(v1.8.1.9013) add Toxoplasma

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 1.8.1.9012
+Version: 1.8.1.9013
-Date: 2022-06-03
+Date: 2022-06-10
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)
     data analysis and to work with microbial and antimicrobial properties by

NEWS.md

@@ -1,5 +1,5 @@
-# `AMR` 1.8.1.9012
+# `AMR` 1.8.1.9013
-## <small>Last updated:  3 June 2022</small>
+## <small>Last updated: 10 June 2022</small>
 
 ### New
 * EUCAST 2022 and CLSI 2022 guidelines have been added for `as.rsi()`. EUCAST 2022 is now the new default guideline for all MIC and disks diffusion interpretations.
@@ -11,6 +11,7 @@
 * Small fix for using `ab_from_text()`
 * Fixes for reading in text files using `set_mo_source()`, which now also allows the source file to contain valid taxonomic names instead of only valid microorganism ID of this package
 * Using any `random_*()` function (such as `random_mic()`) is now possible by directly calling the package without loading it first: `AMR::random_mic(10)`
+* Added *Toxoplasma gondii* (`P_TXPL_GOND`) to the `microorganisms` data set, together with its genus, family, and order
 * Changed value in column `prevalence` of the `microorganisms` data set from 3 to 2 for these genera: *Acholeplasma*, *Alistipes*, *Alloprevotella*, *Bergeyella*, *Borrelia*, *Brachyspira*, *Butyricimonas*, *Cetobacterium*, *Chlamydia*, *Chlamydophila*, *Deinococcus*, *Dysgonomonas*, *Elizabethkingia*, *Empedobacter*, *Haloarcula*, *Halobacterium*, *Halococcus*, *Myroides*, *Odoribacter*, *Ornithobacterium*, *Parabacteroides*, *Pedobacter*, *Phocaeicola*, *Porphyromonas*, *Riemerella*, *Sphingobacterium*, *Streptobacillus*, *Tenacibaculum*, *Terrimonas*, *Victivallis*, *Wautersiella*, *Weeksella*
 
 # `AMR` 1.8.1

R/data.R

@@ -104,6 +104,7 @@
 #' - 11 entries of *Streptococcus* (beta-haemolytic: groups A, B, C, D, F, G, H, K and unspecified; other: viridans, milleri)
 #' - 2 entries of *Staphylococcus* (coagulase-negative (CoNS) and coagulase-positive (CoPS))
 #' - 3 entries of *Trichomonas* (*T. vaginalis*, and its family and genus)
+#' - 4 entries of *Toxoplasma* (*T. gondii*, and its order, family and genus)
 #' - 1 entry of *Candida* (*C.  krusei*), that is not (yet) in the Catalogue of Life
 #' - 1 entry of *Blastocystis* (*B.  hominis*), although it officially does not exist (Noel *et al.* 2005, PMID 15634993)
 #' - 1 entry of *Moraxella* (*M. catarrhalis*), which was formally named *Branhamella catarrhalis* (Catlin, 1970) though this change was never accepted within the field of clinical microbiology
@@ -111,13 +112,10 @@
 #' - 6 families under the Enterobacterales order, according to Adeolu *et al.* (2016, PMID 27620848), that are not (yet) in the Catalogue of Life
 #' 
 #' ## Direct download
-#' This data set is available as 'flat file' for use even without \R - you can find the file here:
+#' This data set is available as 'flat file' for use even without \R - you can find the file here: <https://github.com/msberends/AMR/raw/main/data-raw/microorganisms.txt>. 
 #' 
-#' * <https://github.com/msberends/AMR/raw/main/data-raw/microorganisms.txt>
+#' The file in \R format (with preserved data structure) can be found here: <https://github.com/msberends/AMR/raw/main/data/microorganisms.rda>.
 #' 
-#' The file in \R format (with preserved data structure) can be found here:
-#' 
-#' * <https://github.com/msberends/AMR/raw/main/data/microorganisms.rda>
 #' @section About the Records from LPSN (see *Source*):
 #' The List of Prokaryotic names with Standing in Nomenclature (LPSN) provides comprehensive information on the nomenclature of prokaryotes. LPSN is a free to use service founded by Jean P. Euzeby in 1997 and later on maintained by Aidan C. Parte.
 #' 

R/mo.R

@@ -2208,3 +2208,282 @@ strip_words <- function(text, n, side = "right") {
   })
   vapply(FUN.VALUE = character(1), out, paste, collapse = " ")
 }
+
+
+as.mo2 <- function(x,
+                   Becker = FALSE,
+                   Lancefield = FALSE,
+                   allow_uncertain = TRUE,
+                   reference_df = get_mo_source(),
+                   info = interactive(),
+                   property = "mo",
+                   initial_search = TRUE,
+                   dyslexia_mode = FALSE,
+                   debug = FALSE,
+                   ignore_pattern = getOption("AMR_ignore_pattern"),
+                   reference_data_to_use = MO_lookup,
+                   actual_uncertainty = 1,
+                   actual_input = NULL,
+                   language = get_AMR_locale()) {
+  meet_criteria(x, allow_class = c("mo", "data.frame", "list", "character", "numeric", "integer", "factor"), allow_NA = TRUE)
+  meet_criteria(Becker, allow_class = c("logical", "character"), has_length = 1)
+  meet_criteria(Lancefield, allow_class = c("logical", "character"), has_length = 1)
+  meet_criteria(allow_uncertain, allow_class = c("logical", "numeric", "integer"), has_length = 1)
+  meet_criteria(reference_df, allow_class = "data.frame", allow_NULL = TRUE)
+  meet_criteria(property, allow_class = "character", has_length = 1, is_in = colnames(microorganisms))
+  meet_criteria(initial_search, allow_class = "logical", has_length = 1)
+  meet_criteria(dyslexia_mode, allow_class = "logical", has_length = 1)
+  meet_criteria(debug, allow_class = "logical", has_length = 1)
+  meet_criteria(ignore_pattern, allow_class = "character", has_length = 1, allow_NULL = TRUE)
+  meet_criteria(reference_data_to_use, allow_class = "data.frame")
+  meet_criteria(actual_uncertainty, allow_class = "numeric", has_length = 1)
+  meet_criteria(actual_input, allow_class = "character", allow_NULL = TRUE)
+  meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
+  
+  check_dataset_integrity()
+  
+  if (isTRUE(debug) && initial_search == TRUE) {
+    time_start_tracking()
+  }
+  
+  lookup <- function(needle,
+                     column = property,
+                     haystack = reference_data_to_use,
+                     n = 1,
+                     debug_mode = debug,
+                     initial = initial_search,
+                     uncertainty = actual_uncertainty,
+                     input_actual = actual_input) {
+    
+    if (!is.null(input_actual)) {
+      input <- input_actual
+    } else {
+      input <- tryCatch(x_backup[i], error = function(e) "")
+    }
+    
+    # `column` can be NULL for all columns, or a selection
+    # returns a [character] (vector) - if `column` > length 1 then with columns as names
+    if (isTRUE(debug_mode)) {
+      cat(font_silver("Looking up: ", substitute(needle), collapse = ""), 
+          "\n           ", time_track())
+    }
+    if (length(column) == 1) {
+      res_df <- haystack[which(eval(substitute(needle), envir = haystack, enclos = parent.frame())), , drop = FALSE]
+      if (NROW(res_df) > 1 & uncertainty != -1) {
+        # sort the findings on matching score
+        scores <- mo_matching_score(x = input,
+                                    n = res_df[, "fullname", drop = TRUE])
+        res_df <- res_df[order(scores, decreasing = TRUE), , drop = FALSE]
+      }
+      res <- as.character(res_df[, column, drop = TRUE])
+      if (length(res) == 0) {
+        if (isTRUE(debug_mode)) {
+          cat(font_red(" (no match)\n"))
+        }
+        NA_character_
+      } else {
+        if (isTRUE(debug_mode)) {
+          cat(font_green(paste0(" MATCH (", NROW(res_df), " results)\n")))
+        }
+        if ((length(res) > n | uncertainty > 1) & uncertainty != -1) {
+          # save the other possible results as well, but not for forced certain results (then uncertainty == -1)
+          uncertainties <<- rbind(uncertainties,
+                                  format_uncertainty_as_df(uncertainty_level = uncertainty,
+                                                           input = input,
+                                                           result_mo = res_df[1, "mo", drop = TRUE],
+                                                           candidates = as.character(res_df[, "fullname", drop = TRUE])),
+                                  stringsAsFactors = FALSE)
+        }
+        res[seq_len(min(n, length(res)))]
+      }
+    } else {
+      if (is.null(column)) {
+        column <- names(haystack)
+      }
+      res <- haystack[which(eval(substitute(needle), envir = haystack, enclos = parent.frame())), , drop = FALSE]
+      res <- res[seq_len(min(n, nrow(res))), column, drop = TRUE]
+      if (NROW(res) == 0) {
+        if (isTRUE(debug_mode)) {
+          cat(font_red(" (no rows)\n"))
+        }
+        res <- rep(NA_character_, length(column))
+      } else {
+        if (isTRUE(debug_mode)) {
+          cat(font_green(paste0(" MATCH (", NROW(res), " rows)\n")))
+        }
+      }
+      res <- as.character(res)
+      names(res) <- column
+      res
+    }
+  }
+  
+  # start off with replaced language-specific non-ASCII characters with ASCII characters
+  x <- parse_and_convert(x)
+  # replace mo codes used in older package versions
+  x <- replace_old_mo_codes(x, property)
+  # ignore cases that match the ignore pattern
+  x <- replace_ignore_pattern(x, ignore_pattern)
+  
+  # WHONET: xxx = no growth
+  x[tolower(as.character(paste0(x, ""))) %in% c("", "xxx", "na", "nan")] <- NA_character_
+  # Laboratory systems: remove (translated) entries like "no growth", etc.
+  x[trimws2(x) %like% translate_AMR("no .*growth", language = language)] <- NA_character_
+  x[trimws2(x) %like% paste0("^(", translate_AMR("no|not", language = language), ") [a-z]+")] <- "UNKNOWN"
+  
+  if (initial_search == TRUE) {
+    # keep track of time - give some hints to improve speed if it takes a long time
+    start_time <- Sys.time()
+    
+    pkg_env$mo_failures <- NULL
+    pkg_env$mo_uncertainties <- NULL
+    pkg_env$mo_renamed <- NULL
+  }
+  pkg_env$mo_renamed_last_run <- NULL
+  
+  failures <- character(0)
+  uncertainty_level <- translate_allow_uncertain(allow_uncertain)
+  uncertainties <- data.frame(uncertainty = integer(0),
+                              input = character(0),
+                              fullname = character(0),
+                              renamed_to = character(0),
+                              mo = character(0),
+                              candidates = character(0),
+                              stringsAsFactors = FALSE)
+  
+  x_input <- x
+  # already strip leading and trailing spaces
+  x <- trimws(x)
+  # only check the uniques, which is way faster
+  x <- unique(x)
+  # remove empty values (to later fill them in again with NAs)
+  # ("xxx" is WHONET code for 'no growth')
+  x <- x[!is.na(x)
+         & !is.null(x)
+         & !identical(x, "")
+         & !identical(x, "xxx")]
+  
+  # defined df to check for
+  if (!is.null(reference_df)) {
+    check_validity_mo_source(reference_df)
+    reference_df <- repair_reference_df(reference_df)
+  }
+  
+  # all empty
+  if (all(identical(trimws(x_input), "") | is.na(x_input) | length(x) == 0)) {
+    if (property == "mo") {
+      return(set_clean_class(rep(NA_character_, length(x_input)),
+                             new_class = c("mo", "character")))
+    } else {
+      return(rep(NA_character_, length(x_input)))
+    }
+    
+  } else if (all(x %in% reference_df[, 1][[1]])) {
+    # all in reference df
+    colnames(reference_df)[1] <- "x"
+    suppressWarnings(
+      x <- MO_lookup[match(reference_df[match(x, reference_df$x), "mo", drop = TRUE], MO_lookup$mo), property, drop = TRUE]
+    )
+    
+  } else if (all(x %in% reference_data_to_use$mo)) {
+    x <- MO_lookup[match(x, MO_lookup$mo), property, drop = TRUE]
+    
+  } else if (all(tolower(x) %in% reference_data_to_use$fullname_lower)) {
+    # we need special treatment for very prevalent full names, they are likely!
+    # e.g. as.mo("Staphylococcus aureus")
+    x <- MO_lookup[match(tolower(x), MO_lookup$fullname_lower), property, drop = TRUE]
+    
+  } else if (all(x %in% reference_data_to_use$fullname)) {
+    # we need special treatment for very prevalent full names, they are likely!
+    # e.g. as.mo("Staphylococcus aureus")
+    x <- MO_lookup[match(x, MO_lookup$fullname), property, drop = TRUE]
+    
+  } else if (all(toupper(x) %in% microorganisms.codes$code)) {
+    # commonly used MO codes
+    x <- MO_lookup[match(microorganisms.codes[match(toupper(x),
+                                                    microorganisms.codes$code),
+                                              "mo",
+                                              drop = TRUE],
+                         MO_lookup$mo),
+                   property,
+                   drop = TRUE]
+    
+  } else if (!all(x %in% microorganisms[, property])) {
+    
+    strip_whitespace <- function(x, dyslexia_mode) {
+      # all whitespaces (tab, new lines, etc.) should be one space
+      # and spaces before and after should be left blank
+      trimmed <- trimws2(x)
+      # also, make sure the trailing and leading characters are a-z or 0-9
+      # in case of non-regex
+      if (dyslexia_mode == FALSE) {
+        trimmed <- gsub("^[^a-zA-Z0-9)(]+", "", trimmed, perl = TRUE)
+        trimmed <- gsub("[^a-zA-Z0-9)(]+$", "", trimmed, perl = TRUE)
+      }
+      trimmed
+    }
+    
+    x_backup_untouched <- x
+    x <- strip_whitespace(x, dyslexia_mode)
+    # translate 'unknown' names back to English
+    if (any(tolower(x) %like_case% "unbekannt|onbekend|desconocid|sconosciut|iconnu|desconhecid", na.rm = TRUE)) {
+      trns <- subset(TRANSLATIONS, pattern %like% "unknown")
+      langs <- LANGUAGES_SUPPORTED[LANGUAGES_SUPPORTED != "en"]
+      for (l in langs) {
+        for (i in seq_len(nrow(trns))) {
+          if (!is.na(trns[i, l, drop = TRUE])) {
+            x <- gsub(pattern = trns[i, l, drop = TRUE],
+                      replacement = trns$pattern[i],
+                      x = x,
+                      ignore.case = TRUE,
+                      perl = TRUE)
+          }
+        }
+      }
+    }
+    
+    # remove spp and species
+    x <- gsub("(^| )[ .]*(spp|ssp|ss|sp|subsp|subspecies|biovar|biotype|serovar|species)[ .]*( |$)", "", x, ignore.case = TRUE, perl = TRUE)
+    x <- strip_whitespace(x, dyslexia_mode)
+    
+    x_backup <- x
+    
+    # from here on case-insensitive
+    x <- tolower(x)
+    
+    x_backup[x %like_case% "^(fungus|fungi)$"] <- "(unknown fungus)" # will otherwise become the kingdom
+    x_backup[x_backup_untouched == "Fungi"] <- "Fungi" # is literally the kingdom
+    
+    # Fill in fullnames and MO codes directly
+    known_names <- tolower(x_backup) %in% MO_lookup$fullname_lower
+    x[known_names] <- MO_lookup[match(tolower(x_backup)[known_names], MO_lookup$fullname_lower), property, drop = TRUE]
+    known_codes_mo <- toupper(x_backup) %in% MO_lookup$mo
+    x[known_codes_mo] <- MO_lookup[match(toupper(x_backup)[known_codes_mo], MO_lookup$mo), property, drop = TRUE]
+    known_codes_lis <- toupper(x_backup) %in% microorganisms.codes$code
+    x[known_codes_lis] <- MO_lookup[match(microorganisms.codes[match(toupper(x_backup)[known_codes_lis],
+                                                                     microorganisms.codes$code), "mo", drop = TRUE],
+                                          MO_lookup$mo), property, drop = TRUE]
+    already_known <- known_names | known_codes_mo | known_codes_lis
+    
+    # now only continue where the right taxonomic output is not already known
+    if (any(!already_known)) {
+      x_unknown <- x[!already_known]
+      x_unknown <- gsub(" ?[(].*[)] ?", "", x_unknown, perl = TRUE)
+      x_unknown <- gsub("[^a-z ]", " ", x_unknown, perl = TRUE)
+      x_unknown <- gsub(" +", " ", x_unknown, perl = TRUE)
+      print(x_unknown)
+      x_search <- gsub("([a-z])[a-z]*( ([a-z])[a-z]*)?( ([a-z])[a-z]*)?", "^\\1.* \\3.* \\5.*", x_unknown, perl = TRUE)
+      x_search <- gsub("( [.][*])+$", "", x_search, perl = TRUE)
+      print(x_search)
+      for (i in seq_len(length(x_unknown))) {
+        # search first, second and third part
+        mos_to_search <- MO_lookup[which(MO_lookup$fullname_lower %like_case% x_search[i]), "fullname", drop = TRUE]
+        score <- mo_matching_score(x_unknown[i], mos_to_search)
+        out <- mos_to_search[order(score, decreasing = TRUE)][1:25] # keep first 25
+        print(score[order(score, decreasing = TRUE)][1])
+        x[!already_known][i] <- MO_lookup$mo[match(out[1], MO_lookup$fullname)]
+      }
+    }
+  }
+  x
+}

R/zzz.R

@@ -131,7 +131,12 @@ create_MO_lookup <- function() {
   MO_lookup[which(is.na(MO_lookup$kingdom_index)), "kingdom_index"] <- 5
   
   # use this paste instead of `fullname` to work with Viridans Group Streptococci, etc.
-  MO_lookup$fullname_lower <- MO_FULLNAME_LOWER
+  if (length(MO_FULLNAME_LOWER) == nrow(MO_lookup)) {
+    MO_lookup$fullname_lower <- MO_FULLNAME_LOWER
+  } else {
+    MO_lookup$fullname_lower <- ""
+    warning("MO table updated - Run: source(\"data-raw/_internals.R\")", call. = FALSE)
+  }
   
   # add a column with only "e coli" like combinations
   MO_lookup$g_species <- gsub("^([a-z])[a-z]+ ([a-z]+) ?.*", "\\1 \\2", MO_lookup$fullname_lower, perl = TRUE)

data-raw/_internals.R

@@ -137,6 +137,29 @@ MO_CONS <- create_species_cons_cops("CoNS")
 MO_COPS <- create_species_cons_cops("CoPS")
 MO_STREP_ABCG <- as.mo(MO_lookup[which(MO_lookup$genus == "Streptococcus"), "mo", drop = TRUE], Lancefield = TRUE) %in% c("B_STRPT_GRPA", "B_STRPT_GRPB", "B_STRPT_GRPC", "B_STRPT_GRPG")
 MO_FULLNAME_LOWER <- create_MO_fullname_lower()
+MO_PREVALENT_GENERA <- c("Absidia", "Acholeplasma", "Acremonium", "Actinotignum", "Aedes", "Alistipes", "Alloprevotella",
+                         "Alternaria", "Anaerosalibacter", "Ancylostoma", "Angiostrongylus", "Anisakis", "Anopheles",
+                         "Apophysomyces", "Arachnia", "Aspergillus", "Aureobasidium", "Bacteroides", "Basidiobolus",
+                         "Beauveria", "Bergeyella", "Blastocystis", "Blastomyces", "Borrelia", "Brachyspira", "Branhamella",
+                         "Butyricimonas", "Candida", "Capillaria", "Capnocytophaga", "Catabacter", "Cetobacterium", "Chaetomium",
+                         "Chlamydia", "Chlamydophila", "Chryseobacterium", "Chrysonilia", "Cladophialophora", "Cladosporium",
+                         "Conidiobolus", "Contracaecum", "Cordylobia", "Cryptococcus", "Curvularia", "Deinococcus", "Demodex",
+                         "Dermatobia", "Diphyllobothrium", "Dirofilaria", "Dysgonomonas", "Echinostoma", "Elizabethkingia",
+                         "Empedobacter", "Enterobius", "Exophiala", "Exserohilum", "Fasciola", "Flavobacterium", "Fonsecaea",
+                         "Fusarium", "Fusobacterium", "Giardia", "Haloarcula", "Halobacterium", "Halococcus", "Hendersonula",
+                         "Heterophyes", "Histoplasma", "Hymenolepis", "Hypomyces", "Hysterothylacium", "Lelliottia",
+                         "Leptosphaeria", "Leptotrichia", "Lucilia", "Lumbricus", "Malassezia", "Malbranchea", "Metagonimus",
+                         "Microsporum", "Mortierella", "Mucor", "Mycocentrospora", "Mycoplasma", "Myroides", "Necator",
+                         "Nectria", "Ochroconis", "Odoribacter", "Oesophagostomum", "Oidiodendron", "Opisthorchis",
+                         "Ornithobacterium", "Parabacteroides", "Pediculus", "Pedobacter", "Phlebotomus", "Phocaeicola",
+                         "Phocanema", "Phoma", "Piedraia", "Pithomyces", "Pityrosporum", "Porphyromonas", "Prevotella",
+                         "Pseudallescheria", "Pseudoterranova", "Pulex", "Rhizomucor", "Rhizopus", "Rhodotorula", "Riemerella",
+                         "Saccharomyces", "Sarcoptes", "Scolecobasidium", "Scopulariopsis", "Scytalidium", "Sphingobacterium",
+                         "Spirometra", "Spiroplasma", "Sporobolomyces", "Stachybotrys", "Streptobacillus", "Strongyloides",
+                         "Syngamus", "Taenia", "Tannerella", "Tenacibaculum", "Terrimonas", "Toxocara", "Treponema", "Trichinella",
+                         "Trichobilharzia", "Trichoderma", "Trichomonas", "Trichophyton", "Trichosporon", "Trichostrongylus",
+                         "Trichuris", "Tritirachium", "Trombicula", "Tunga", "Ureaplasma", "Victivallis", "Wautersiella",
+                         "Weeksella", "Wuchereria")
 
 # antibiotic groups
 # (these will also be used for eucast_rules() and understanding data-raw/eucast_rules.tsv)
@@ -200,6 +223,7 @@ usethis::use_data(EUCAST_RULES_DF,
                   MO_COPS,
                   MO_STREP_ABCG,
                   MO_FULLNAME_LOWER,
+                  MO_PREVALENT_GENERA,
                   AB_LOOKUP,
                   AB_AMINOGLYCOSIDES,
                   AB_AMINOPENICILLINS,
@@ -275,7 +299,7 @@ if (changed_md5(mo)) {
   try(haven::write_sas(dplyr::select(mo, -snomed), "data-raw/microorganisms.sas"), silent = TRUE)
   try(haven::write_sav(dplyr::select(mo, -snomed), "data-raw/microorganisms.sav"), silent = TRUE)
   try(haven::write_dta(dplyr::select(mo, -snomed), "data-raw/microorganisms.dta"), silent = TRUE)
-  try(openxlsx::write.xlsx(mo, "data-raw/microorganisms.xlsx"), silent = TRUE)
+  try(openxlsx::write.xlsx(dplyr::select(mo, -snomed), "data-raw/microorganisms.xlsx"), silent = TRUE)
 }
 
 if (changed_md5(microorganisms.old)) {

data-raw/microorganisms.txt

@@ -22446,6 +22446,7 @@
 "C_ECHTN_SNTN"	"Euchitonia santonica"	"Chromista"	"Radiozoa"	"Polycystina"	"Nassellaria"	"Plagiacanthidae"	"Euchitonia"	"santonica"	""	"species"	"Lipman, 1952"		"CoL"	3	"character(0)"
 "C_ECHTN_TRRD"	"Euchitonia triradiata"	"Chromista"	"Radiozoa"	"Polycystina"	"Nassellaria"	"Plagiacanthidae"	"Euchitonia"	"triradiata"	""	"species"	"Lipman, 1960"		"CoL"	3	"character(0)"
 "C_[ORD]_EUCCCDRD"	"Eucoccidiorida"	"Chromista"	"Miozoa"	"Conoidasida"	"Eucoccidiorida"	"(unknown family)"	""	""	""	"order"	""		"CoL"	2	"717355005"
+"[ORD]_EUCCCDRD"	"Eucoccidiorida"	"(unknown kingdom)"	"Apicomplexa"	"Conoidasida"	"Eucoccidiorida"	""	""	""	""	"order"	"Leger et al., 1910"		"manually added"	2	"NULL"
 "C_ECCCN"	"Eucocconeis"	"Chromista"	"Ochrophyta"	"Bacillariophyceae"	"Achnanthales"	"Achnanthidiaceae"	"Eucocconeis"	""	""	"genus"	""		"CoL"	3	"character(0)"
 "C_ECCCN_DPRS"	"Eucocconeis depressa"	"Chromista"	"Ochrophyta"	"Bacillariophyceae"	"Achnanthales"	"Achnanthidiaceae"	"Eucocconeis"	"depressa"	""	"species"	"Hust"		"CoL"	3	"character(0)"
 "C_ECCCN_FLXL"	"Eucocconeis flexella"	"Chromista"	"Ochrophyta"	"Bacillariophyceae"	"Achnanthales"	"Achnanthidiaceae"	"Eucocconeis"	"flexella"	""	"species"	"Cleve"		"CoL"	3	"character(0)"
@@ -58199,6 +58200,7 @@
 "B_SARCN"	"Sarcina"	"Bacteria"	"Firmicutes"	"Clostridia"	"Eubacteriales"	"Clostridiaceae"	"Sarcina"	""	""	"genus"	""	516554	"LPSN"	2	"58039002"
 "B_SARCN_MAXM"	"Sarcina maxima"	"Bacteria"	"Firmicutes"	"Clostridia"	"Eubacteriales"	"Clostridiaceae"	"Sarcina"	"maxima"	""	"species"	"Lindner, 1888"	780788	"LPSN"	2	"15560003"
 "B_SARCN_VNTR"	"Sarcina ventriculi"	"Bacteria"	"Firmicutes"	"Clostridia"	"Eubacteriales"	"Clostridiaceae"	"Sarcina"	"ventriculi"	""	"species"	"Goodsir, 1842"	780795	"LPSN"	2	"22267009"
+"[FAM]_SRCCYSTD"	"Sarcocystidae"	"(unknown kingdom)"	"Apicomplexa"	"Conoidasida"	"Eucoccidiorida"	"Sarcocystidae"	""	""	""	"family"	"Poche, 1913"		"manually added"	2	"NULL"
 "P_[PHL]_SRCMSTGP"	"Sarcomastigophora"	"Protozoa"	"Sarcomastigophora"	"(unknown class)"	"(unknown order)"	"(unknown family)"	""	""	""	"phylum"	""		"CoL"	3	"428002001"
 "AN_SRCPT"	"Sarcoptes"	"Animalia"	"Arthropoda"	"Arachnida"	"Astigmata"	"Sarcoptidae"	"Sarcoptes"	""	""	"genus"	""		"CoL"	2	"character(0)"
 "AN_SRCPT_SCAB"	"Sarcoptes scabiei"	"Animalia"	"Arthropoda"	"Arachnida"	"Astigmata"	"Sarcoptidae"	"Sarcoptes"	"scabiei"	""	"species"	"Linnaeus, 1758"		"CoL"	2	"788310009"
@@ -66464,6 +66466,8 @@
 "C_TOXND_CHLL"	"Toxonidea challengerensis"	"Chromista"	"Ochrophyta"	"Bacillariophyceae"	"Naviculales"	"Pleurosigmataceae"	"Toxonidea"	"challengerensis"	""	"species"	""		"CoL"	3	"character(0)"
 "C_TOXND_GRGR"	"Toxonidea gregoriana"	"Chromista"	"Ochrophyta"	"Bacillariophyceae"	"Naviculales"	"Pleurosigmataceae"	"Toxonidea"	"gregoriana"	""	"species"	""		"CoL"	3	"character(0)"
 "C_TOXND_INSG"	"Toxonidea insignis"	"Chromista"	"Ochrophyta"	"Bacillariophyceae"	"Naviculales"	"Pleurosigmataceae"	"Toxonidea"	"insignis"	""	"species"	""		"CoL"	3	"character(0)"
+"P_TXPL"	"Toxoplasma"	"(unknown kingdom)"	"Apicomplexa"	"Conoidasida"	"Eucoccidiorida"	"Sarcocystidae"	"Toxoplasma"	""	""	"genus"	"Nicolle et al., 1909"		"manually added"	2	"NULL"
+"P_TXPL_GOND"	"Toxoplasma gondii"	"(unknown kingdom)"	"Apicomplexa"	"Conoidasida"	"Eucoccidiorida"	"Sarcocystidae"	"Toxoplasma"	"gondii"	""	"species"	"Nicolle et al., 1908"		"manually added"	2	"NULL"
 "P_TXSPR"	"Toxospora"	"Protozoa"	"Microsporidia"	"Microsporea"	"(unknown order)"	"Toxoglugeidae"	"Toxospora"	""	""	"genus"	""		"CoL"	3	"character(0)"
 "P_TXSPR_VIBR"	"Toxospora vibrio"	"Protozoa"	"Microsporidia"	"Microsporea"	"(unknown order)"	"Toxoglugeidae"	"Toxospora"	"vibrio"	""	"species"	"Kudo, 1925"		"CoL"	3	"character(0)"
 "P_TXSPR_VOLG"	"Toxospora volgae"	"Protozoa"	"Microsporidia"	"Microsporea"	"(unknown order)"	"Toxoglugeidae"	"Toxospora"	"volgae"	""	"species"	"Voronin, 1993"		"CoL"	3	"character(0)"

data-raw/mo.md5

@@ -1 +1 @@
-532f52b6cbe1cdb25268122fa0608714
+4709adde8932f9e887fbd892a27ad929

data-raw/reproduction_of_microorganisms.R

@@ -168,41 +168,6 @@ rm(ref_taxonomy)
 rm(data_col.bak)
 rm(data_dsmz.bak)
 
-mo_found_in_NL <- c("Absidia", "Acholeplasma", "Acremonium", "Actinotignum", "Aedes", "Alistipes",
-                    "Alloprevotella", "Alternaria", "Anaerosalibacter", "Ancylostoma", "Angiostrongylus",
-                    "Anisakis", "Anopheles", "Apophysomyces", "Arachnia", "Ascaris", "Aspergillus",
-                    "Aureobacterium", "Aureobasidium", "Bacteroides", "Balantidum", "Basidiobolus",
-                    "Beauveria", "Bergeyella", "Bilophilia", "Blastocystis", "Borrelia", "Brachyspira",
-                    "Branhamella", "Brochontrix", "Brugia", "Butyricimonas", "Calymmatobacterium",
-                    "Candida", "Capillaria", "Capnocytophaga", "Catabacter", "Cdc", "Cetobacterium",
-                    "Chaetomium", "Chilomastix", "Chlamydia", "Chlamydophila", "Chryseobacterium",
-                    "Chryseomonas", "Chrysonilia", "Cladophialophora", "Cladosporium", "Clonorchis",
-                    "Conidiobolus", "Contracaecum", "Cordylobia", "Cryptococcus", "Curvularia", "Deinococcus",
-                    "Demodex", "Dermatobia", "Dicrocoelium", "Dioctophyma", "Diphyllobothrium", "Dipylidium",
-                    "Dirofilaria", "Dracunculus", "Dysgonomonas", "Echinococcus", "Echinostoma",
-                    "Elisabethkingia", "Elizabethkingia", "Empedobacter", "Enterobius", "Enteromonas",
-                    "Euascomycetes", "Exophiala", "Exserohilum", "Fasciola", "Fasciolopsis", "Flavobacterium",
-                    "Fonsecaea", "Fusarium", "Fusobacterium", "Giardia", "Gnathostoma", "Haloarcula",
-                    "Halobacterium", "Halococcus", "Hendersonula", "Heterophyes", "Hymenolepis", "Hypomyces",
-                    "Hysterothylacium", "Kloeckera", "Koserella", "Larva", "Lecythophora", "Leishmania",
-                    "Lelliottia", "Leptomyxida", "Leptosphaeria", "Leptotrichia", "Loa", "Lucilia", "Lumbricus",
-                    "Malassezia", "Malbranchea", "Mansonella", "Mesocestoides", "Metagonimus", "Metarrhizium",
-                    "Molonomonas", "Mortierella", "Mucor", "Multiceps", "Mycocentrospora", "Mycoplasma",
-                    "Myroides", "Nanophetus", "Nattrassia", "Necator", "Nectria", "Novospingobium", "Ochroconis",
-                    "Odoribacter", "Oesophagostomum", "Oidiodendron", "Onchocerca", "Opisthorchis",
-                    "Opistorchis", "Ornithobacterium", "Parabacteroides", "Paragonimus", "Paramyxovirus",
-                    "Pediculus", "Pedobacter", "Phlebotomus", "Phocaeicola", "Phocanema", "Phoma",
-                    "Phthirus", "Piedraia", "Pithomyces", "Pityrosporum", "Porphyromonas", "Prevotella",
-                    "Pseudallescheria", "Pseudoterranova", "Pulex", "Retortamonas", "Rhizomucor", "Rhizopus",
-                    "Rhodotorula", "Riemerella", "Salinococcus", "Sanguibacteroides", "Sarcophagidae", "Sarcoptes",
-                    "Schistosoma", "Scolecobasidium", "Scopulariopsis", "Scytalidium", "Sphingobacterium",
-                    "Spirometra", "Sporobolomyces", "Stachybotrys", "Stenotrophomononas", "Stomatococcus",
-                    "Streptobacillus", "Strongyloides", "Syncephalastraceae", "Syngamus", "Taenia",
-                    "Tenacibaculum", "Ternidens", "Terrimonas", "Torulopsis", "Toxocara", "Toxoplasma",
-                    "Treponema", "Trichinella", "Trichobilharzia", "Trichoderma", "Trichomonas", "Trichophyton",
-                    "Trichosporon", "Trichostrongylus", "Trichuris", "Tritirachium", "Trombicula", "Trypanosoma",
-                    "Tunga", "Ureaplasma", "Victivallis", "Wautersiella", "Weeksella", "Wuchereria")
-
 MOs <- data_total %>%
   filter(
     (
@@ -214,7 +179,7 @@ MOs <- data_total %>%
           & !order %in% c("Eurotiales", "Microascales", "Mucorales", "Saccharomycetales", "Schizosaccharomycetales", "Tremellales", "Onygenales", "Pneumocystales"))
     )
     # or the genus has to be one of the genera we found in our hospitals last decades (Northern Netherlands, 2002-2018)
-    | genus %in% mo_found_in_NL
+    | genus %in% MO_PREVALENT_GENERA
   ) %>%
   # really no Plantae (e.g. Dracunculus exist both as worm and as plant)
   filter(kingdom != "Plantae") %>% 
@@ -407,7 +372,7 @@ MOs <- MOs %>%
                      "Firmicutes",
                      "Actinobacteria",
                      "Sarcomastigophora")
-       | genus %in% mo_found_in_NL
+       | genus %in% MO_PREVALENT_GENERA
        | rank %in% c("kingdom", "phylum", "class", "order", "family"))
     ~ 2,
     TRUE ~ 3

data-raw/reproduction_of_microorganisms_update.R

@@ -276,40 +276,7 @@ MOs <- MOs %>%
                      "Firmicutes",
                      "Actinobacteria",
                      "Sarcomastigophora")
-       | genus %in% c("Absidia", "Acholeplasma", "Acremonium", "Actinotignum", "Aedes", "Alistipes",
+       | genus %in% MO_PREVALENT_GENERA
-                      "Alloprevotella", "Alternaria", "Anaerosalibacter", "Ancylostoma", "Angiostrongylus",
-                      "Anisakis", "Anopheles", "Apophysomyces", "Arachnia", "Ascaris", "Aspergillus",
-                      "Aureobacterium", "Aureobasidium", "Bacteroides", "Balantidum", "Basidiobolus",
-                      "Beauveria", "Bergeyella", "Bilophilia", "Blastocystis", "Borrelia", "Brachyspira",
-                      "Branhamella", "Brochontrix", "Brugia", "Butyricimonas", "Calymmatobacterium",
-                      "Candida", "Capillaria", "Capnocytophaga", "Catabacter", "Cdc", "Cetobacterium",
-                      "Chaetomium", "Chilomastix", "Chlamydia", "Chlamydophila", "Chryseobacterium",
-                      "Chryseomonas", "Chrysonilia", "Cladophialophora", "Cladosporium", "Clonorchis",
-                      "Conidiobolus", "Contracaecum", "Cordylobia", "Cryptococcus", "Curvularia", "Deinococcus",
-                      "Demodex", "Dermatobia", "Dicrocoelium", "Dioctophyma", "Diphyllobothrium", "Dipylidium",
-                      "Dirofilaria", "Dracunculus", "Dysgonomonas", "Echinococcus", "Echinostoma",
-                      "Elisabethkingia", "Elizabethkingia", "Empedobacter", "Enterobius", "Enteromonas",
-                      "Euascomycetes", "Exophiala", "Exserohilum", "Fasciola", "Fasciolopsis", "Flavobacterium",
-                      "Fonsecaea", "Fusarium", "Fusobacterium", "Giardia", "Gnathostoma", "Haloarcula",
-                      "Halobacterium", "Halococcus", "Hendersonula", "Heterophyes", "Hymenolepis", "Hypomyces",
-                      "Hysterothylacium", "Kloeckera", "Koserella", "Larva", "Lecythophora", "Leishmania",
-                      "Lelliottia", "Leptomyxida", "Leptosphaeria", "Leptotrichia", "Loa", "Lucilia", "Lumbricus",
-                      "Malassezia", "Malbranchea", "Mansonella", "Mesocestoides", "Metagonimus", "Metarrhizium",
-                      "Molonomonas", "Mortierella", "Mucor", "Multiceps", "Mycocentrospora", "Mycoplasma",
-                      "Myroides", "Nanophetus", "Nattrassia", "Necator", "Nectria", "Novospingobium", "Ochroconis",
-                      "Odoribacter", "Oesophagostomum", "Oidiodendron", "Onchocerca", "Opisthorchis",
-                      "Opistorchis", "Ornithobacterium", "Parabacteroides", "Paragonimus", "Paramyxovirus",
-                      "Pediculus", "Pedobacter", "Phlebotomus", "Phocaeicola", "Phocanema", "Phoma",
-                      "Phthirus", "Piedraia", "Pithomyces", "Pityrosporum", "Porphyromonas", "Prevotella",
-                      "Pseudallescheria", "Pseudoterranova", "Pulex", "Retortamonas", "Rhizomucor", "Rhizopus",
-                      "Rhodotorula", "Riemerella", "Salinococcus", "Sanguibacteroides", "Sarcophagidae", "Sarcoptes",
-                      "Schistosoma", "Scolecobasidium", "Scopulariopsis", "Scytalidium", "Sphingobacterium",
-                      "Spirometra", "Sporobolomyces", "Stachybotrys", "Stenotrophomononas", "Stomatococcus",
-                      "Streptobacillus", "Strongyloides", "Syncephalastraceae", "Syngamus", "Taenia",
-                      "Tenacibaculum", "Ternidens", "Terrimonas", "Torulopsis", "Toxocara", "Toxoplasma",
-                      "Treponema", "Trichinella", "Trichobilharzia", "Trichoderma", "Trichomonas", "Trichophyton",
-                      "Trichosporon", "Trichostrongylus", "Trichuris", "Tritirachium", "Trombicula", "Trypanosoma",
-                      "Tunga", "Ureaplasma", "Victivallis", "Wautersiella", "Weeksella", "Wuchereria")
        | rank %in% c("kingdom", "phylum", "class", "order", "family"))
     ~ 2,
     TRUE ~ 3

data-raw/toxoplasma.R

@@ -0,0 +1,68 @@
+microorganisms <- microorganisms |> bind_rows(
+  # Toxoplasma
+  data.frame(mo = "P_TXPL_GOND", # species
+             fullname = "Toxoplasma gondii",
+             kingdom = "(unknown kingdom)",
+             phylum = "Apicomplexa",
+             class = "Conoidasida",
+             order = "Eucoccidiorida",
+             family = "Sarcocystidae",
+             genus = "Toxoplasma",
+             species = "gondii",
+             subspecies = "",
+             rank = "species",
+             ref = "Nicolle et al., 1908",
+             species_id = NA_real_,
+             source = "manually added",
+             prevalence = 2,
+             stringsAsFactors = FALSE),
+  data.frame(mo = "P_TXPL", # genus
+             fullname = "Toxoplasma",
+             kingdom = "(unknown kingdom)",
+             phylum = "Apicomplexa",
+             class = "Conoidasida",
+             order = "Eucoccidiorida",
+             family = "Sarcocystidae",
+             genus = "Toxoplasma",
+             species = "",
+             subspecies = "",
+             rank = "genus",
+             ref = "Nicolle et al., 1909",
+             species_id = NA_real_,
+             source = "manually added",
+             prevalence = 2,
+             stringsAsFactors = FALSE),
+  data.frame(mo = "[FAM]_SRCCYSTD", # family
+             fullname = "Sarcocystidae",
+             kingdom = "(unknown kingdom)",
+             phylum = "Apicomplexa",
+             class = "Conoidasida",
+             order = "Eucoccidiorida",
+             family = "Sarcocystidae",
+             genus = "",
+             species = "",
+             subspecies = "",
+             rank = "family",
+             ref = "Poche, 1913",
+             species_id = NA_real_,
+             source = "manually added",
+             prevalence = 2,
+             stringsAsFactors = FALSE),
+  data.frame(mo = "[ORD]_EUCCCDRD", # order
+             fullname = "Eucoccidiorida",
+             kingdom = "(unknown kingdom)",
+             phylum = "Apicomplexa",
+             class = "Conoidasida",
+             order = "Eucoccidiorida",
+             family = "",
+             genus = "",
+             species = "",
+             subspecies = "",
+             rank = "order",
+             ref = "Leger et al., 1910",
+             species_id = NA_real_,
+             source = "manually added",
+             prevalence = 2,
+             stringsAsFactors = FALSE),
+  ) |> 
+  arrange(fullname)

docs/404.html

@@ -43,7 +43,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9012</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9013</span>
       </span>
     </div>
 

docs/LICENSE-text.html

@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9012</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9013</span>
       </span>
     </div>
 

docs/articles/datasets.html

@@ -44,7 +44,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9012</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9013</span>
       </span>
     </div>
 
@@ -190,7 +190,7 @@
     <div class="page-header toc-ignore">
       <h1 data-toc-skip>Data sets for download / own use</h1>
             
-            <h4 data-toc-skip class="date">03 June 2022</h4>
+            <h4 data-toc-skip class="date">10 June 2022</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
       <div class="hidden name"><code>datasets.Rmd</code></div>
@@ -224,15 +224,15 @@ column names:<br><em>mo</em>, <em>fullname</em>, <em>kingdom</em>, <em>phylum</e
 <em>snomed</em>.</p>
 <p>This data set is in R available as <code>microorganisms</code>, after
 you load the <code>AMR</code> package.</p>
-<p>It was last updated on 3 June 2022 11:18:29 UTC. Find more info about
+<p>It was last updated on 10 June 2022 11:09:45 UTC. Find more info
-the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
+about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.rds" class="external-link">R
 file</a> (1.3 MB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.xlsx" class="external-link">Excel
-file</a> (5.1 MB)<br>
+file</a> (4.8 MB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.txt" class="external-link">plain
 text file</a> (13.1 MB)<br>

docs/authors.html

@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9012</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9013</span>
       </span>
     </div>
 

docs/index.html

@@ -47,7 +47,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9012</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9013</span>
       </span>
     </div>
 

docs/news/index.html

@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9012</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9013</span>
       </span>
     </div>
 
@@ -157,16 +157,16 @@
     </div>
 
     <div class="section level2">
-<h2 class="page-header" data-toc-text="1.8.1.9012" id="amr-1819012">
+<h2 class="page-header" data-toc-text="1.8.1.9013" id="amr-1819013">
-<code>AMR</code> 1.8.1.9012<a class="anchor" aria-label="anchor" href="#amr-1819012"></a></h2>
+<code>AMR</code> 1.8.1.9013<a class="anchor" aria-label="anchor" href="#amr-1819013"></a></h2>
 <div class="section level3">
-<h3 id="last-updated-june-1-8-1-9012"><small>Last updated: 3 June 2022</small><a class="anchor" aria-label="anchor" href="#last-updated-june-1-8-1-9012"></a></h3>
+<h3 id="last-updated-june-1-8-1-9013"><small>Last updated: 10 June 2022</small><a class="anchor" aria-label="anchor" href="#last-updated-june-1-8-1-9013"></a></h3>
 <div class="section level4">
-<h4 id="new-1-8-1-9012">New<a class="anchor" aria-label="anchor" href="#new-1-8-1-9012"></a></h4>
+<h4 id="new-1-8-1-9013">New<a class="anchor" aria-label="anchor" href="#new-1-8-1-9013"></a></h4>
 <ul><li>EUCAST 2022 and CLSI 2022 guidelines have been added for <code><a href="../reference/as.rsi.html">as.rsi()</a></code>. EUCAST 2022 is now the new default guideline for all MIC and disks diffusion interpretations.</li>
 </ul></div>
 <div class="section level4">
-<h4 id="changed-1-8-1-9012">Changed<a class="anchor" aria-label="anchor" href="#changed-1-8-1-9012"></a></h4>
+<h4 id="changed-1-8-1-9013">Changed<a class="anchor" aria-label="anchor" href="#changed-1-8-1-9013"></a></h4>
 <ul><li>Fix for <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on certain EUCAST breakpoints for MIC values</li>
 <li>Removed <code><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer()</a></code> for MIC values, since MIC are not integer values and running <code><a href="https://rdrr.io/r/base/table.html" class="external-link">table()</a></code> on MIC values consequently failed for not being able to retrieve the level position (as that’s how normally <code><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer()</a></code> on <code>factor</code>s work)</li>
 <li>
@@ -176,6 +176,7 @@
 <li>Fixes for reading in text files using <code><a href="../reference/mo_source.html">set_mo_source()</a></code>, which now also allows the source file to contain valid taxonomic names instead of only valid microorganism ID of this package</li>
 <li>Using any <code>random_*()</code> function (such as <code><a href="../reference/random.html">random_mic()</a></code>) is now possible by directly calling the package without loading it first: <code>AMR::random_mic(10)</code>
 </li>
+<li>Added <em>Toxoplasma gondii</em> (<code>P_TXPL_GOND</code>) to the <code>microorganisms</code> data set, together with its genus, family, and order</li>
 <li>Changed value in column <code>prevalence</code> of the <code>microorganisms</code> data set from 3 to 2 for these genera: <em>Acholeplasma</em>, <em>Alistipes</em>, <em>Alloprevotella</em>, <em>Bergeyella</em>, <em>Borrelia</em>, <em>Brachyspira</em>, <em>Butyricimonas</em>, <em>Cetobacterium</em>, <em>Chlamydia</em>, <em>Chlamydophila</em>, <em>Deinococcus</em>, <em>Dysgonomonas</em>, <em>Elizabethkingia</em>, <em>Empedobacter</em>, <em>Haloarcula</em>, <em>Halobacterium</em>, <em>Halococcus</em>, <em>Myroides</em>, <em>Odoribacter</em>, <em>Ornithobacterium</em>, <em>Parabacteroides</em>, <em>Pedobacter</em>, <em>Phocaeicola</em>, <em>Porphyromonas</em>, <em>Riemerella</em>, <em>Sphingobacterium</em>, <em>Streptobacillus</em>, <em>Tenacibaculum</em>, <em>Terrimonas</em>, <em>Victivallis</em>, <em>Wautersiella</em>, <em>Weeksella</em>
 </li>
 </ul></div>

docs/reference/index.html

@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9012</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9013</span>
       </span>
     </div>
 
@@ -282,7 +282,7 @@
       </tr><tr><td>
           <p><code><a href="microorganisms.html">microorganisms</a></code> </p>
         </td>
-        <td><p>Data Set with 70,760 Microorganisms</p></td>
+        <td><p>Data Set with 70,764 Microorganisms</p></td>
       </tr><tr><td>
           <p><code><a href="microorganisms.codes.html">microorganisms.codes</a></code> </p>
         </td>

docs/reference/microorganisms.html

@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Data Set with 70,760 Microorganisms — microorganisms • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Data Set with 70,760 Microorganisms — microorganisms"><meta property="og:description" content="A data set containing the full microbial taxonomy (last updated: 5 October 2021) of six kingdoms from the Catalogue of Life (CoL) and the List of Prokaryotic names with Standing in Nomenclature (LPSN). MO codes can be looked up using as.mo()."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"><meta name="twitter:card" content="summary_large_image"><meta name="twitter:creator" content="@msberends"><meta name="twitter:site" content="@univgroningen"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Data Set with 70,764 Microorganisms — microorganisms • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Data Set with 70,764 Microorganisms — microorganisms"><meta property="og:description" content="A data set containing the full microbial taxonomy (last updated: 5 October 2021) of six kingdoms from the Catalogue of Life (CoL) and the List of Prokaryotic names with Standing in Nomenclature (LPSN). MO codes can be looked up using as.mo()."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"><meta name="twitter:card" content="summary_large_image"><meta name="twitter:creator" content="@msberends"><meta name="twitter:site" content="@univgroningen"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body data-spy="scroll" data-target="#toc">
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9007</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9013</span>
       </span>
     </div>
 
@@ -152,7 +152,7 @@
       </header><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
-    <h1>Data Set with 70,760 Microorganisms</h1>
+    <h1>Data Set with 70,764 Microorganisms</h1>
     <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/data.R" class="external-link"><code>R/data.R</code></a></small>
     <div class="hidden name"><code>microorganisms.Rd</code></div>
     </div>
@@ -167,7 +167,7 @@
 
     <div id="format">
     <h2>Format</h2>
-    <p>A <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> with 70,760 observations and 16 variables:</p><ul><li><p><code>mo</code><br> ID of microorganism as used by this package</p></li>
+    <p>A <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> with 70,764 observations and 16 variables:</p><ul><li><p><code>mo</code><br> ID of microorganism as used by this package</p></li>
 <li><p><code>fullname</code><br> Full name, like <code>"Escherichia coli"</code></p></li>
 <li><p><code>kingdom</code>, <code>phylum</code>, <code>class</code>, <code>order</code>, <code>family</code>, <code>genus</code>, <code>species</code>, <code>subspecies</code><br> Taxonomic rank of the microorganism</p></li>
 <li><p><code>rank</code><br> Text of the taxonomic rank of the microorganism, like <code>"species"</code> or <code>"genus"</code></p></li>
@@ -180,17 +180,17 @@
     <div id="source">
     <h2>Source</h2>
     <p>Catalogue of Life: 2019 Annual Checklist as currently implemented in this <code>AMR</code> package:</p><ul><li><p>Annual Checklist (public online taxonomic database), <a href="http://www.catalogueoflife.org" class="external-link">http://www.catalogueoflife.org</a></p></li>
-</ul><p>List of Prokaryotic names with Standing in Nomenclature (5 October 2021) as currently implemented in this <code>AMR</code> package:</p><ul><li><p>Parte, A.C., Sarda Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Goker, M. (2020). List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. International Journal of Systematic and Evolutionary Microbiology, 70, 5607-5612; doi: <a href="https://doi.org/10.1099/ijsem.0.004332" class="external-link">10.1099/ijsem.0.004332</a></p></li>
+</ul><p>List of Prokaryotic names with Standing in Nomenclature (5 October 2021) as currently implemented in this <code>AMR</code> package:</p><ul><li><p>Parte, A.C., Sarda Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Goker, M. (2020). List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. International Journal of Systematic and Evolutionary Microbiology, 70, 5607-5612; <a href="https://doi.org/10.1099/ijsem.0.004332" class="external-link">doi:10.1099/ijsem.0.004332</a></p></li>
-<li><p>Parte, A.C. (2018). LPSN - List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. International Journal of Systematic and Evolutionary Microbiology, 68, 1825-1829; doi: <a href="https://doi.org/10.1099/ijsem.0.002786" class="external-link">10.1099/ijsem.0.002786</a></p></li>
+<li><p>Parte, A.C. (2018). LPSN - List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. International Journal of Systematic and Evolutionary Microbiology, 68, 1825-1829; <a href="https://doi.org/10.1099/ijsem.0.002786" class="external-link">doi:10.1099/ijsem.0.002786</a></p></li>
-<li><p>Parte, A.C. (2014). LPSN - List of Prokaryotic names with Standing in Nomenclature. Nucleic Acids Research, 42, Issue D1, D613-D616; doi: <a href="https://doi.org/10.1093/nar/gkt1111" class="external-link">10.1093/nar/gkt1111</a></p></li>
+<li><p>Parte, A.C. (2014). LPSN - List of Prokaryotic names with Standing in Nomenclature. Nucleic Acids Research, 42, Issue D1, D613-D616; <a href="https://doi.org/10.1093/nar/gkt1111" class="external-link">doi:10.1093/nar/gkt1111</a></p></li>
-<li><p>Euzeby, J.P. (1997). List of Bacterial Names with Standing in Nomenclature: a Folder Available on the Internet. International Journal of Systematic Bacteriology, 47, 590-592; doi: <a href="https://doi.org/10.1099/00207713-47-2-590" class="external-link">10.1099/00207713-47-2-590</a></p></li>
+<li><p>Euzeby, J.P. (1997). List of Bacterial Names with Standing in Nomenclature: a Folder Available on the Internet. International Journal of Systematic Bacteriology, 47, 590-592; <a href="https://doi.org/10.1099/00207713-47-2-590" class="external-link">doi:10.1099/00207713-47-2-590</a></p></li>
 </ul><p>US Edition of SNOMED CT from 1 September 2020 as currently implemented in this <code>AMR</code> package:</p><ul><li><p>Retrieved from the Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS), OID 2.16.840.1.114222.4.11.1009, version 12; url: <a href="https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009" class="external-link">https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009</a></p></li>
 </ul></div>
     <div id="details">
     <h2>Details</h2>
     <p>Please note that entries are only based on the Catalogue of Life and the LPSN (see below). Since these sources incorporate entries based on (recent) publications in the International Journal of Systematic and Evolutionary Microbiology (IJSEM), it can happen that the year of publication is sometimes later than one might expect.</p>
-<p>For example, <em>Staphylococcus pettenkoferi</em> was described for the first time in Diagnostic Microbiology and Infectious Disease in 2002 (doi: <a href="https://doi.org/10.1016/s0732-8893(02)00399-1" class="external-link">10.1016/s0732-8893(02)00399-1</a>
+<p>For example, <em>Staphylococcus pettenkoferi</em> was described for the first time in Diagnostic Microbiology and Infectious Disease in 2002 (<a href="https://doi.org/10.1016/s0732-8893%2802%2900399-1" class="external-link">doi:10.1016/s0732-8893(02)00399-1</a>
-), but it was not before 2007 that a publication in IJSEM followed (doi: <a href="https://doi.org/10.1099/ijs.0.64381-0" class="external-link">10.1099/ijs.0.64381-0</a>
+), but it was not before 2007 that a publication in IJSEM followed (<a href="https://doi.org/10.1099/ijs.0.64381-0" class="external-link">doi:10.1099/ijs.0.64381-0</a>
 ). Consequently, the <code>AMR</code> package returns 2007 for <code>mo_year("S. pettenkoferi")</code>.</p><div class="section">
 <h3 id="manual-additions">Manual additions<a class="anchor" aria-label="anchor" href="#manual-additions"></a></h3>
 
@@ -198,6 +198,7 @@
 <p>For convenience, some entries were added manually:</p><ul><li><p>11 entries of <em>Streptococcus</em> (beta-haemolytic: groups A, B, C, D, F, G, H, K and unspecified; other: viridans, milleri)</p></li>
 <li><p>2 entries of <em>Staphylococcus</em> (coagulase-negative (CoNS) and coagulase-positive (CoPS))</p></li>
 <li><p>3 entries of <em>Trichomonas</em> (<em>T. vaginalis</em>, and its family and genus)</p></li>
+<li><p>4 entries of <em>Toxoplasma</em> (<em>T. gondii</em>, and its order, family and genus)</p></li>
 <li><p>1 entry of <em>Candida</em> (<em>C.  krusei</em>), that is not (yet) in the Catalogue of Life</p></li>
 <li><p>1 entry of <em>Blastocystis</em> (<em>B.  hominis</em>), although it officially does not exist (Noel <em>et al.</em> 2005, PMID 15634993)</p></li>
 <li><p>1 entry of <em>Moraxella</em> (<em>M. catarrhalis</em>), which was formally named <em>Branhamella catarrhalis</em> (Catlin, 1970) though this change was never accepted within the field of clinical microbiology</p></li>
@@ -209,9 +210,9 @@
 <h3 id="direct-download">Direct download<a class="anchor" aria-label="anchor" href="#direct-download"></a></h3>
 
 
-<p>This data set is available as 'flat file' for use even without <span style="R">R</span> - you can find the file here:</p><ul><li><p><a href="https://github.com/msberends/AMR/raw/main/data-raw/microorganisms.txt" class="external-link">https://github.com/msberends/AMR/raw/main/data-raw/microorganisms.txt</a></p></li>
+<p>This data set is available as 'flat file' for use even without <span style="R">R</span> - you can find the file here: <a href="https://github.com/msberends/AMR/raw/main/data-raw/microorganisms.txt" class="external-link">https://github.com/msberends/AMR/raw/main/data-raw/microorganisms.txt</a>.</p>
-</ul><p>The file in <span style="R">R</span> format (with preserved data structure) can be found here:</p><ul><li><p><a href="https://github.com/msberends/AMR/raw/main/data/microorganisms.rda" class="external-link">https://github.com/msberends/AMR/raw/main/data/microorganisms.rda</a></p></li>
+<p>The file in <span style="R">R</span> format (with preserved data structure) can be found here: <a href="https://github.com/msberends/AMR/raw/main/data/microorganisms.rda" class="external-link">https://github.com/msberends/AMR/raw/main/data/microorganisms.rda</a>.</p>
-</ul></div>
+</div>
 
     </div>
     <div id="about-the-records-from-lpsn-see-source-">

docs/survey.html

@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9012</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9013</span>
       </span>
     </div>
 

man/microorganisms.Rd

@@ -3,9 +3,9 @@
 \docType{data}
 \name{microorganisms}
 \alias{microorganisms}
-\title{Data Set with 70,760 Microorganisms}
+\title{Data Set with 70,764 Microorganisms}
 \format{
-A \link{data.frame} with 70,760 observations and 16 variables:
+A \link{data.frame} with 70,764 observations and 16 variables:
 \itemize{
 \item \code{mo}\cr ID of microorganism as used by this package
 \item \code{fullname}\cr Full name, like \code{"Escherichia coli"}
@@ -54,6 +54,7 @@ For convenience, some entries were added manually:
 \item 11 entries of \emph{Streptococcus} (beta-haemolytic: groups A, B, C, D, F, G, H, K and unspecified; other: viridans, milleri)
 \item 2 entries of \emph{Staphylococcus} (coagulase-negative (CoNS) and coagulase-positive (CoPS))
 \item 3 entries of \emph{Trichomonas} (\emph{T. vaginalis}, and its family and genus)
+\item 4 entries of \emph{Toxoplasma} (\emph{T. gondii}, and its order, family and genus)
 \item 1 entry of \emph{Candida} (\emph{C.  krusei}), that is not (yet) in the Catalogue of Life
 \item 1 entry of \emph{Blastocystis} (\emph{B.  hominis}), although it officially does not exist (Noel \emph{et al.} 2005, PMID 15634993)
 \item 1 entry of \emph{Moraxella} (\emph{M. catarrhalis}), which was formally named \emph{Branhamella catarrhalis} (Catlin, 1970) though this change was never accepted within the field of clinical microbiology
@@ -64,15 +65,9 @@ For convenience, some entries were added manually:
 
 \subsection{Direct download}{
 
-This data set is available as 'flat file' for use even without \R - you can find the file here:
+This data set is available as 'flat file' for use even without \R - you can find the file here: \url{https://github.com/msberends/AMR/raw/main/data-raw/microorganisms.txt}.
-\itemize{
-\item \url{https://github.com/msberends/AMR/raw/main/data-raw/microorganisms.txt}
-}
 
-The file in \R format (with preserved data structure) can be found here:
+The file in \R format (with preserved data structure) can be found here: \url{https://github.com/msberends/AMR/raw/main/data/microorganisms.rda}.
-\itemize{
-\item \url{https://github.com/msberends/AMR/raw/main/data/microorganisms.rda}
-}
 }
 }
 \section{About the Records from LPSN (see \emph{Source})}{