobe", "anaerobe") %in% oxygen) ~ "facultative anaerobe",
|
|
TRUE ~ NA_character_))
|
|
# now find all synonyms and copy them from their current taxonomic names
|
|
synonyms <- as.mo(unique(unlist(mo_synonyms(bacdive$mo, keep_synonyms = TRUE))),
|
|
keep_synonyms = TRUE)
|
|
syns <- tibble(species = synonyms,
|
|
mo = synonyms %>% mo_current() %>% as.mo()) %>%
|
|
filter(species != mo) %>%
|
|
mutate(species = mo_name(species, keep_synonyms = TRUE)) %>%
|
|
left_join(bacdive %>% select(mo, oxygen_tolerance)) %>%
|
|
# set mo to mo of the synonym
|
|
mutate(mo = as.mo(species, keep_synonyms = TRUE)) %>%
|
|
select(all_of(colnames(bacdive)))
|
|
|
|
bacdive <- bacdive %>%
|
|
bind_rows(syns) %>%
|
|
distinct()
|
|
|
|
bacdive_genus <- bacdive %>%
|
|
mutate(oxygen = oxygen_tolerance) %>%
|
|
group_by(species = mo_genus(mo)) %>%
|
|
summarise(oxygen_tolerance = case_when(any(oxygen == "facultative anaerobe") ~ "facultative anaerobe",
|
|
any(oxygen == "anaerobe/microaerophile") ~ "anaerobe/microaerophile",
|
|
all(oxygen == "microaerophile") ~ "microaerophile",
|
|
all(oxygen == "anaerobe") ~ "anaerobe",
|
|
all(oxygen == "aerobe") ~ "aerobe",
|
|
TRUE ~ "facultative anaerobe"))
|
|
|
|
bacdive <- bacdive %>%
|
|
filter(species %unlike% " sp[.]") %>%
|
|
bind_rows(bacdive_genus) %>%
|
|
arrange(species) %>%
|
|
mutate(mo = as.mo(species, keep_synonyms = TRUE))
|
|
|
|
other_species <- microorganisms %>%
|
|
filter(kingdom == "Bacteria", rank == "species", !mo %in% bacdive$mo, genus %in% bacdive$species) %>%
|
|
select(species = fullname, genus, mo2 = mo) %>%
|
|
left_join(bacdive, by = c("genus" = "species")) %>%
|
|
mutate(oxygen_tolerance = ifelse(oxygen_tolerance %in% c("aerobe", "anaerobe", "microaerophile", "anaerobe/microaerophile"),
|
|
oxygen_tolerance,
|
|
paste("likely", oxygen_tolerance))) %>%
|
|
select(species, oxygen_tolerance, mo = mo2) %>%
|
|
distinct(species, .keep_all = TRUE)
|
|
|
|
bacdive <- bacdive %>%
|
|
bind_rows(other_species) %>%
|
|
arrange(species) %>%
|
|
distinct(mo, .keep_all = TRUE) %>%
|
|
select(-species)
|
|
|
|
taxonomy <- taxonomy %>%
|
|
left_join(bacdive, by = "mo") %>%
|
|
relocate(oxygen_tolerance, .after = ref)
|
|
|
|
|
|
# Clean data set ----------------------------------------------------------
|
|
|
|
# format to tibble and check again for invalid characters
|
|
taxonomy <- taxonomy %>%
|
|
select(mo, fullname, status, kingdom:subspecies, rank, ref, source, starts_with("lpsn"), starts_with("gbif"), prevalence, snomed) %>%
|
|
df_remove_nonASCII()
|
|
|
|
# set class <mo>
|
|
class(taxonomy$mo) <- c("mo", "character")
|
|
microorganisms <- taxonomy
|
|
|
|
|
|
# Restore 'synonym' microorganisms to 'accepted' --------------------------
|
|
|
|
# according to LPSN: Stenotrophomonas maltophilia is the correct name if this species is regarded as a separate species (i.e., if its nomenclatural type is not assigned to another species whose name is validly published, legitimate and not rejected and has priority) within a separate genus Stenotrophomonas.
|
|
# https://lpsn.dsmz.de/species/stenotrophomonas-maltophilia
|
|
|
|
# all MO's to keep as 'accepted', not as 'synonym':
|
|
to_restore <- c(
|
|
"Stenotrophomonas maltophilia",
|
|
"Moraxella catarrhalis"
|
|
)
|
|
all(to_restore %in% microorganisms$fullname)
|
|
for (nm in to_restore) {
|
|
microorganisms$lpsn_renamed_to[which(microorganisms$fullname == nm)] <- NA
|
|
microorganisms$gbif_renamed_to[which(microorganisms$fullname == nm)] <- NA
|
|
microorganisms$status[which(microorganisms$fullname == nm)] <- "accepted"
|
|
}
|
|
|
|
|
|
# Save to package ---------------------------------------------------------
|
|
|
|
# set class <mo> if still needed (if you run only this part coming from other scripts)
|
|
class(microorganisms$mo) <- c("mo", "character")
|
|
microorganisms <- microorganisms %>% arrange(fullname)
|
|
usethis::use_data(microorganisms, overwrite = TRUE, version = 2, compress = "xz")
|
|
rm(microorganisms)
|
|
|
|
# DON'T FORGET TO UPDATE R/_globals.R!
|
|
|
|
|
|
# Test updates ------------------------------------------------------------
|
|
|
|
# and check: these codes should not be missing (will otherwise throw a unit test error):
|
|
AMR::microorganisms.codes %>% filter(!mo %in% taxonomy$mo)
|
|
AMR::clinical_breakpoints %>% filter(!mo %in% taxonomy$mo)
|
|
AMR::example_isolates %>% filter(!mo %in% taxonomy$mo)
|
|
AMR::intrinsic_resistant %>% filter(!mo %in% taxonomy$mo)
|
|
|
|
# load new data sets
|
|
devtools::load_all(".")
|
|
|
|
|
|
# reset previously changed mo codes
|
|
if (!identical(clinical_breakpoints$mo, as.mo(clinical_breakpoints$mo, language = NULL))) {
|
|
clinical_breakpoints$mo <- as.mo(clinical_breakpoints$mo, language = NULL)
|
|
usethis::use_data(clinical_breakpoints, overwrite = TRUE, version = 2, compress = "xz")
|
|
rm(clinical_breakpoints)
|
|
}
|
|
|
|
if (!identical(microorganisms.codes$mo, as.mo(microorganisms.codes$mo, language = NULL))) {
|
|
microorganisms.codes <- microorganisms.codes %>% filter(mo %in% microorganisms$mo)
|
|
microorganisms.codes$mo <- as.mo(microorganisms.codes$mo, language = NULL)
|
|
usethis::use_data(microorganisms.codes, overwrite = TRUE, version = 2, compress = "xz")
|
|
rm(microorganisms.codes)
|
|
}
|
|
|
|
if (!identical(example_isolates$mo, as.mo(example_isolates$mo, language = NULL))) {
|
|
example_isolates$mo <- as.mo(example_isolates$mo, language = NULL)
|
|
usethis::use_data(example_isolates, overwrite = TRUE, version = 2)
|
|
rm(example_isolates)
|
|
}
|
|
|
|
# load new data sets again
|
|
devtools::load_all(".")
|
|
source("data-raw/_pre_commit_checks.R")
|
|
devtools::load_all(".")
|
|
|
|
if (!identical(intrinsic_resistant$mo, as.mo(intrinsic_resistant$mo, language = NULL))) {
|
|
stop("Run data-raw/reproduction_of_intrinsic_resistant.R again")
|
|
}
|
|
|
|
|
|
# run the unit tests
|
|
Sys.setenv(NOT_CRAN = "true")
|
|
testthat::test_file("tests/testthat/test-data.R")
|
|
testthat::test_file("tests/testthat/test-mo.R")
|
|
testthat::test_file("tests/testthat/test-mo_property.R")
|