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mirror of https://github.com/msberends/AMR.git synced 2024-12-24 04:06:12 +01:00

(v1.8.1.9013) add Toxoplasma

This commit is contained in:
dr. M.S. (Matthijs) Berends 2022-06-10 13:15:23 +02:00
parent b84d647cac
commit 7f981e7778
29 changed files with 432 additions and 124 deletions

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@ -1,6 +1,6 @@
Package: AMR
Version: 1.8.1.9012
Date: 2022-06-03
Version: 1.8.1.9013
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

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@ -1,5 +1,5 @@
# `AMR` 1.8.1.9012
## <small>Last updated: 3 June 2022</small>
# `AMR` 1.8.1.9013
## <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

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@ -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.
#'

279
R/mo.R
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@ -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
}

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@ -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)

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@ -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)) {

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@ -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)"

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@ -1 +1 @@
532f52b6cbe1cdb25268122fa0608714
4709adde8932f9e887fbd892a27ad929

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@ -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

View File

@ -276,40 +276,7 @@ MOs <- MOs %>%
"Firmicutes",
"Actinobacteria",
"Sarcomastigophora")
| genus %in% 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")
| genus %in% MO_PREVALENT_GENERA
| rank %in% c("kingdom", "phylum", "class", "order", "family"))
~ 2,
TRUE ~ 3

68
data-raw/toxoplasma.R Normal file
View File

@ -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)

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@ -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>

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@ -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>

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@ -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
the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
<p>It was last updated on 10 June 2022 11:09:45 UTC. Find more info
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>

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@ -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>

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@ -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>

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@ -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">
<code>AMR</code> 1.8.1.9012<a class="anchor" aria-label="anchor" href="#amr-1819012"></a></h2>
<h2 class="page-header" data-toc-text="1.8.1.9013" id="amr-1819013">
<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 thats 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>

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@ -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>

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<!DOCTYPE html>
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<div class="col-md-9 contents">
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<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>
<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. (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>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>
</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; <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; <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; <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>
), 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>
<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 (<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>
</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>
</ul></div>
<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>
<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>
</div>
</div>
<div id="about-the-records-from-lpsn-see-source-">

View File

@ -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>
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View File

@ -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:
\itemize{
\item \url{https://github.com/msberends/AMR/raw/main/data-raw/microorganisms.txt}
}
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}.
The file in \R format (with preserved data structure) can be found here:
\itemize{
\item \url{https://github.com/msberends/AMR/raw/main/data/microorganisms.rda}
}
The file in \R format (with preserved data structure) can be found here: \url{https://github.com/msberends/AMR/raw/main/data/microorganisms.rda}.
}
}
\section{About the Records from LPSN (see \emph{Source})}{