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AMR
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fixes #58 

fixes #54
fixes #51
This commit is contained in:
dr. M.S. (Matthijs) Berends 2022-09-23 12:55:52 +02:00
parent 96a9fd0382
commit 1724e6d3f3
36 changed files with 233 additions and 252 deletions
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4
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR
Version: 1.8.1.9058
Date: 2022-09-19
Version: 1.8.1.9059
Date: 2022-09-23
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

3
NAMESPACE
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@ -119,7 +119,6 @@ S3method(print,custom_mdro_guideline)
S3method(print,disk)
S3method(print,mic)
S3method(print,mo)
S3method(print,mo_renamed)
S3method(print,mo_uncertainties)
S3method(print,pca)
S3method(print,rsi)
@ -267,7 +266,6 @@ export(mean_amr_distance)
export(mo_authors)
export(mo_class)
export(mo_domain)
export(mo_failures)
export(mo_family)
export(mo_fullname)
export(mo_gbif)
@ -287,7 +285,6 @@ export(mo_phylum)
export(mo_property)
export(mo_rank)
export(mo_ref)
export(mo_renamed)
export(mo_reset_session)
export(mo_shortname)
export(mo_snomed)

2
NEWS.md
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@ -1,4 +1,4 @@
# AMR 1.8.1.9058
# AMR 1.8.1.9059
This version will eventually become v2.0! We're happy to reach a new major milestone soon!

23
R/ab_selectors.R
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@ -562,15 +562,22 @@ ab_select_exec <- function(function_name,
message_("No antimicrobial agents found in the data.")
return(NULL)
}
if (is.null(ab_class_args)) {
# their upper case equivalent are vectors with class <ab>, created in data-raw/_pre_commit_hook.R
# carbapenems() gets its codes from AMR:::AB_CARBAPENEMS
abx <- get(paste0("AB_", toupper(function_name)), envir = asNamespace("AMR"))
ab_group <- function_name
if (is.null(ab_class_args) || function_name %in% c("antifungals", "antimycobacterials")) {
ab_group <- NULL
if (function_name == "antifungals") {
abx <- antibiotics$ab[which(antibiotics$group == "Antifungals")]
} else if (function_name == "antimycobacterials") {
abx <- antibiotics$ab[which(antibiotics$group == "Antimycobacterials")]
} else {
# their upper case equivalent are vectors with class <ab>, created in data-raw/_pre_commit_hook.R
# carbapenems() gets its codes from AMR:::AB_CARBAPENEMS
abx <- get(paste0("AB_", toupper(function_name)), envir = asNamespace("AMR"))
ab_group <- function_name
}
examples <- paste0(" (such as ", vector_or(ab_name(sample(abx, size = min(2, length(abx)), replace = FALSE),
tolower = TRUE,
language = NULL
tolower = TRUE,
language = NULL
),
quotes = FALSE
), ")")

10
R/data.R
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@ -98,14 +98,14 @@
#'
#' @section Included Taxa:
#' Included taxonomic data are:
#' - All `r format_included_data_number(microorganisms[which(microorganisms$kingdom %in% c("Archeae", "Bacteria", "Protozoa")), , drop = FALSE])` (sub)species from the kingdoms of Archaea, Bacteria and Protozoa
#' - All `r format_included_data_number(microorganisms[which(microorganisms$kingdom == "Fungi"), , drop = FALSE])` (sub)species from `r format_included_data_number(microorganisms[which(microorganisms$kingdom == "Fungi"), "order", drop = TRUE])` relevant orders of the kingdom of Fungi. The kingdom of Fungi is a very large taxon with almost 300,000 different (sub)species, of which most are not microbial (but rather macroscopic, like mushrooms). Because of this, not all fungi fit the scope of this package and including everything would tremendously slow down our algorithms too. By only including relevant taxonomic orders, the most relevant fungi are covered (such as all species of *Aspergillus*, *Candida*, *Cryptococcus*, *Histplasma*, *Pneumocystis*, *Saccharomyces* and *Trichophyton*).
#' - All `r format_included_data_number(microorganisms[which(microorganisms$kingdom == "Animalia"), , drop = FALSE])` (sub)species from `r format_included_data_number(microorganisms[which(microorganisms$kingdom == "Animalia"), "genus", drop = TRUE])` other relevant genera from the kingdom of Animalia (such as *Strongyloides* and *Taenia*)
#' - All `r format_included_data_number(microorganisms[which(microorganisms$kingdom == "Plantae"), , drop = FALSE])` (sub)species from `r format_included_data_number(microorganisms[which(microorganisms$kingdom == "Animalia"), "genus", drop = TRUE])` other relevant genera from the kingdom of Animalia (such as *Strongyloides* and *Taenia*)
#' - All `r format_included_data_number(microorganisms[which(microorganisms$kingdom %in% c("Archeae", "Bacteria")), , drop = FALSE])` (sub)species from the kingdoms of Archaea and Bacteria
#' - `r format_included_data_number(microorganisms[which(microorganisms$kingdom == "Fungi"), , drop = FALSE])` (sub)species from the kingdom of Fungi. The kingdom of Fungi is a very large taxon with almost 300,000 different (sub)species, of which most are not microbial (but rather macroscopic, like mushrooms). Because of this, not all fungi fit the scope of this package. Only relevant fungi are covered (such as all species of *Aspergillus*, *Candida*, *Cryptococcus*, *Histoplasma*, *Pneumocystis*, *Saccharomyces* and *Trichophyton*).
#' - `r format_included_data_number(microorganisms[which(microorganisms$kingdom == "Protozoa"), , drop = FALSE])` (sub)species from the kingdom of Protozoa
#' - `r format_included_data_number(microorganisms[which(microorganisms$kingdom == "Animalia"), , drop = FALSE])` (sub)species from `r format_included_data_number(microorganisms[which(microorganisms$kingdom == "Animalia"), "genus", drop = TRUE])` other relevant genera from the kingdom of Animalia (such as *Strongyloides* and *Taenia*)
#' - All `r format_included_data_number(microorganisms[which(microorganisms$status != "accepted"), , drop = FALSE])` previously accepted names of all included (sub)species (these were taxonomically renamed)
#' - The complete taxonomic tree of all included (sub)species: from kingdom to subspecies
#' - The identifier of the parent taxons
#' - The responsible author(s) and year of scientific publication
#' - The year and first author of the related scientific publication
#'
#' ## Manual additions
#' For convenience, some entries were added manually:

2
R/mdro.R
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@ -175,7 +175,7 @@ mdro <- function(x = NULL,
...) {
if (is_null_or_grouped_tbl(x)) {
# when `x` is left blank, auto determine it (get_current_data() also contains dplyr::cur_data_all())
# is also fix for using a grouped df as input (a dot as first argument)
# is also a fix for using a grouped df as input (i.e., a dot as first argument)
x <- tryCatch(get_current_data(arg_name = "x", call = -2), error = function(e) x)
}
meet_criteria(x, allow_class = "data.frame") # also checks dimensions to be >0

30
R/mic.R
View File

@ -24,23 +24,27 @@
# ==================================================================== #
# these are allowed MIC values and will become [factor] levels
ops <- c("<", "<=", "", ">=", ">")
operators <- c("<", "<=", "", ">=", ">")
valid_mic_levels <- c(
c(t(vapply(
FUN.VALUE = character(9), ops,
function(x) paste0(x, "0.00", 1:9)
FUN.VALUE = character(6), operators,
function(x) paste0(x, "0.000", c(1:4, 6, 8))
))),
c(t(vapply(
FUN.VALUE = character(90), operators,
function(x) paste0(x, "0.00", c(1:9, 11:19, 21:29, 31:39, 41:49, 51:59, 61:69, 71:79, 81:89, 91:99))
))),
unique(c(t(vapply(
FUN.VALUE = character(104), ops,
FUN.VALUE = character(106), operators,
function(x) {
paste0(x, sort(as.double(paste0(
"0.0",
sort(c(1:99, 125, 128, 256, 512, 625))
sort(c(1:99, 125, 128, 156, 165, 256, 512, 625))
))))
}
)))),
unique(c(t(vapply(
FUN.VALUE = character(103), ops,
FUN.VALUE = character(103), operators,
function(x) {
paste0(x, sort(as.double(paste0(
"0.",
@ -49,15 +53,15 @@ valid_mic_levels <- c(
}
)))),
c(t(vapply(
FUN.VALUE = character(10), ops,
FUN.VALUE = character(10), operators,
function(x) paste0(x, sort(c(1:9, 1.5)))
))),
c(t(vapply(
FUN.VALUE = character(45), ops,
FUN.VALUE = character(45), operators,
function(x) paste0(x, c(10:98)[9:98 %% 2 == TRUE])
))),
c(t(vapply(
FUN.VALUE = character(17), ops,
FUN.VALUE = character(17), operators,
function(x) paste0(x, sort(c(2^c(7:11), 192, 80 * c(2:12))))
)))
)
@ -159,11 +163,15 @@ valid_mic_levels <- c(
as.mic <- function(x, na.rm = FALSE) {
meet_criteria(x, allow_class = c("mic", "character", "numeric", "integer", "factor"), allow_NA = TRUE)
meet_criteria(na.rm, allow_class = "logical", has_length = 1)
if (is.mic(x)) {
x
} else {
x <- as.character(unlist(x))
if (is.numeric(x)) {
x <- format(x, scientific = FALSE)
} else {
x <- as.character(unlist(x))
}
if (na.rm == TRUE) {
x <- x[!is.na(x)]
}

169
R/mo.R
View File

@ -88,9 +88,9 @@
#' The level of uncertainty can be set using the argument `allow_uncertain`. The default is `allow_uncertain = TRUE`, which is equal to uncertainty level 2. Using `allow_uncertain = FALSE` is equal to uncertainty level 0 and will skip all rules. You can also use e.g. `as.mo(..., allow_uncertain = 1)` to only allow up to level 1 uncertainty.
#'
#' With the default setting (`allow_uncertain = TRUE`, level 2), below examples will lead to valid results:
#' - `"Streptococcus group B (known as S. agalactiae)"`. The text between brackets will be removed and a warning will be thrown that the result *Streptococcus group B* (``r as.mo("Streptococcus group B")``) needs review.
#' - `"S. aureus - please mind: MRSA"`. The last word will be stripped, after which the function will try to find a match. If it does not, the second last word will be stripped, etc. Again, a warning will be thrown that the result *Staphylococcus aureus* (``r as.mo("Staphylococcus aureus")``) needs review.
#' - `"Fluoroquinolone-resistant Neisseria gonorrhoeae"`. The first word will be stripped, after which the function will try to find a match. A warning will be thrown that the result *Neisseria gonorrhoeae* (``r as.mo("Neisseria gonorrhoeae")``) needs review.
#' - `"Streptococcus group B (known as S. agalactiae)"`. The text between brackets will be removed and a warning will be thrown that the result *Streptococcus group B* (`B_STRPT_GRPB`) needs review.
#' - `"S. aureus - please mind: MRSA"`. The last word will be stripped, after which the function will try to find a match. If it does not, the second last word will be stripped, etc. Again, a warning will be thrown that the result *Staphylococcus aureus* (`B_STPHY_AURS`) needs review.
#' - `"Fluoroquinolone-resistant Neisseria gonorrhoeae"`. The first word will be stripped, after which the function will try to find a match. A warning will be thrown that the result *Neisseria gonorrhoeae* (`B_NESSR_GNRR`) needs review.
#'
#' There are three helper functions that can be run after using the [as.mo()] function:
#' - Use [mo_uncertainties()] to get a [data.frame] that prints in a pretty format with all taxonomic names that were guessed. The output contains the matching score for all matches (see *Matching Score for Microorganisms* below).
@ -197,22 +197,6 @@ as.mo <- function(x,
# WHONET: xxx = no growth
x[tolower(x) %in% c("", "xxx", "na", "nan")] <- NA_character_
if (tryCatch(all(x == "" | gsub(".*(unknown ).*", "unknown name", tolower(x), perl = TRUE) %in% MO_lookup$fullname_lower, na.rm = TRUE) &&
isFALSE(Becker) &&
isTRUE(keep_synonyms) &&
isFALSE(Lancefield), error = function(e) FALSE)) {
# to improve speed, special case for taxonomically correct full names (case-insensitive)
return(set_clean_class(MO_lookup[match(
gsub(".*(unknown ).*", "unknown name",
tolower(x),
perl = TRUE
),
MO_lookup$fullname_lower
), "mo", drop = TRUE],
new_class = c("mo", "character")
))
}
out <- rep(NA_character_, length(x))
# below we use base R's match(), known for powering '%in%', and incredibly fast!
@ -233,6 +217,9 @@ as.mo <- function(x,
# found this extremely fast gem here: https://stackoverflow.com/a/11002456/4575331
out[is.na(out) & x %in% unlist(microorganisms$snomed)] <- microorganisms$mo[rep(seq_along(microorganisms$snomed), vapply(FUN.VALUE = double(1), microorganisms$snomed, length))[match(x[is.na(out) & x %in% unlist(microorganisms$snomed)], unlist(microorganisms$snomed))]]
}
# From other familiar output ----
# such as Salmonella groups, colloquial names, etc.
out[is.na(out)] <- convert_colloquial_input(x[is.na(out)])
# From previous hits in this session ----
old <- out
out[is.na(out) & x %in% pkg_env$mo_previously_coerced$x] <- pkg_env$mo_previously_coerced$mo[match(x[is.na(out) & x %in% pkg_env$mo_previously_coerced$x], pkg_env$mo_previously_coerced$x)]
@ -310,7 +297,7 @@ as.mo <- function(x,
m[m < minimum_matching_score_current] <- NA_real_
top_hits <- mo_to_search[order(m, decreasing = TRUE, na.last = NA)] # na.last = NA will remove the NAs
if (length(top_hits) == 0) {
warning_("No hits found for \"", x_search, "\" with minimum_matching_score = ", ifelse(is.null(minimum_matching_score), "NULL", minimum_matching_score), ". Try setting this value higher.")
warning_("No hits found for \"", x_search, "\" with minimum_matching_score = ", ifelse(is.null(minimum_matching_score), "NULL", minimum_matching_score), ". Try setting this value lower or even to 0.")
result_mo <- NA_character_
} else {
result_mo <- MO_lookup$mo[match(top_hits[1], MO_lookup$fullname)]
@ -409,13 +396,11 @@ as.mo <- function(x,
)
)
}
} else {
} else if (is.null(getOption("AMR_keep_synonyms")) && any(!is.na(c(gbif_matches, lpsn_matches))) && message_not_thrown_before("as.mo", "keep_synonyms_warning", entire_session = TRUE)) {
# keep synonyms is TRUE, so check if any do have synonyms
if (any(!is.na(c(gbif_matches, lpsn_matches))) && message_not_thrown_before("as.mo", unique(c(gbif_matches, lpsn_matches)))) {
warning_("Function `as.mo()` returned some old taxonomic names. Use `as.mo(..., keep_synonyms = FALSE)` to clean the input to currently accepted taxonomic names, or set the R option `AMR_keep_synonyms` to `FALSE`.")
}
warning_("Function `as.mo()` returned some old taxonomic names. Use `as.mo(..., keep_synonyms = FALSE)` to clean the input to currently accepted taxonomic names, or set the R option `AMR_keep_synonyms` to `FALSE`. This warning will be shown once per session.")
}
# Apply Becker ----
if (isTRUE(Becker) || Becker == "all") {
# warn when species found that are not in:
@ -615,19 +600,18 @@ print.mo <- function(x, print.shortnames = FALSE, ...) {
#' @noRd
summary.mo <- function(object, ...) {
# unique and top 1-3
x <- as.mo(object) # force again, could be mo from older pkg version
top <- as.data.frame(table(x), responseName = "n", stringsAsFactors = FALSE)
top_3 <- top[order(-top$n), 1, drop = TRUE][1:3]
value <- c(
x <- object
top_3 <- names(sort(-table(x[!is.na(x)])))[1:3]
out <- c(
"Class" = "mo",
"<NA>" = length(x[is.na(x)]),
"Unique" = pm_n_distinct(x[!is.na(x)]),
"Unique" = length(unique(x[!is.na(x)])),
"#1" = top_3[1],
"#2" = top_3[2],
"#3" = top_3[3]
)
class(value) <- c("summaryDefault", "table")
value
class(out) <- c("summaryDefault", "table")
out
}
#' @method as.data.frame mo
@ -710,12 +694,6 @@ rep.mo <- function(x, ...) {
y
}
#' @rdname as.mo
#' @export
mo_failures <- function() {
pkg_env$mo_failures
}
#' @rdname as.mo
#' @export
mo_uncertainties <- function() {
@ -833,51 +811,6 @@ mo_reset_session <- function() {
}
}
#' @rdname as.mo
#' @export
mo_renamed <- function() {
items <- pkg_env$mo_renamed
if (is.null(items)) {
items <- data.frame(stringsAsFactors = FALSE)
} else {
items <- pm_distinct(items, old_name, .keep_all = TRUE)
}
set_clean_class(as.data.frame(items,
stringsAsFactors = FALSE
),
new_class = c("mo_renamed", "data.frame")
)
}
#' @method print mo_renamed
#' @export
#' @noRd
print.mo_renamed <- function(x, ...) {
if (NROW(x) == 0) {
return(invisible())
}
for (i in seq_len(nrow(x))) {
message_(
font_italic(x$old_name[i]),
ifelse(x$old_ref[i] %in% c("", NA),
"",
paste0(" (", gsub("et al.", font_italic("et al."), x$old_ref[i]), ")")
),
" was renamed ",
ifelse(!x$new_ref[i] %in% c("", NA) && as.integer(gsub("[^0-9]", "", x$new_ref[i])) < as.integer(gsub("[^0-9]", "", x$old_ref[i])),
font_bold("back to "),
""
),
font_italic(x$new_name[i]),
ifelse(x$new_ref[i] %in% c("", NA),
"",
paste0(" (", gsub("et al.", font_italic("et al."), x$new_ref[i]), ")")
),
" [", x$mo[i], "]"
)
}
}
nr2char <- function(x) {
if (x %in% c(1:10)) {
v <- c(
@ -890,10 +823,6 @@ nr2char <- function(x) {
}
}
unregex <- function(x) {
gsub("[^a-zA-Z0-9 -]", "", x)
}
translate_allow_uncertain <- function(allow_uncertain) {
if (isTRUE(allow_uncertain)) {
# default to uncertainty level 2
@ -911,22 +840,14 @@ translate_allow_uncertain <- function(allow_uncertain) {
}
get_mo_failures_uncertainties_renamed <- function() {
remember <- list(
failures = pkg_env$mo_failures,
uncertainties = pkg_env$mo_uncertainties,
renamed = pkg_env$mo_renamed
)
# empty them, otherwise mo_shortname("Chlamydophila psittaci") will give 3 notes
pkg_env$mo_failures <- NULL
remember <- list(uncertainties = pkg_env$mo_uncertainties)
# empty them, otherwise e.g. mo_shortname("Chlamydophila psittaci") will give 3 notes
pkg_env$mo_uncertainties <- NULL
pkg_env$mo_renamed <- NULL
remember
}
load_mo_failures_uncertainties_renamed <- function(metadata) {
pkg_env$mo_failures <- metadata$failures
pkg_env$mo_uncertainties <- metadata$uncertainties
pkg_env$mo_renamed <- metadata$renamed
}
trimws2 <- function(x) {
@ -934,6 +855,9 @@ trimws2 <- function(x) {
}
parse_and_convert <- function(x) {
if (tryCatch(is.character(x) && Encoding(x) == "unknown", error = function(e) FALSE)) {
return(x)
}
tryCatch(
{
if (!is.null(dim(x))) {
@ -966,7 +890,7 @@ replace_old_mo_codes <- function(x, property) {
# this function transform old MO codes to current codes, such as:
# B_ESCH_COL (AMR v0.5.0) -> B_ESCHR_COLI
ind <- x %like_case% "^[A-Z]_[A-Z_]+$" & !x %in% AMR::microorganisms$mo
if (any(ind)) {
if (any(ind, na.rm = TRUE)) {
# get the ones that match
affected <- x[ind]
affected_unique <- unique(affected)
@ -1067,13 +991,44 @@ repair_reference_df <- function(reference_df) {
reference_df
}
strip_words <- function(text, n, side = "right") {
out <- lapply(strsplit(text, " "), function(x) {
if (side %like% "^r" & length(x) > n) {
x[seq_len(length(x) - n)]
} else if (side %like% "^l" & length(x) > n) {
x[2:length(x)]
}
})
vapply(FUN.VALUE = character(1), out, paste, collapse = " ")
convert_colloquial_input <- function(x) {
x.bak <- trimws(x)
x <- trimws(tolower(x))
out <- rep(NA_character_, length(x))
# Streptococci, like GBS = Group B Streptococci (B_STRPT_GRPB)
out[x %like_case% "^g[abcdfghkl]s$"] <- gsub("g([abcdfghkl])s",
"B_STRPT_GRP\\U\\1",
x[x %like_case% "^g[abcdfghkl]s$"],
perl = TRUE)
# Streptococci in different languages, like "estreptococos grupo B"
out[x %like_case% "strepto[ck]o[ck].* [abcdfghkl]$"] <- gsub(".*e?strepto[ck]o[ck].* ([abcdfghkl])$",
"B_STRPT_GRP\\U\\1",
x[x %like_case% "strepto[ck]o[ck].* [abcdfghkl]$"],
perl = TRUE)
out[x %like_case% "group [abcdfghkl] strepto[ck]o[ck]"] <- gsub(".*group ([abcdfghkl]) strepto[ck]o[ck].*",
"B_STRPT_GRP\\U\\1",
x[x %like_case% "group [abcdfghkl] strepto[ck]o[ck]"],
perl = TRUE)
out[x %like_case% "ha?emoly.*strep"] <- "B_STRPT_HAEM"
out[x %like_case% "(strepto.* mil+er+i|^mgs[^a-z]*$)"] <- "B_STRPT_MILL"
out[x %like_case% "((strepto|^s).* viridans|^vgs[^a-z]*$)"] <- "B_STRPT_VIRI"
# CoNS/CoPS in different languages (support for German, Dutch, Spanish, Portuguese)
out[x %like_case% "([ck]oagulas[ea].negatie?[vf]|^[ck]o?ns[^a-z]*$)"] <- "B_STPHY_CONS"
out[x %like_case% "([ck]oagulas[ea].positie?[vf]|^[ck]o?ps[^a-z]*$)"] <- "B_STPHY_COPS"
# Gram stains
out[x %like_case% "gram[ -]?neg.*|negatie?[vf]"] <- "B_GRAMN"
out[x %like_case% "gram[ -]?pos.*|positie?[vf]"] <- "B_GRAMP"
# Salmonella city names, starting with capital species name - they are all S. enterica
out[x.bak %like_case% "[sS]almonella [A-Z][a-z]+ ?.*" & x %unlike% "typhi"] <- "B_SLMNL_ENTR"
# trivial names known to the field
out[x %like_case% "meningo[ck]o[ck]"] <- "B_NESSR_MNNG"
out[x %like_case% "gono[ck]o[ck]"] <- "B_NESSR_GNRR"
out[x %like_case% "pneumo[ck]o[ck]"] <- "B_STRPT_PNMN"
out
}

24
R/rsi.R
View File

@ -327,31 +327,35 @@ as.rsi.default <- function(x, ...) {
# remove other invalid characters
# set to capitals
x <- toupper(x)
x <- gsub("[^RSIHDU]+", "", x, perl = TRUE)
x <- gsub("[^A-Z]+", "", x, perl = TRUE)
# some labs now report "H" instead of "I" to not interfere with EUCAST prior to 2019
x <- gsub("^H$", "I", x, perl = TRUE)
x <- gsub("H", "I", x, fixed = TRUE)
# and MIPS uses D for Dose-dependent (which is I, but it will throw a note)
x <- gsub("^D$", "I", x, perl = TRUE)
x <- gsub("D", "I", x, fixed = TRUE)
# and MIPS uses U for "susceptible urine"
x <- gsub("^U$", "S", x, perl = TRUE)
x <- gsub("U", "S", x, fixed = TRUE)
# in cases of "S;S" keep S, but in case of "S;I" make it NA
x <- gsub("^S+$", "S", x)
x <- gsub("^I+$", "I", x)
x <- gsub("^R+$", "R", x)
x[!x %in% c("S", "I", "R")] <- NA_character_
na_after <- length(x[is.na(x) | x == ""])
if (!isFALSE(list(...)$warn)) { # so as.rsi(..., warn = FALSE) will never throw a warning
if (na_before != na_after) {
list_missing <- x.bak[is.na(x) & !is.na(x.bak) & x.bak != ""] %pm>%
unique() %pm>%
sort() %pm>%
vector_and(quotes = TRUE)
warning_("in `as.rsi()`: ", na_after - na_before, " results truncated (",
round(((na_after - na_before) / length(x)) * 100),
"%) that were invalid antimicrobial interpretations: ",
list_missing,
call = FALSE
cur_col <- get_current_column()
warning_("in `as.rsi()`: ", na_after - na_before, " result",
ifelse(na_after - na_before > 1, "s", ""),
ifelse(is.null(cur_col), "", paste0(" in column '", cur_col, "'")),
" truncated (",
round(((na_after - na_before) / length(x)) * 100),
"%) that were invalid antimicrobial interpretations: ",
list_missing,
call = FALSE
)
}
if (any(toupper(x.bak[!is.na(x.bak)]) == "U") && message_not_thrown_before("as.rsi", "U")) {

2
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@ -10,7 +10,7 @@
`AMR` is a free, open-source and independent R package to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. Our aim is to provide a standard for clean and reproducible antimicrobial resistance data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. It is currently being used in over 175 countries.
After installing this package, R knows ~63,000 distinct microbial species and all ~570 antibiotic, antimycotic, and antiviral drugs by name and code (including ATC, WHONET/EARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data. Antimicrobial names and group names are available in Danish, Dutch, English, French, German, Italian, Portuguese and Spanish.
After installing this package, R knows ~49,000 distinct microbial species and all ~570 antibiotic, antimycotic, and antiviral drugs by name and code (including ATC, WHONET/EARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data. Antimicrobial names and group names are available in Danish, Dutch, English, French, German, Italian, Portuguese and Spanish.
This package is fully independent of any other R package and works on Windows, macOS and Linux with all versions of R since R-3.0.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice Foundation and University Medical Center Groningen. This R package is actively maintained and free software; you can freely use and distribute it for both personal and commercial (but not patent) purposes under the terms of the GNU General Public License version 2.0 (GPL-2), as published by the Free Software Foundation.

2
data-raw/_pre_commit_hook.R
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@ -177,7 +177,7 @@ MO_PREVALENT_GENERA <- c(
"Microsporidium", "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",
"Phocanema", "Phoma", "Piedraia", "Pithomyces", "Pityrosporum", "Pneumocystis", "Porphyromonas", "Prevotella",
"Pseudallescheria", "Pseudoterranova", "Pulex", "Rhizomucor", "Rhizopus", "Rhodotorula", "Riemerella",
"Saccharomyces", "Sarcoptes", "Scolecobasidium", "Scopulariopsis", "Scytalidium", "Sphingobacterium",
"Spirometra", "Spiroplasma", "Sporobolomyces", "Stachybotrys", "Streptobacillus", "Strongyloides",

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data-raw/reproduction_of_microorganisms.R
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@ -997,13 +997,25 @@ taxonomy <- taxonomy %>%
arrange(fullname) %>%
distinct(fullname, .keep_all = TRUE)
# Remove unwanted taxonomic entries from Protoza/Fungi --------------------
# this must be done after the microbial ID generation, since it will otherwise generate a lot of different IDs
taxonomy <- taxonomy %>%
filter(
# Protozoa:
!(phylum %in% c("Choanozoa", "Mycetozoa") & prevalence == 3),
# Fungi:
!(phylum %in% c("Ascomycota", "Zygomycota", "Basidiomycota") & prevalence == 3),
!(genus %in% c("Phoma", "Leptosphaeria") & rank %in% c("species", "subspecies")), # only genus of this rare fungus, with resp. 1300 and 800 species
# (leave Alternaria in there, part of human mycobiome and opportunistic pathogen)
# Animalia:
!genus %in% c("Lucilia", "Lumbricus"),
!(genus %in% c("Aedes", "Anopheles") & rank %in% c("species", "subspecies")), # only genus of the many hundreds of mosquitoes species
kingdom != "Plantae") # this kingdom only contained Curvularia and Hymenolepis, which have coincidental twin names with Fungi
message("\nCongratulations! The new taxonomic table will contain ", format(nrow(taxonomy), big.mark = ","), " rows.\n")
# taxonomy <- taxonomy %>%
# bind_rows(taxonomy %>%
# filter(mo == "B_STRPT_GRPK") %>%
# mutate(mo = gsub("GRPK", "GRPL", as.character(mo)), fullname = "Streptococcus group L", species = "group L")) %>%
# arrange(fullname)
# Add SNOMED CT -----------------------------------------------------------
@ -1035,12 +1047,10 @@ snomed <- snomed %>%
summarise(snomed = list(snomed))
taxonomy <- taxonomy %>%
left_join(snomed, by = "fullname") %>%
# just to be sure:
AMR:::dataset_UTF8_to_ASCII()
left_join(snomed, by = "fullname")
# Save to package ---------------------------------------------------------
# Clean data set ----------------------------------------------------------
# format to tibble and check again for invalid characters
taxonomy <- taxonomy %>%
@ -1050,20 +1060,26 @@ taxonomy <- taxonomy %>%
# set class <mo>
class(taxonomy$mo) <- c("mo", "character")
# --- Moraxella catarrhalis was named Branhamella catarrhalis (Catlin, 1970), but this is unaccepted in clinical microbiology
# Moraxella catarrhalis was named Branhamella catarrhalis (Catlin, 1970), but this is unaccepted in clinical microbiology
# we keep them both
taxonomy$status[which(taxonomy$fullname == "Moraxella catarrhalis")]
taxonomy$lpsn_renamed_to[which(taxonomy$fullname == "Moraxella catarrhalis")]
taxonomy$status[which(taxonomy$fullname == "Moraxella catarrhalis")] <- "accepted"
taxonomy$lpsn_renamed_to[which(taxonomy$fullname == "Moraxella catarrhalis")] <- NA_character_
taxonomy <- taxonomy %>%
AMR:::dataset_UTF8_to_ASCII()
# Save to package ---------------------------------------------------------
microorganisms <- taxonomy
usethis::use_data(microorganisms, overwrite = TRUE, version = 2, compress = "xz")
rm(microorganisms)
# DON'T FORGET TO UPDATE R/globals.R!
# Test updates ------------------------------------------------------------
# and check: these codes should not be missing (will otherwise throw a unit test error):

2
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data-raw/rsi_translation.txt
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@ -8,7 +8,7 @@
"EUCAST 2022" "MIC" "F_CANDD_PRPS" "Candida parapsilosis" 2 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2022" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2022" "MIC" "F_CRYPT_NFRM" "Cryptococcus neoformans" 2 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2022" "MIC" "F_PICHI" "Pichia" 3 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2022" "MIC" "F_PICHI" "Pithomyces djbhatii" 3 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2022" "DISK" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "AMC" "Amoxicillin/clavulanic acid" "Enterobacteriaceae" "20-10" 19 19 FALSE
"EUCAST 2022" "DISK" "UTI" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "AMC" "Amoxicillin/clavulanic acid" "Enterobacteriaceae" "20-10" 16 16 TRUE
"EUCAST 2022" "MIC" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "AMC" "Amoxicillin/clavulanic acid" "Enterobacteriaceae" 8 8 FALSE
@ -82,7 +82,7 @@
"EUCAST 2022" "MIC" "F_CANDD_KRUS" "Candida krusei" 2 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2022" "MIC" "F_CANDD_PRPS" "Candida parapsilosis" 2 "ANI" "Anidulafungin" "Candida" 4 4 FALSE
"EUCAST 2022" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2022" "MIC" "F_PICHI" "Pichia" 3 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2022" "MIC" "F_PICHI" "Pithomyces djbhatii" 3 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2022" "DISK" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "ATM" "Aztreonam" "Enterobacteriaceae" "30" 26 21 FALSE
"EUCAST 2022" "MIC" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "ATM" "Aztreonam" "Enterobacteriaceae" 1 4 FALSE
"EUCAST 2022" "DISK" "B_PSDMN" "Pseudomonas" 3 "ATM" "Aztreonam" "Pseudo" "30" 50 18 FALSE
@ -1068,7 +1068,7 @@
"EUCAST 2021" "MIC" "F_CANDD_KRUS" "Candida krusei" 2 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2021" "MIC" "F_CANDD_PRPS" "Candida parapsilosis" 2 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2021" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2021" "MIC" "F_PICHI" "Pichia" 3 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2021" "MIC" "F_PICHI" "Pithomyces djbhatii" 3 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2021" "DISK" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "AMC" "Amoxicillin/clavulanic acid" "Enterobacteriaceae" "20-10" 19 19 FALSE
"EUCAST 2021" "DISK" "UTI" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "AMC" "Amoxicillin/clavulanic acid" "Enterobacteriaceae" "20-10" 16 16 TRUE
"EUCAST 2021" "MIC" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "AMC" "Amoxicillin/clavulanic acid" "Enterobacteriaceae" 8 8 FALSE
@ -1140,7 +1140,7 @@
"EUCAST 2021" "MIC" "F_CANDD_KRUS" "Candida krusei" 2 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2021" "MIC" "F_CANDD_PRPS" "Candida parapsilosis" 2 "ANI" "Anidulafungin" "Candida" 0.002 4 FALSE
"EUCAST 2021" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2021" "MIC" "F_PICHI" "Pichia" 3 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2021" "MIC" "F_PICHI" "Pithomyces djbhatii" 3 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2021" "DISK" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "ATM" "Aztreonam" "Enterobacteriaceae" "30" 26 21 FALSE
"EUCAST 2021" "MIC" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "ATM" "Aztreonam" "Enterobacteriaceae" 1 4 FALSE
"EUCAST 2021" "DISK" "B_PSDMN" "Pseudomonas" 3 "ATM" "Aztreonam" "Pseudo" "30" 50 18 FALSE
@ -1957,7 +1957,7 @@
"EUCAST 2020" "MIC" "F_CANDD_KRUS" "Candida krusei" 2 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2020" "MIC" "F_CANDD_PRPS" "Candida parapsilosis" 2 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2020" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2020" "MIC" "F_PICHI" "Pichia" 3 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2020" "MIC" "F_PICHI" "Pithomyces djbhatii" 3 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2020" "DISK" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "AMC" "Amoxicillin/clavulanic acid" "Enterobacteriaceae" "20-10" 19 19 FALSE
"EUCAST 2020" "DISK" "UTI" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "AMC" "Amoxicillin/clavulanic acid" "Enterobacteriaceae" "20-10" 16 16 TRUE
"EUCAST 2020" "MIC" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "AMC" "Amoxicillin/clavulanic acid" "Enterobacteriaceae" 8 8 FALSE
@ -2027,7 +2027,7 @@
"EUCAST 2020" "MIC" "F_CANDD_KRUS" "Candida krusei" 2 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2020" "MIC" "F_CANDD_PRPS" "Candida parapsilosis" 2 "ANI" "Anidulafungin" "Candida" 0.002 4 FALSE
"EUCAST 2020" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2020" "MIC" "F_PICHI" "Pichia" 3 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2020" "MIC" "F_PICHI" "Pithomyces djbhatii" 3 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2020" "DISK" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "ATM" "Aztreonam" "Enterobacteriaceae" "30" 26 21 FALSE
"EUCAST 2020" "MIC" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "ATM" "Aztreonam" "Enterobacteriaceae" 1 4 FALSE
"EUCAST 2020" "DISK" "B_PSDMN" "Pseudomonas" 3 "ATM" "Aztreonam" "Pseudo" "30" 50 18 FALSE
@ -2765,7 +2765,7 @@
"EUCAST 2019" "MIC" "F_CANDD_KRUS" "Candida krusei" 2 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2019" "MIC" "F_CANDD_PRPS" "Candida parapsilosis" 2 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2019" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2019" "MIC" "F_PICHI" "Pichia" 3 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2019" "MIC" "F_PICHI" "Pithomyces djbhatii" 3 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2019" "DISK" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "AMC" "Amoxicillin/clavulanic acid" "Enterobacteriaceae" "20-10" 19 19 FALSE
"EUCAST 2019" "DISK" "UTI" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "AMC" "Amoxicillin/clavulanic acid" "Enterobacteriaceae" "20-10" 16 16 TRUE
"EUCAST 2019" "MIC" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "AMC" "Amoxicillin/clavulanic acid" "Enterobacteriaceae" 8 8 FALSE
@ -2824,7 +2824,7 @@
"EUCAST 2019" "MIC" "F_CANDD_KRUS" "Candida krusei" 2 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2019" "MIC" "F_CANDD_PRPS" "Candida parapsilosis" 2 "ANI" "Anidulafungin" "Candida" 0.002 4 FALSE
"EUCAST 2019" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2019" "MIC" "F_PICHI" "Pichia" 3 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2019" "MIC" "F_PICHI" "Pithomyces djbhatii" 3 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2019" "DISK" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "ATM" "Aztreonam" "Enterobacteriaceae" "30" 26 21 FALSE
"EUCAST 2019" "MIC" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "ATM" "Aztreonam" "Enterobacteriaceae" 1 4 FALSE
"EUCAST 2019" "DISK" "B_PSDMN" "Pseudomonas" 3 "ATM" "Aztreonam" "Pseudo" "30" 18 18 FALSE
@ -3506,7 +3506,7 @@
"EUCAST 2018" "MIC" "F_CANDD_KRUS" "Candida krusei" 2 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2018" "MIC" "F_CANDD_PRPS" "Candida parapsilosis" 2 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2018" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2018" "MIC" "F_PICHI" "Pichia" 3 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2018" "MIC" "F_PICHI" "Pithomyces djbhatii" 3 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2018" "DISK" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "AMC" "Amoxicillin/clavulanic acid" "Enterobacteriaceae" "20-10" 19 19 FALSE
"EUCAST 2018" "DISK" "UTI" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "AMC" "Amoxicillin/clavulanic acid" "Enterobacteriaceae" "20-10" 16 16 TRUE
"EUCAST 2018" "MIC" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "AMC" "Amoxicillin/clavulanic acid" "Enterobacteriaceae" 8 8 FALSE
@ -3562,7 +3562,7 @@
"EUCAST 2018" "MIC" "F_CANDD_KRUS" "Candida krusei" 2 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2018" "MIC" "F_CANDD_PRPS" "Candida parapsilosis" 2 "ANI" "Anidulafungin" "Candida" 0.002 4 FALSE
"EUCAST 2018" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2018" "MIC" "F_PICHI" "Pichia" 3 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2018" "MIC" "F_PICHI" "Pithomyces djbhatii" 3 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2018" "DISK" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "ATM" "Aztreonam" "Enterobacteriaceae" "30" 26 21 FALSE
"EUCAST 2018" "MIC" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "ATM" "Aztreonam" "Enterobacteriaceae" 1 4 FALSE
"EUCAST 2018" "DISK" "B_PSDMN" "Pseudomonas" 3 "ATM" "Aztreonam" "Pseudo" "30" 50 16 FALSE
@ -4231,7 +4231,7 @@
"EUCAST 2017" "MIC" "F_CANDD_KRUS" "Candida krusei" 2 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2017" "MIC" "F_CANDD_PRPS" "Candida parapsilosis" 2 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2017" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2017" "MIC" "F_PICHI" "Pichia" 3 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2017" "MIC" "F_PICHI" "Pithomyces djbhatii" 3 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2017" "DISK" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "AMC" "Amoxicillin/clavulanic acid" "Enterobacteriaceae" "20-10" 19 19 FALSE
"EUCAST 2017" "DISK" "UTI" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "AMC" "Amoxicillin/clavulanic acid" "Enterobacteriaceae" "20-10" 16 16 TRUE
"EUCAST 2017" "MIC" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "AMC" "Amoxicillin/clavulanic acid" "Enterobacteriaceae" 8 8 FALSE
@ -4287,7 +4287,7 @@
"EUCAST 2017" "MIC" "F_CANDD_KRUS" "Candida krusei" 2 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2017" "MIC" "F_CANDD_PRPS" "Candida parapsilosis" 2 "ANI" "Anidulafungin" "Candida" 0.002 4 FALSE
"EUCAST 2017" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2017" "MIC" "F_PICHI" "Pichia" 3 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2017" "MIC" "F_PICHI" "Pithomyces djbhatii" 3 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2017" "DISK" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "ATM" "Aztreonam" "Enterobacteriaceae" "30" 26 21 FALSE
"EUCAST 2017" "MIC" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "ATM" "Aztreonam" "Enterobacteriaceae" 1 4 FALSE
"EUCAST 2017" "DISK" "B_PSDMN" "Pseudomonas" 3 "ATM" "Aztreonam" "Pseudo" "30" 50 16 FALSE
@ -4946,7 +4946,7 @@
"EUCAST 2016" "MIC" "F_CANDD_KRUS" "Candida krusei" 2 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2016" "MIC" "F_CANDD_PRPS" "Candida parapsilosis" 2 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2016" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2016" "MIC" "F_PICHI" "Pichia" 3 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2016" "MIC" "F_PICHI" "Pithomyces djbhatii" 3 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2016" "DISK" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "AMC" "Amoxicillin/clavulanic acid" "Enterobacteriaceae" "20-10" 19 19 FALSE
"EUCAST 2016" "DISK" "UTI" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "AMC" "Amoxicillin/clavulanic acid" "Enterobacteriaceae" "20-10" 16 16 TRUE
"EUCAST 2016" "MIC" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "AMC" "Amoxicillin/clavulanic acid" "Enterobacteriaceae" 8 8 FALSE
@ -4999,7 +4999,7 @@
"EUCAST 2016" "MIC" "F_CANDD_KRUS" "Candida krusei" 2 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2016" "MIC" "F_CANDD_PRPS" "Candida parapsilosis" 2 "ANI" "Anidulafungin" "Candida" 0.002 4 FALSE
"EUCAST 2016" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2016" "MIC" "F_PICHI" "Pichia" 3 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2016" "MIC" "F_PICHI" "Pithomyces djbhatii" 3 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2016" "DISK" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "ATM" "Aztreonam" "Enterobacteriaceae" "30" 24 21 FALSE
"EUCAST 2016" "MIC" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "ATM" "Aztreonam" "Enterobacteriaceae" 1 4 FALSE
"EUCAST 2016" "DISK" "B_PSDMN" "Pseudomonas" 3 "ATM" "Aztreonam" "Pseudo" "30" 50 16 FALSE
@ -5597,7 +5597,7 @@
"EUCAST 2015" "MIC" "F_CANDD_KRUS" "Candida krusei" 2 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2015" "MIC" "F_CANDD_PRPS" "Candida parapsilosis" 2 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2015" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2015" "MIC" "F_PICHI" "Pichia" 3 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2015" "MIC" "F_PICHI" "Pithomyces djbhatii" 3 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2015" "DISK" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "AMC" "Amoxicillin/clavulanic acid" "Enterobacteriaceae" "20-10" 19 19 FALSE
"EUCAST 2015" "DISK" "UTI" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "AMC" "Amoxicillin/clavulanic acid" "Enterobacteriaceae" "20-10" 16 16 TRUE
"EUCAST 2015" "MIC" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "AMC" "Amoxicillin/clavulanic acid" "Enterobacteriaceae" 8 8 FALSE
@ -5650,7 +5650,7 @@
"EUCAST 2015" "MIC" "F_CANDD_KRUS" "Candida krusei" 2 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2015" "MIC" "F_CANDD_PRPS" "Candida parapsilosis" 2 "ANI" "Anidulafungin" "Candida" 0.002 4 FALSE
"EUCAST 2015" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2015" "MIC" "F_PICHI" "Pichia" 3 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2015" "MIC" "F_PICHI" "Pithomyces djbhatii" 3 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2015" "DISK" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "ATM" "Aztreonam" "Enterobacteriaceae" "30" 24 21 FALSE
"EUCAST 2015" "MIC" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "ATM" "Aztreonam" "Enterobacteriaceae" 1 4 FALSE
"EUCAST 2015" "DISK" "B_PSDMN" "Pseudomonas" 3 "ATM" "Aztreonam" "Pseudo" "30" 50 16 FALSE
@ -6224,7 +6224,7 @@
"EUCAST 2014" "MIC" "F_CANDD_KRUS" "Candida krusei" 2 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2014" "MIC" "F_CANDD_PRPS" "Candida parapsilosis" 2 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2014" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2014" "MIC" "F_PICHI" "Pichia" 3 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2014" "MIC" "F_PICHI" "Pithomyces djbhatii" 3 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2014" "DISK" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "AMC" "Amoxicillin/clavulanic acid" "Enterobacteriaceae" "20-10" 19 19 FALSE
"EUCAST 2014" "DISK" "UTI" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "AMC" "Amoxicillin/clavulanic acid" "Enterobacteriaceae" "20-10" 16 16 TRUE
"EUCAST 2014" "MIC" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "AMC" "Amoxicillin/clavulanic acid" "Enterobacteriaceae" 8 8 FALSE
@ -6277,7 +6277,7 @@
"EUCAST 2014" "MIC" "F_CANDD_KRUS" "Candida krusei" 2 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2014" "MIC" "F_CANDD_PRPS" "Candida parapsilosis" 2 "ANI" "Anidulafungin" "Candida" 0.002 4 FALSE
"EUCAST 2014" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2014" "MIC" "F_PICHI" "Pichia" 3 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2014" "MIC" "F_PICHI" "Pithomyces djbhatii" 3 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2014" "DISK" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "ATM" "Aztreonam" "Enterobacteriaceae" "30" 24 21 FALSE
"EUCAST 2014" "MIC" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "ATM" "Aztreonam" "Enterobacteriaceae" 1 4 FALSE
"EUCAST 2014" "DISK" "B_PSDMN" "Pseudomonas" 3 "ATM" "Aztreonam" "Pseudo" "30" 50 16 FALSE
@ -6846,7 +6846,7 @@
"EUCAST 2013" "MIC" "F_CANDD_KRUS" "Candida krusei" 2 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2013" "MIC" "F_CANDD_PRPS" "Candida parapsilosis" 2 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2013" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2013" "MIC" "F_PICHI" "Pichia" 3 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2013" "MIC" "F_PICHI" "Pithomyces djbhatii" 3 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2013" "DISK" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "AMC" "Amoxicillin/clavulanic acid" "Enterobacteriaceae" "20/10ug" 17 17 FALSE
"EUCAST 2013" "MIC" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "AMC" "Amoxicillin/clavulanic acid" "Enterobacteriaceae" 8 8 FALSE
"EUCAST 2013" "MIC" "B_ENTRC" "Enterococcus" 3 "AMC" "Amoxicillin/clavulanic acid" "Enterococcus" 4 8 FALSE
@ -6896,7 +6896,7 @@
"EUCAST 2013" "MIC" "F_CANDD_ALBC" "Candida albicans" 2 "ANI" "Anidulafungin" "Candida" 0.032 0.032 FALSE
"EUCAST 2013" "MIC" "F_CANDD_KRUS" "Candida krusei" 2 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2013" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2013" "MIC" "F_PICHI" "Pichia" 3 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2013" "MIC" "F_PICHI" "Pithomyces djbhatii" 3 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2013" "DISK" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "ATM" "Aztreonam" "Enterobacteriaceae" "30ug" 24 21 FALSE
"EUCAST 2013" "MIC" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "ATM" "Aztreonam" "Enterobacteriaceae" 1 4 FALSE
"EUCAST 2013" "DISK" "B_PSDMN" "Pseudomonas" 3 "ATM" "Aztreonam" "Pseud" "30ug" 50 16 FALSE
@ -8481,8 +8481,8 @@
"CLSI 2022" "MIC" "F_CANDD_KRUS" "Candida krusei" 2 "ANI" "Anidulafungin" "Table 1" 0.25 1 FALSE
"CLSI 2022" "MIC" "F_CANDD_PRPS" "Candida parapsilosis" 2 "ANI" "Anidulafungin" "Table 1" 2 8 FALSE
"CLSI 2022" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "ANI" "Anidulafungin" "Table 1" 0.25 1 FALSE
"CLSI 2022" "MIC" "F_MYRZY_GLLR" "Meyerozyma guilliermondii" 2 "ANI" "Anidulafungin" "Table 1" 2 8 FALSE
"CLSI 2022" "MIC" "F_PICHI" "Pichia" 3 "ANI" "Anidulafungin" "Table 1" 0.25 1 FALSE
"CLSI 2022" "MIC" "F_MYRZY_GLLR" 2 "ANI" "Anidulafungin" "Table 1" 2 8 FALSE
"CLSI 2022" "MIC" "F_PICHI" "Pithomyces djbhatii" 3 "ANI" "Anidulafungin" "Table 1" 0.25 1 FALSE
"CLSI 2022" "DISK" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "ATM" "Aztreonam" "Table 2A" "30ug" 21 17 FALSE
"CLSI 2022" "MIC" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "ATM" "Aztreonam" "Table 2A" 4 16 FALSE
"CLSI 2022" "DISK" "B_AERMN" "Aeromonas" 3 "ATM" "Aztreonam" "M45 Table 2" "30ug" 21 17 FALSE
@ -8532,10 +8532,10 @@
"CLSI 2022" "MIC" "F_CANDD_PRPS" "Candida parapsilosis" 2 "CAS" "Caspofungin" "Table 1" 2 8 FALSE
"CLSI 2022" "DISK" "F_CANDD_TRPC" "Candida tropicalis" 2 "CAS" "Caspofungin" "Table 1" 17 14 FALSE
"CLSI 2022" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "CAS" "Caspofungin" "Table 1" 0.25 1 FALSE
"CLSI 2022" "DISK" "F_MYRZY_GLLR" "Meyerozyma guilliermondii" 2 "CAS" "Caspofungin" "Table 1" 13 10 FALSE
"CLSI 2022" "MIC" "F_MYRZY_GLLR" "Meyerozyma guilliermondii" 2 "CAS" "Caspofungin" "Table 1" 2 8 FALSE
"CLSI 2022" "DISK" "F_PICHI" "Pichia" 3 "CAS" "Caspofungin" "Table 1" 17 14 FALSE
"CLSI 2022" "MIC" "F_PICHI" "Pichia" 3 "CAS" "Caspofungin" "Table 1" 0.25 1 FALSE
"CLSI 2022" "DISK" "F_MYRZY_GLLR" 2 "CAS" "Caspofungin" "Table 1" 13 10 FALSE
"CLSI 2022" "MIC" "F_MYRZY_GLLR" 2 "CAS" "Caspofungin" "Table 1" 2 8 FALSE
"CLSI 2022" "DISK" "F_PICHI" "Pithomyces djbhatii" 3 "CAS" "Caspofungin" "Table 1" 17 14 FALSE
"CLSI 2022" "MIC" "F_PICHI" "Pithomyces djbhatii" 3 "CAS" "Caspofungin" "Table 1" 0.25 1 FALSE
"CLSI 2022" "DISK" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "CAT" "Cefetamet" "Table 2A" "10ug" 18 14 FALSE
"CLSI 2022" "MIC" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "CAT" "Cefetamet" "Table 2A" 4 16 FALSE
"CLSI 2022" "DISK" "B_HMPHL_INFL" "Haemophilus influenzae" 2 "CAT" "Cefetamet" "Table 2E" "10ug" 18 14 FALSE
@ -9292,10 +9292,10 @@
"CLSI 2022" "MIC" "F_CANDD_PRPS" "Candida parapsilosis" 2 "MIF" "Micafungin" "Table 1" 2 8 FALSE
"CLSI 2022" "DISK" "F_CANDD_TRPC" "Candida tropicalis" 2 "MIF" "Micafungin" "Table 1" 22 19 FALSE
"CLSI 2022" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "MIF" "Micafungin" "Table 1" 0.25 1 FALSE
"CLSI 2022" "DISK" "F_MYRZY_GLLR" "Meyerozyma guilliermondii" 2 "MIF" "Micafungin" "Table 1" 16 13 FALSE
"CLSI 2022" "MIC" "F_MYRZY_GLLR" "Meyerozyma guilliermondii" 2 "MIF" "Micafungin" "Table 1" 2 8 FALSE
"CLSI 2022" "DISK" "F_PICHI" "Pichia" 3 "MIF" "Micafungin" "Table 1" 22 19 FALSE
"CLSI 2022" "MIC" "F_PICHI" "Pichia" 3 "MIF" "Micafungin" "Table 1" 0.25 1 FALSE
"CLSI 2022" "DISK" "F_MYRZY_GLLR" 2 "MIF" "Micafungin" "Table 1" 16 13 FALSE
"CLSI 2022" "MIC" "F_MYRZY_GLLR" 2 "MIF" "Micafungin" "Table 1" 2 8 FALSE
"CLSI 2022" "DISK" "F_PICHI" "Pithomyces djbhatii" 3 "MIF" "Micafungin" "Table 1" 22 19 FALSE
"CLSI 2022" "MIC" "F_PICHI" "Pithomyces djbhatii" 3 "MIF" "Micafungin" "Table 1" 0.25 1 FALSE
"CLSI 2022" "DISK" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "MNO" "Minocycline" "Table 2A" "30ug" 16 12 FALSE
"CLSI 2022" "MIC" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "MNO" "Minocycline" "Table 2A" 4 16 FALSE
"CLSI 2022" "DISK" "B_ACNTB" "Acinetobacter" 3 "MNO" "Minocycline" "Table 2B-2" "30ug" 16 12 FALSE
@ -9679,8 +9679,8 @@
"CLSI 2022" "MIC" "F_CANDD_PRPS" "Candida parapsilosis" 2 "VOR" "Voriconazole" "Table 1" 0.125 1 FALSE
"CLSI 2022" "DISK" "F_CANDD_TRPC" "Candida tropicalis" 2 "VOR" "Voriconazole" "Table 1" 17 14 FALSE
"CLSI 2022" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "VOR" "Voriconazole" "Table 1" 0.125 1 FALSE
"CLSI 2022" "DISK" "F_PICHI" "Pichia" 3 "VOR" "Voriconazole" "Table 1" 15 12 FALSE
"CLSI 2022" "MIC" "F_PICHI" "Pichia" 3 "VOR" "Voriconazole" "Table 1" 0.5 2 FALSE
"CLSI 2022" "DISK" "F_PICHI" "Pithomyces djbhatii" 3 "VOR" "Voriconazole" "Table 1" 15 12 FALSE
"CLSI 2022" "MIC" "F_PICHI" "Pithomyces djbhatii" 3 "VOR" "Voriconazole" "Table 1" 0.5 2 FALSE
"CLSI 2021" "DISK" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "AMC" "Amoxicillin/clavulanic acid" "Table 2A" "20ug/10ug" 18 13 FALSE
"CLSI 2021" "MIC" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "AMC" "Amoxicillin/clavulanic acid" "Table 2A" 8 32 FALSE
"CLSI 2021" "DISK" "B_AERMN" "Aeromonas" 3 "AMC" "Amoxicillin/clavulanic acid" "M45 Table 2" "20ug" 18 13 FALSE
@ -9745,8 +9745,8 @@
"CLSI 2021" "MIC" "F_CANDD_KRUS" "Candida krusei" 2 "ANI" "Anidulafungin" "Table 1" 0.25 1 FALSE
"CLSI 2021" "MIC" "F_CANDD_PRPS" "Candida parapsilosis" 2 "ANI" "Anidulafungin" "Table 1" 2 8 FALSE
"CLSI 2021" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "ANI" "Anidulafungin" "Table 1" 0.25 1 FALSE
"CLSI 2021" "MIC" "F_MYRZY_GLLR" "Meyerozyma guilliermondii" 2 "ANI" "Anidulafungin" "Table 1" 2 8 FALSE
"CLSI 2021" "MIC" "F_PICHI" "Pichia" 3 "ANI" "Anidulafungin" "Table 1" 0.25 1 FALSE
"CLSI 2021" "MIC" "F_MYRZY_GLLR" 2 "ANI" "Anidulafungin" "Table 1" 2 8 FALSE
"CLSI 2021" "MIC" "F_PICHI" "Pithomyces djbhatii" 3 "ANI" "Anidulafungin" "Table 1" 0.25 1 FALSE
"CLSI 2021" "DISK" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "ATM" "Aztreonam" "Table 2A" "30ug" 21 17 FALSE
"CLSI 2021" "MIC" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "ATM" "Aztreonam" "Table 2A" 4 16 FALSE
"CLSI 2021" "DISK" "B_AERMN" "Aeromonas" 3 "ATM" "Aztreonam" "M45 Table 2" "30ug" 21 17 FALSE
@ -9792,10 +9792,10 @@
"CLSI 2021" "MIC" "F_CANDD_PRPS" "Candida parapsilosis" 2 "CAS" "Caspofungin" "Table 1" 2 8 FALSE
"CLSI 2021" "DISK" "F_CANDD_TRPC" "Candida tropicalis" 2 "CAS" "Caspofungin" "Table 1" 17 14 FALSE
"CLSI 2021" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "CAS" "Caspofungin" "Table 1" 0.25 1 FALSE
"CLSI 2021" "DISK" "F_MYRZY_GLLR" "Meyerozyma guilliermondii" 2 "CAS" "Caspofungin" "Table 1" 13 10 FALSE
"CLSI 2021" "MIC" "F_MYRZY_GLLR" "Meyerozyma guilliermondii" 2 "CAS" "Caspofungin" "Table 1" 2 8 FALSE
"CLSI 2021" "DISK" "F_PICHI" "Pichia" 3 "CAS" "Caspofungin" "Table 1" 17 14 FALSE
"CLSI 2021" "MIC" "F_PICHI" "Pichia" 3 "CAS" "Caspofungin" "Table 1" 0.25 1 FALSE
"CLSI 2021" "DISK" "F_MYRZY_GLLR" 2 "CAS" "Caspofungin" "Table 1" 13 10 FALSE
"CLSI 2021" "MIC" "F_MYRZY_GLLR" 2 "CAS" "Caspofungin" "Table 1" 2 8 FALSE
"CLSI 2021" "DISK" "F_PICHI" "Pithomyces djbhatii" 3 "CAS" "Caspofungin" "Table 1" 17 14 FALSE
"CLSI 2021" "MIC" "F_PICHI" "Pithomyces djbhatii" 3 "CAS" "Caspofungin" "Table 1" 0.25 1 FALSE
"CLSI 2021" "DISK" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "CAT" "Cefetamet" "Table 2A" "10ug" 18 14 FALSE
"CLSI 2021" "MIC" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "CAT" "Cefetamet" "Table 2A" 4 16 FALSE
"CLSI 2021" "DISK" "B_HMPHL" "Haemophilus" 3 "CAT" "Cefetamet" "Table 2E" "10ug" 18 14 FALSE
@ -10488,10 +10488,10 @@
"CLSI 2021" "MIC" "F_CANDD_PRPS" "Candida parapsilosis" 2 "MIF" "Micafungin" "Table 1" 2 8 FALSE
"CLSI 2021" "DISK" "F_CANDD_TRPC" "Candida tropicalis" 2 "MIF" "Micafungin" "Table 1" 22 19 FALSE
"CLSI 2021" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "MIF" "Micafungin" "Table 1" 0.25 1 FALSE
"CLSI 2021" "DISK" "F_MYRZY_GLLR" "Meyerozyma guilliermondii" 2 "MIF" "Micafungin" "Table 1" 16 13 FALSE
"CLSI 2021" "MIC" "F_MYRZY_GLLR" "Meyerozyma guilliermondii" 2 "MIF" "Micafungin" "Table 1" 2 8 FALSE
"CLSI 2021" "DISK" "F_PICHI" "Pichia" 3 "MIF" "Micafungin" "Table 1" 22 19 FALSE
"CLSI 2021" "MIC" "F_PICHI" "Pichia" 3 "MIF" "Micafungin" "Table 1" 0.25 1 FALSE
"CLSI 2021" "DISK" "F_MYRZY_GLLR" 2 "MIF" "Micafungin" "Table 1" 16 13 FALSE
"CLSI 2021" "MIC" "F_MYRZY_GLLR" 2 "MIF" "Micafungin" "Table 1" 2 8 FALSE
"CLSI 2021" "DISK" "F_PICHI" "Pithomyces djbhatii" 3 "MIF" "Micafungin" "Table 1" 22 19 FALSE
"CLSI 2021" "MIC" "F_PICHI" "Pithomyces djbhatii" 3 "MIF" "Micafungin" "Table 1" 0.25 1 FALSE
"CLSI 2021" "DISK" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "MNO" "Minocycline" "Table 2A" "30ug" 16 12 FALSE
"CLSI 2021" "MIC" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "MNO" "Minocycline" "Table 2A" 4 16 FALSE
"CLSI 2021" "DISK" "B_ACNTB" "Acinetobacter" 3 "MNO" "Minocycline" "Table 2B-2" "30ug" 16 12 FALSE
@ -10861,8 +10861,8 @@
"CLSI 2021" "MIC" "F_CANDD_PRPS" "Candida parapsilosis" 2 "VOR" "Voriconazole" "Table 1" 0.125 1 FALSE
"CLSI 2021" "DISK" "F_CANDD_TRPC" "Candida tropicalis" 2 "VOR" "Voriconazole" "Table 1" 17 14 FALSE
"CLSI 2021" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "VOR" "Voriconazole" "Table 1" 0.125 1 FALSE
"CLSI 2021" "DISK" "F_PICHI" "Pichia" 3 "VOR" "Voriconazole" "Table 1" 15 12 FALSE
"CLSI 2021" "MIC" "F_PICHI" "Pichia" 3 "VOR" "Voriconazole" "Table 1" 0.5 2 FALSE
"CLSI 2021" "DISK" "F_PICHI" "Pithomyces djbhatii" 3 "VOR" "Voriconazole" "Table 1" 15 12 FALSE
"CLSI 2021" "MIC" "F_PICHI" "Pithomyces djbhatii" 3 "VOR" "Voriconazole" "Table 1" 0.5 2 FALSE
"CLSI 2020" "DISK" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "AMC" "Amoxicillin/clavulanic acid" "Table 2A" "20ug/10ug" 18 13 FALSE
"CLSI 2020" "MIC" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "AMC" "Amoxicillin/clavulanic acid" "Table 2A" 8 32 FALSE
"CLSI 2020" "DISK" "B_AERMN" "Aeromonas" 3 "AMC" "Amoxicillin/clavulanic acid" "M45 Table 2" "20ug" 18 13 FALSE
@ -10927,8 +10927,8 @@
"CLSI 2020" "MIC" "F_CANDD_KRUS" "Candida krusei" 2 "ANI" "Anidulafungin" "Table 1" 0.25 1 FALSE
"CLSI 2020" "MIC" "F_CANDD_PRPS" "Candida parapsilosis" 2 "ANI" "Anidulafungin" "Table 1" 2 8 FALSE
"CLSI 2020" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "ANI" "Anidulafungin" "Table 1" 0.25 1 FALSE
"CLSI 2020" "MIC" "F_MYRZY_GLLR" "Meyerozyma guilliermondii" 2 "ANI" "Anidulafungin" "Table 1" 2 8 FALSE
"CLSI 2020" "MIC" "F_PICHI" "Pichia" 3 "ANI" "Anidulafungin" "Table 1" 0.25 1 FALSE
"CLSI 2020" "MIC" "F_MYRZY_GLLR" 2 "ANI" "Anidulafungin" "Table 1" 2 8 FALSE
"CLSI 2020" "MIC" "F_PICHI" "Pithomyces djbhatii" 3 "ANI" "Anidulafungin" "Table 1" 0.25 1 FALSE
"CLSI 2020" "DISK" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "ATM" "Aztreonam" "Table 2A" "30ug" 21 17 FALSE
"CLSI 2020" "MIC" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "ATM" "Aztreonam" "Table 2A" 4 16 FALSE
"CLSI 2020" "DISK" "B_AERMN" "Aeromonas" 3 "ATM" "Aztreonam" "M45 Table 2" "30ug" 21 17 FALSE
@ -10971,10 +10971,10 @@
"CLSI 2020" "MIC" "F_CANDD_PRPS" "Candida parapsilosis" 2 "CAS" "Caspofungin" "Table 1" 2 8 FALSE
"CLSI 2020" "DISK" "F_CANDD_TRPC" "Candida tropicalis" 2 "CAS" "Caspofungin" "Table 1" 17 14 FALSE
"CLSI 2020" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "CAS" "Caspofungin" "Table 1" 0.25 1 FALSE
"CLSI 2020" "DISK" "F_MYRZY_GLLR" "Meyerozyma guilliermondii" 2 "CAS" "Caspofungin" "Table 1" 13 10 FALSE
"CLSI 2020" "MIC" "F_MYRZY_GLLR" "Meyerozyma guilliermondii" 2 "CAS" "Caspofungin" "Table 1" 2 8 FALSE
"CLSI 2020" "DISK" "F_PICHI" "Pichia" 3 "CAS" "Caspofungin" "Table 1" 17 14 FALSE
"CLSI 2020" "MIC" "F_PICHI" "Pichia" 3 "CAS" "Caspofungin" "Table 1" 0.25 1 FALSE
"CLSI 2020" "DISK" "F_MYRZY_GLLR" 2 "CAS" "Caspofungin" "Table 1" 13 10 FALSE
"CLSI 2020" "MIC" "F_MYRZY_GLLR" 2 "CAS" "Caspofungin" "Table 1" 2 8 FALSE
"CLSI 2020" "DISK" "F_PICHI" "Pithomyces djbhatii" 3 "CAS" "Caspofungin" "Table 1" 17 14 FALSE
"CLSI 2020" "MIC" "F_PICHI" "Pithomyces djbhatii" 3 "CAS" "Caspofungin" "Table 1" 0.25 1 FALSE
"CLSI 2020" "DISK" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "CAT" "Cefetamet" "Table 2A" "10ug" 18 14 FALSE
"CLSI 2020" "MIC" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "CAT" "Cefetamet" "Table 2A" 4 16 FALSE
"CLSI 2020" "DISK" "B_HMPHL" "Haemophilus" 3 "CAT" "Cefetamet" "Table 2E" "10ug" 18 14 FALSE
@ -11658,10 +11658,10 @@
"CLSI 2020" "MIC" "F_CANDD_PRPS" "Candida parapsilosis" 2 "MIF" "Micafungin" "Table 1" 2 8 FALSE
"CLSI 2020" "DISK" "F_CANDD_TRPC" "Candida tropicalis" 2 "MIF" "Micafungin" "Table 1" 22 19 FALSE
"CLSI 2020" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "MIF" "Micafungin" "Table 1" 0.25 1 FALSE
"CLSI 2020" "DISK" "F_MYRZY_GLLR" "Meyerozyma guilliermondii" 2 "MIF" "Micafungin" "Table 1" 16 13 FALSE
"CLSI 2020" "MIC" "F_MYRZY_GLLR" "Meyerozyma guilliermondii" 2 "MIF" "Micafungin" "Table 1" 2 8 FALSE
"CLSI 2020" "DISK" "F_PICHI" "Pichia" 3 "MIF" "Micafungin" "Table 1" 22 19 FALSE
"CLSI 2020" "MIC" "F_PICHI" "Pichia" 3 "MIF" "Micafungin" "Table 1" 0.25 1 FALSE
"CLSI 2020" "DISK" "F_MYRZY_GLLR" 2 "MIF" "Micafungin" "Table 1" 16 13 FALSE
"CLSI 2020" "MIC" "F_MYRZY_GLLR" 2 "MIF" "Micafungin" "Table 1" 2 8 FALSE
"CLSI 2020" "DISK" "F_PICHI" "Pithomyces djbhatii" 3 "MIF" "Micafungin" "Table 1" 22 19 FALSE
"CLSI 2020" "MIC" "F_PICHI" "Pithomyces djbhatii" 3 "MIF" "Micafungin" "Table 1" 0.25 1 FALSE
"CLSI 2020" "DISK" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "MNO" "Minocycline" "Table 2A" "30ug" 16 12 FALSE
"CLSI 2020" "MIC" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "MNO" "Minocycline" "Table 2A" 4 16 FALSE
"CLSI 2020" "DISK" "B_ACNTB" "Acinetobacter" 3 "MNO" "Minocycline" "Table 2B-2" "30ug" 16 12 FALSE
@ -12038,8 +12038,8 @@
"CLSI 2020" "MIC" "F_CANDD_PRPS" "Candida parapsilosis" 2 "VOR" "Voriconazole" "Table 1" 0.125 1 FALSE
"CLSI 2020" "DISK" "F_CANDD_TRPC" "Candida tropicalis" 2 "VOR" "Voriconazole" "Table 1" 17 14 FALSE
"CLSI 2020" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "VOR" "Voriconazole" "Table 1" 0.125 1 FALSE
"CLSI 2020" "DISK" "F_PICHI" "Pichia" 3 "VOR" "Voriconazole" "Table 1" 15 12 FALSE
"CLSI 2020" "MIC" "F_PICHI" "Pichia" 3 "VOR" "Voriconazole" "Table 1" 0.5 2 FALSE
"CLSI 2020" "DISK" "F_PICHI" "Pithomyces djbhatii" 3 "VOR" "Voriconazole" "Table 1" 15 12 FALSE
"CLSI 2020" "MIC" "F_PICHI" "Pithomyces djbhatii" 3 "VOR" "Voriconazole" "Table 1" 0.5 2 FALSE
"CLSI 2019" "DISK" "B_AERMN" "Aeromonas" 3 "AMC" "Amoxicillin/clavulanic acid" "M45 Table 2" "20ug" 18 13 FALSE
"CLSI 2019" "MIC" "B_AGGRG" "Aggregatibacter" 3 "AMC" "Amoxicillin/clavulanic acid" "M45 Table 9" 4 8 FALSE
"CLSI 2019" "MIC" "B_BRKHL_PSDM" "Burkholderia pseudomallei" 2 "AMC" "Amoxicillin/clavulanic acid" "M45 Table 21" 8 32 FALSE
@ -12098,8 +12098,8 @@
"CLSI 2019" "MIC" "F_CANDD_KRUS" "Candida krusei" 2 "ANI" "Anidulafungin" "Table 1" 0.25 1 FALSE
"CLSI 2019" "MIC" "F_CANDD_PRPS" "Candida parapsilosis" 2 "ANI" "Anidulafungin" "Table 1" 2 8 FALSE
"CLSI 2019" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "ANI" "Anidulafungin" "Table 1" 0.25 1 FALSE
"CLSI 2019" "MIC" "F_MYRZY_GLLR" "Meyerozyma guilliermondii" 2 "ANI" "Anidulafungin" "Table 1" 2 8 FALSE
"CLSI 2019" "MIC" "F_PICHI" "Pichia" 3 "ANI" "Anidulafungin" "Table 1" 0.25 1 FALSE
"CLSI 2019" "MIC" "F_MYRZY_GLLR" 2 "ANI" "Anidulafungin" "Table 1" 2 8 FALSE
"CLSI 2019" "MIC" "F_PICHI" "Pithomyces djbhatii" 3 "ANI" "Anidulafungin" "Table 1" 0.25 1 FALSE
"CLSI 2019" "DISK" "B_AERMN" "Aeromonas" 3 "ATM" "Aztreonam" "M45 Table 2" "30ug" 21 17 FALSE
"CLSI 2019" "MIC" "B_AERMN" "Aeromonas" 3 "ATM" "Aztreonam" "M45 Table 3" 4 16 FALSE
"CLSI 2019" "MIC" "B_GRAMN" "(unknown Gram-negatives)" 2 "ATM" "Aztreonam" "Table 2B-5" 8 32 FALSE
@ -12140,10 +12140,10 @@
"CLSI 2019" "MIC" "F_CANDD_PRPS" "Candida parapsilosis" 2 "CAS" "Caspofungin" "Table 1" 2 8 FALSE
"CLSI 2019" "DISK" "F_CANDD_TRPC" "Candida tropicalis" 2 "CAS" "Caspofungin" "Table 1" 17 14 FALSE
"CLSI 2019" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "CAS" "Caspofungin" "Table 1" 0.25 1 FALSE
"CLSI 2019" "DISK" "F_MYRZY_GLLR" "Meyerozyma guilliermondii" 2 "CAS" "Caspofungin" "Table 1" 13 10 FALSE
"CLSI 2019" "MIC" "F_MYRZY_GLLR" "Meyerozyma guilliermondii" 2 "CAS" "Caspofungin" "Table 1" 2 8 FALSE
"CLSI 2019" "DISK" "F_PICHI" "Pichia" 3 "CAS" "Caspofungin" "Table 1" 17 14 FALSE
"CLSI 2019" "MIC" "F_PICHI" "Pichia" 3 "CAS" "Caspofungin" "Table 1" 0.25 1 FALSE
"CLSI 2019" "DISK" "F_MYRZY_GLLR" 2 "CAS" "Caspofungin" "Table 1" 13 10 FALSE
"CLSI 2019" "MIC" "F_MYRZY_GLLR" 2 "CAS" "Caspofungin" "Table 1" 2 8 FALSE
"CLSI 2019" "DISK" "F_PICHI" "Pithomyces djbhatii" 3 "CAS" "Caspofungin" "Table 1" 17 14 FALSE
"CLSI 2019" "MIC" "F_PICHI" "Pithomyces djbhatii" 3 "CAS" "Caspofungin" "Table 1" 0.25 1 FALSE
"CLSI 2019" "DISK" "B_HMPHL" "Haemophilus" 3 "CAT" "Cefetamet" "Table 2E" "10ug" 18 14 FALSE
"CLSI 2019" "MIC" "B_HMPHL" "Haemophilus" 3 "CAT" "Cefetamet" "Table 2E" 4 16 FALSE
"CLSI 2019" "DISK" "B_ACNTB" "Acinetobacter" 3 "CAZ" "Ceftazidime" "Table 2B-2" "30ug" 18 14 FALSE
@ -12740,10 +12740,10 @@
"CLSI 2019" "MIC" "F_CANDD_PRPS" "Candida parapsilosis" 2 "MIF" "Micafungin" "Table 1" 2 8 FALSE
"CLSI 2019" "DISK" "F_CANDD_TRPC" "Candida tropicalis" 2 "MIF" "Micafungin" "Table 1" 22 19 FALSE
"CLSI 2019" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "MIF" "Micafungin" "Table 1" 0.25 1 FALSE
"CLSI 2019" "DISK" "F_MYRZY_GLLR" "Meyerozyma guilliermondii" 2 "MIF" "Micafungin" "Table 1" 16 13 FALSE
"CLSI 2019" "MIC" "F_MYRZY_GLLR" "Meyerozyma guilliermondii" 2 "MIF" "Micafungin" "Table 1" 2 8 FALSE
"CLSI 2019" "DISK" "F_PICHI" "Pichia" 3 "MIF" "Micafungin" "Table 1" 22 19 FALSE
"CLSI 2019" "MIC" "F_PICHI" "Pichia" 3 "MIF" "Micafungin" "Table 1" 0.25 1 FALSE
"CLSI 2019" "DISK" "F_MYRZY_GLLR" 2 "MIF" "Micafungin" "Table 1" 16 13 FALSE
"CLSI 2019" "MIC" "F_MYRZY_GLLR" 2 "MIF" "Micafungin" "Table 1" 2 8 FALSE
"CLSI 2019" "DISK" "F_PICHI" "Pithomyces djbhatii" 3 "MIF" "Micafungin" "Table 1" 22 19 FALSE
"CLSI 2019" "MIC" "F_PICHI" "Pithomyces djbhatii" 3 "MIF" "Micafungin" "Table 1" 0.25 1 FALSE
"CLSI 2019" "DISK" "B_ACNTB" "Acinetobacter" 3 "MNO" "Minocycline" "Table 2B-2" "30ug" 16 12 FALSE
"CLSI 2019" "MIC" "B_ACNTB" "Acinetobacter" 3 "MNO" "Minocycline" "Table 2B-2" 4 16 FALSE
"CLSI 2019" "DISK" "B_BRKHL_CEPC" "Burkholderia cepacia" 2 "MNO" "Minocycline" "Table 2B-3" "30ug" 19 14 FALSE
@ -13074,8 +13074,8 @@
"CLSI 2019" "MIC" "F_CANDD_PRPS" "Candida parapsilosis" 2 "VOR" "Voriconazole" "Table 1" 0.125 1 FALSE
"CLSI 2019" "DISK" "F_CANDD_TRPC" "Candida tropicalis" 2 "VOR" "Voriconazole" "Table 1" 17 14 FALSE
"CLSI 2019" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "VOR" "Voriconazole" "Table 1" 0.125 1 FALSE
"CLSI 2019" "DISK" "F_PICHI" "Pichia" 3 "VOR" "Voriconazole" "Table 1" 15 12 FALSE
"CLSI 2019" "MIC" "F_PICHI" "Pichia" 3 "VOR" "Voriconazole" "Table 1" 0.5 2 FALSE
"CLSI 2019" "DISK" "F_PICHI" "Pithomyces djbhatii" 3 "VOR" "Voriconazole" "Table 1" 15 12 FALSE
"CLSI 2019" "MIC" "F_PICHI" "Pithomyces djbhatii" 3 "VOR" "Voriconazole" "Table 1" 0.5 2 FALSE
"CLSI 2018" "DISK" "B_AERMN" "Aeromonas" 3 "AMC" "Amoxicillin/clavulanic acid" "M45 Table 2" "20ug" 18 13 FALSE
"CLSI 2018" "MIC" "B_AERMN" "Aeromonas" 3 "AMC" "Amoxicillin/clavulanic acid" "M45 Table 2" 8 32 FALSE
"CLSI 2018" "MIC" "B_AGGRG" "Aggregatibacter" 3 "AMC" "Amoxicillin/clavulanic acid" "M45 Table 7" 4 8 FALSE

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@ -4,7 +4,7 @@
The `AMR` package is a [free and open-source](#copyright) R package with [zero dependencies](https://en.wikipedia.org/wiki/Dependency_hell) to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. **Our aim is to provide a standard** for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. The rationale behind this package was scientifically described in the Journal of Statistical Software (Volume xx, Issue xx; [DOI 10.18637/jss.v000.i00](https://doi.org/10.18637/jss.v000.i00) *- waiting for copy-editing to finish*).
After installing this package, R knows [**~63,000 distinct microbial species**](./reference/microorganisms.html) and all [**~570 antibiotic, antimycotic and antiviral drugs**](./reference/antibiotics.html) by name and code (including ATC, WHONET/EARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). **It was designed to work in any setting, including those with very limited resources**. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the [University of Groningen](https://www.rug.nl), in collaboration with non-profit organisations [Certe Medical Diagnostics and Advice Foundation](https://www.certe.nl) and [University Medical Center Groningen](https://www.umcg.nl). This R package formed the basis of two PhD theses ([DOI 10.33612/diss.177417131](https://doi.org/10.33612/diss.177417131) and [DOI 10.33612/diss.192486375](https://doi.org/10.33612/diss.192486375)) but is [actively and durably maintained](./news) by two public healthcare organisations in the Netherlands.
After installing this package, R knows [**~49,000 distinct microbial species**](./reference/microorganisms.html) and all [**~570 antibiotic, antimycotic and antiviral drugs**](./reference/antibiotics.html) by name and code (including ATC, WHONET/EARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). **It was designed to work in any setting, including those with very limited resources**. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the [University of Groningen](https://www.rug.nl), in collaboration with non-profit organisations [Certe Medical Diagnostics and Advice Foundation](https://www.certe.nl) and [University Medical Center Groningen](https://www.umcg.nl). This R package formed the basis of two PhD theses ([DOI 10.33612/diss.177417131](https://doi.org/10.33612/diss.177417131) and [DOI 10.33612/diss.192486375](https://doi.org/10.33612/diss.192486375)) but is [actively and durably maintained](./news) by two public healthcare organisations in the Netherlands.
##### Used in 175 countries, translated to 16 languages

2
man/AMR.Rd
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@ -9,7 +9,7 @@ Welcome to the \code{AMR} package.
\details{
\code{AMR} is a free, open-source and independent \R package to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. Our aim is to provide a standard for clean and reproducible antimicrobial resistance data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting.
After installing this package, \R knows ~63,000 distinct microbial species and all ~570 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-NET, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.
After installing this package, \R knows ~49,000 distinct microbial species and all ~570 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-NET, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.
This package is fully independent of any other \R package and works on Windows, macOS and Linux with all versions of \R since R-3.0.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice and University Medical Center Groningen. This \R package is actively maintained and free software; you can freely use and distribute it for both personal and commercial (but not patent) purposes under the terms of the GNU General Public License version 2.0 (GPL-2), as published by the Free Software Foundation.

10
man/as.mo.Rd
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@ -4,10 +4,8 @@
\alias{as.mo}
\alias{mo}
\alias{is.mo}
\alias{mo_failures}
\alias{mo_uncertainties}
\alias{mo_reset_session}
\alias{mo_renamed}
\title{Transform Input to a Microorganism Code}
\usage{
as.mo(
@ -26,13 +24,9 @@ as.mo(
is.mo(x)
mo_failures()
mo_uncertainties()
mo_reset_session()
mo_renamed()
}
\arguments{
\item{x}{a \link{character} vector or a \link{data.frame} with one or two columns}
@ -65,7 +59,7 @@ This excludes enterococci at default (who are in group D), use \code{Lancefield
A \link{character} \link{vector} with additional class \code{\link{mo}}
}
\description{
Use this function to determine a valid microorganism code (\code{\link{mo}}). Determination is done using intelligent rules and the complete taxonomic kingdoms Animalia, Archaea, Bacteria, Plantae and Protozoa, and most microbial species from the kingdom Fungi (see \emph{Source}). The input can be almost anything: a full name (like \code{"Staphylococcus aureus"}), an abbreviated name (such as \code{"S. aureus"}), an abbreviation known in the field (such as \code{"MRSA"}), or just a genus. See \emph{Examples}.
Use this function to determine a valid microorganism code (\code{\link{mo}}). Determination is done using intelligent rules and the complete taxonomic kingdoms Animalia, Archaea, Bacteria and Protozoa, and most microbial species from the kingdom Fungi (see \emph{Source}). The input can be almost anything: a full name (like \code{"Staphylococcus aureus"}), an abbreviated name (such as \code{"S. aureus"}), an abbreviation known in the field (such as \code{"MRSA"}), or just a genus. See \emph{Examples}.
}
\details{
\subsection{General Info}{
@ -168,7 +162,7 @@ The grouping into human pathogenic prevalence (\eqn{p}) is based on experience f
\strong{Group 1} (most prevalent microorganisms) consists of all microorganisms where the taxonomic class is Gammaproteobacteria or where the taxonomic genus is \emph{Enterococcus}, \emph{Staphylococcus} or \emph{Streptococcus}. This group consequently contains all common Gram-negative bacteria, such as \emph{Pseudomonas} and \emph{Legionella} and all species within the order Enterobacterales.
\strong{Group 2} consists of all microorganisms where the taxonomic phylum is Proteobacteria, Firmicutes, Actinobacteria or Sarcomastigophora, or where the taxonomic genus is \emph{Absidia}, \emph{Acanthamoeba}, \emph{Acholeplasma}, \emph{Acremonium}, \emph{Actinotignum}, \emph{Aedes}, \emph{Alistipes}, \emph{Alloprevotella}, \emph{Alternaria}, \emph{Amoeba}, \emph{Anaerosalibacter}, \emph{Ancylostoma}, \emph{Angiostrongylus}, \emph{Anisakis}, \emph{Anopheles}, \emph{Apophysomyces}, \emph{Arachnia}, \emph{Aspergillus}, \emph{Aureobasidium}, \emph{Bacteroides}, \emph{Basidiobolus}, \emph{Beauveria}, \emph{Bergeyella}, \emph{Blastocystis}, \emph{Blastomyces}, \emph{Borrelia}, \emph{Brachyspira}, \emph{Branhamella}, \emph{Butyricimonas}, \emph{Candida}, \emph{Capillaria}, \emph{Capnocytophaga}, \emph{Catabacter}, \emph{Cetobacterium}, \emph{Chaetomium}, \emph{Chlamydia}, \emph{Chlamydophila}, \emph{Chryseobacterium}, \emph{Chrysonilia}, \emph{Cladophialophora}, \emph{Cladosporium}, \emph{Conidiobolus}, \emph{Contracaecum}, \emph{Cordylobia}, \emph{Cryptococcus}, \emph{Curvularia}, \emph{Deinococcus}, \emph{Demodex}, \emph{Dermatobia}, \emph{Dientamoeba}, \emph{Diphyllobothrium}, \emph{Dirofilaria}, \emph{Dysgonomonas}, \emph{Echinostoma}, \emph{Elizabethkingia}, \emph{Empedobacter}, \emph{Entamoeba}, \emph{Enterobius}, \emph{Exophiala}, \emph{Exserohilum}, \emph{Fasciola}, \emph{Flavobacterium}, \emph{Fonsecaea}, \emph{Fusarium}, \emph{Fusobacterium}, \emph{Giardia}, \emph{Haloarcula}, \emph{Halobacterium}, \emph{Halococcus}, \emph{Hendersonula}, \emph{Heterophyes}, \emph{Histomonas}, \emph{Histoplasma}, \emph{Hymenolepis}, \emph{Hypomyces}, \emph{Hysterothylacium}, \emph{Leishmania}, \emph{Lelliottia}, \emph{Leptosphaeria}, \emph{Leptotrichia}, \emph{Lucilia}, \emph{Lumbricus}, \emph{Malassezia}, \emph{Malbranchea}, \emph{Metagonimus}, \emph{Microsporidium}, \emph{Microsporum}, \emph{Mortierella}, \emph{Mucor}, \emph{Mycocentrospora}, \emph{Mycoplasma}, \emph{Myroides}, \emph{Necator}, \emph{Nectria}, \emph{Ochroconis}, \emph{Odoribacter}, \emph{Oesophagostomum}, \emph{Oidiodendron}, \emph{Opisthorchis}, \emph{Ornithobacterium}, \emph{Parabacteroides}, \emph{Pediculus}, \emph{Pedobacter}, \emph{Phlebotomus}, \emph{Phocaeicola}, \emph{Phocanema}, \emph{Phoma}, \emph{Piedraia}, \emph{Pithomyces}, \emph{Pityrosporum}, \emph{Porphyromonas}, \emph{Prevotella}, \emph{Pseudallescheria}, \emph{Pseudoterranova}, \emph{Pulex}, \emph{Rhizomucor}, \emph{Rhizopus}, \emph{Rhodotorula}, \emph{Riemerella}, \emph{Saccharomyces}, \emph{Sarcoptes}, \emph{Scolecobasidium}, \emph{Scopulariopsis}, \emph{Scytalidium}, \emph{Sphingobacterium}, \emph{Spirometra}, \emph{Spiroplasma}, \emph{Sporobolomyces}, \emph{Stachybotrys}, \emph{Streptobacillus}, \emph{Strongyloides}, \emph{Syngamus}, \emph{Taenia}, \emph{Tannerella}, \emph{Tenacibaculum}, \emph{Terrimonas}, \emph{Toxocara}, \emph{Treponema}, \emph{Trichinella}, \emph{Trichobilharzia}, \emph{Trichoderma}, \emph{Trichomonas}, \emph{Trichophyton}, \emph{Trichosporon}, \emph{Trichostrongylus}, \emph{Trichuris}, \emph{Tritirachium}, \emph{Trombicula}, \emph{Trypanosoma}, \emph{Tunga}, \emph{Ureaplasma}, \emph{Victivallis}, \emph{Wautersiella}, \emph{Weeksella} or \emph{Wuchereria}.
\strong{Group 2} consists of all microorganisms where the taxonomic phylum is Proteobacteria, Firmicutes, Actinobacteria or Sarcomastigophora, or where the taxonomic genus is \emph{Absidia}, \emph{Acanthamoeba}, \emph{Acholeplasma}, \emph{Acremonium}, \emph{Actinotignum}, \emph{Aedes}, \emph{Alistipes}, \emph{Alloprevotella}, \emph{Alternaria}, \emph{Amoeba}, \emph{Anaerosalibacter}, \emph{Ancylostoma}, \emph{Angiostrongylus}, \emph{Anisakis}, \emph{Anopheles}, \emph{Apophysomyces}, \emph{Arachnia}, \emph{Aspergillus}, \emph{Aureobasidium}, \emph{Bacteroides}, \emph{Basidiobolus}, \emph{Beauveria}, \emph{Bergeyella}, \emph{Blastocystis}, \emph{Blastomyces}, \emph{Borrelia}, \emph{Brachyspira}, \emph{Branhamella}, \emph{Butyricimonas}, \emph{Candida}, \emph{Capillaria}, \emph{Capnocytophaga}, \emph{Catabacter}, \emph{Cetobacterium}, \emph{Chaetomium}, \emph{Chlamydia}, \emph{Chlamydophila}, \emph{Chryseobacterium}, \emph{Chrysonilia}, \emph{Cladophialophora}, \emph{Cladosporium}, \emph{Conidiobolus}, \emph{Contracaecum}, \emph{Cordylobia}, \emph{Cryptococcus}, \emph{Curvularia}, \emph{Deinococcus}, \emph{Demodex}, \emph{Dermatobia}, \emph{Dientamoeba}, \emph{Diphyllobothrium}, \emph{Dirofilaria}, \emph{Dysgonomonas}, \emph{Echinostoma}, \emph{Elizabethkingia}, \emph{Empedobacter}, \emph{Entamoeba}, \emph{Enterobius}, \emph{Exophiala}, \emph{Exserohilum}, \emph{Fasciola}, \emph{Flavobacterium}, \emph{Fonsecaea}, \emph{Fusarium}, \emph{Fusobacterium}, \emph{Giardia}, \emph{Haloarcula}, \emph{Halobacterium}, \emph{Halococcus}, \emph{Hendersonula}, \emph{Heterophyes}, \emph{Histomonas}, \emph{Histoplasma}, \emph{Hymenolepis}, \emph{Hypomyces}, \emph{Hysterothylacium}, \emph{Leishmania}, \emph{Lelliottia}, \emph{Leptosphaeria}, \emph{Leptotrichia}, \emph{Lucilia}, \emph{Lumbricus}, \emph{Malassezia}, \emph{Malbranchea}, \emph{Metagonimus}, \emph{Microsporidium}, \emph{Microsporum}, \emph{Mortierella}, \emph{Mucor}, \emph{Mycocentrospora}, \emph{Mycoplasma}, \emph{Myroides}, \emph{Necator}, \emph{Nectria}, \emph{Ochroconis}, \emph{Odoribacter}, \emph{Oesophagostomum}, \emph{Oidiodendron}, \emph{Opisthorchis}, \emph{Ornithobacterium}, \emph{Parabacteroides}, \emph{Pediculus}, \emph{Pedobacter}, \emph{Phlebotomus}, \emph{Phocaeicola}, \emph{Phocanema}, \emph{Phoma}, \emph{Piedraia}, \emph{Pithomyces}, \emph{Pityrosporum}, \emph{Pneumocystis}, \emph{Porphyromonas}, \emph{Prevotella}, \emph{Pseudallescheria}, \emph{Pseudoterranova}, \emph{Pulex}, \emph{Rhizomucor}, \emph{Rhizopus}, \emph{Rhodotorula}, \emph{Riemerella}, \emph{Saccharomyces}, \emph{Sarcoptes}, \emph{Scolecobasidium}, \emph{Scopulariopsis}, \emph{Scytalidium}, \emph{Sphingobacterium}, \emph{Spirometra}, \emph{Spiroplasma}, \emph{Sporobolomyces}, \emph{Stachybotrys}, \emph{Streptobacillus}, \emph{Strongyloides}, \emph{Syngamus}, \emph{Taenia}, \emph{Tannerella}, \emph{Tenacibaculum}, \emph{Terrimonas}, \emph{Toxocara}, \emph{Treponema}, \emph{Trichinella}, \emph{Trichobilharzia}, \emph{Trichoderma}, \emph{Trichomonas}, \emph{Trichophyton}, \emph{Trichosporon}, \emph{Trichostrongylus}, \emph{Trichuris}, \emph{Tritirachium}, \emph{Trombicula}, \emph{Trypanosoma}, \emph{Tunga}, \emph{Ureaplasma}, \emph{Victivallis}, \emph{Wautersiella}, \emph{Weeksella} or \emph{Wuchereria}.
\strong{Group 3} consists of all other microorganisms.

18
man/microorganisms.Rd
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@ -3,9 +3,9 @@
\docType{data}
\name{microorganisms}
\alias{microorganisms}
\title{Data Set with 63,472 Microorganisms}
\title{Data Set with 48,651 Microorganisms}
\format{
A \link[tibble:tibble]{tibble} with 63,472 observations and 22 variables:
A \link[tibble:tibble]{tibble} with 48,651 observations and 22 variables:
\itemize{
\item \code{mo}\cr ID of microorganism as used by this package
\item \code{fullname}\cr Full name, like \code{"Escherichia coli"}. For the taxonomic ranks genus, species and subspecies, this is the 'pasted' text of genus, species, and subspecies. For all taxonomic ranks higher than genus, this is the name of the taxon.
@ -35,7 +35,7 @@ A \link[tibble:tibble]{tibble} with 63,472 observations and 22 variables:
microorganisms
}
\description{
A data set containing the full microbial taxonomy (\strong{last updated: 12 September, 2022}) of six kingdoms from the List of Prokaryotic names with Standing in Nomenclature (LPSN) and the Global Biodiversity Information Facility (GBIF). This data set is the backbone of this \code{AMR} package. MO codes can be looked up using \code{\link[=as.mo]{as.mo()}}.
A data set containing the full microbial taxonomy (\strong{last updated: 12 September, 2022}) of five kingdoms from the List of Prokaryotic names with Standing in Nomenclature (LPSN) and the Global Biodiversity Information Facility (GBIF). This data set is the backbone of this \code{AMR} package. MO codes can be looked up using \code{\link[=as.mo]{as.mo()}}.
}
\details{
Please note that entries are only based on the List of Prokaryotic names with Standing in Nomenclature (LPSN) and the Global Biodiversity Information Facility (GBIF) (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.
@ -46,14 +46,14 @@ For example, \emph{Staphylococcus pettenkoferi} was described for the first time
Included taxonomic data are:
\itemize{
\item All ~42,000 (sub)species from the kingdoms of Archaea, Bacteria and Protozoa
\item All ~16,000 (sub)species from ~30 relevant orders of the kingdom of Fungi. The kingdom of Fungi is a very large taxon with almost 300,000 different (sub)species, of which most are not microbial (but rather macroscopic, like mushrooms). Because of this, not all fungi fit the scope of this package and including everything would tremendously slow down our algorithms too. By only including relevant taxonomic orders, the most relevant fungi are covered (such as all species of \emph{Aspergillus}, \emph{Candida}, \emph{Cryptococcus}, \emph{Histplasma}, \emph{Pneumocystis}, \emph{Saccharomyces} and \emph{Trichophyton}).
\item All ~4,200 (sub)species from ~50 other relevant genera from the kingdom of Animalia (such as \emph{Strongyloides} and \emph{Taenia})
\item All ~60 (sub)species from ~50 other relevant genera from the kingdom of Animalia (such as \emph{Strongyloides} and \emph{Taenia})
\item All ~14,000 previously accepted names of all included (sub)species (these were taxonomically renamed)
\item All ~34,000 (sub)species from the kingdoms of Archaea and Bacteria
\item ~7,200 (sub)species from the kingdom of Fungi. The kingdom of Fungi is a very large taxon with almost 300,000 different (sub)species, of which most are not microbial (but rather macroscopic, like mushrooms). Because of this, not all fungi fit the scope of this package. Only relevant fungi are covered (such as all species of \emph{Aspergillus}, \emph{Candida}, \emph{Cryptococcus}, \emph{Histoplasma}, \emph{Pneumocystis}, \emph{Saccharomyces} and \emph{Trichophyton}).
\item ~4,900 (sub)species from the kingdom of Protozoa
\item ~1,500 (sub)species from ~50 other relevant genera from the kingdom of Animalia (such as \emph{Strongyloides} and \emph{Taenia})
\item All ~9,400 previously accepted names of all included (sub)species (these were taxonomically renamed)
\item The complete taxonomic tree of all included (sub)species: from kingdom to subspecies
\item The identifier of the parent taxons
\item The responsible author(s) and year of scientific publication
\item The year and first author of the related scientific publication
}
\subsection{Manual additions}{

2
man/mo_matching_score.Rd
View File

@ -34,7 +34,7 @@ The grouping into human pathogenic prevalence (\eqn{p}) is based on experience f
\strong{Group 1} (most prevalent microorganisms) consists of all microorganisms where the taxonomic class is Gammaproteobacteria or where the taxonomic genus is \emph{Enterococcus}, \emph{Staphylococcus} or \emph{Streptococcus}. This group consequently contains all common Gram-negative bacteria, such as \emph{Pseudomonas} and \emph{Legionella} and all species within the order Enterobacterales.
\strong{Group 2} consists of all microorganisms where the taxonomic phylum is Proteobacteria, Firmicutes, Actinobacteria or Sarcomastigophora, or where the taxonomic genus is \emph{Absidia}, \emph{Acanthamoeba}, \emph{Acholeplasma}, \emph{Acremonium}, \emph{Actinotignum}, \emph{Aedes}, \emph{Alistipes}, \emph{Alloprevotella}, \emph{Alternaria}, \emph{Amoeba}, \emph{Anaerosalibacter}, \emph{Ancylostoma}, \emph{Angiostrongylus}, \emph{Anisakis}, \emph{Anopheles}, \emph{Apophysomyces}, \emph{Arachnia}, \emph{Aspergillus}, \emph{Aureobasidium}, \emph{Bacteroides}, \emph{Basidiobolus}, \emph{Beauveria}, \emph{Bergeyella}, \emph{Blastocystis}, \emph{Blastomyces}, \emph{Borrelia}, \emph{Brachyspira}, \emph{Branhamella}, \emph{Butyricimonas}, \emph{Candida}, \emph{Capillaria}, \emph{Capnocytophaga}, \emph{Catabacter}, \emph{Cetobacterium}, \emph{Chaetomium}, \emph{Chlamydia}, \emph{Chlamydophila}, \emph{Chryseobacterium}, \emph{Chrysonilia}, \emph{Cladophialophora}, \emph{Cladosporium}, \emph{Conidiobolus}, \emph{Contracaecum}, \emph{Cordylobia}, \emph{Cryptococcus}, \emph{Curvularia}, \emph{Deinococcus}, \emph{Demodex}, \emph{Dermatobia}, \emph{Dientamoeba}, \emph{Diphyllobothrium}, \emph{Dirofilaria}, \emph{Dysgonomonas}, \emph{Echinostoma}, \emph{Elizabethkingia}, \emph{Empedobacter}, \emph{Entamoeba}, \emph{Enterobius}, \emph{Exophiala}, \emph{Exserohilum}, \emph{Fasciola}, \emph{Flavobacterium}, \emph{Fonsecaea}, \emph{Fusarium}, \emph{Fusobacterium}, \emph{Giardia}, \emph{Haloarcula}, \emph{Halobacterium}, \emph{Halococcus}, \emph{Hendersonula}, \emph{Heterophyes}, \emph{Histomonas}, \emph{Histoplasma}, \emph{Hymenolepis}, \emph{Hypomyces}, \emph{Hysterothylacium}, \emph{Leishmania}, \emph{Lelliottia}, \emph{Leptosphaeria}, \emph{Leptotrichia}, \emph{Lucilia}, \emph{Lumbricus}, \emph{Malassezia}, \emph{Malbranchea}, \emph{Metagonimus}, \emph{Microsporidium}, \emph{Microsporum}, \emph{Mortierella}, \emph{Mucor}, \emph{Mycocentrospora}, \emph{Mycoplasma}, \emph{Myroides}, \emph{Necator}, \emph{Nectria}, \emph{Ochroconis}, \emph{Odoribacter}, \emph{Oesophagostomum}, \emph{Oidiodendron}, \emph{Opisthorchis}, \emph{Ornithobacterium}, \emph{Parabacteroides}, \emph{Pediculus}, \emph{Pedobacter}, \emph{Phlebotomus}, \emph{Phocaeicola}, \emph{Phocanema}, \emph{Phoma}, \emph{Piedraia}, \emph{Pithomyces}, \emph{Pityrosporum}, \emph{Porphyromonas}, \emph{Prevotella}, \emph{Pseudallescheria}, \emph{Pseudoterranova}, \emph{Pulex}, \emph{Rhizomucor}, \emph{Rhizopus}, \emph{Rhodotorula}, \emph{Riemerella}, \emph{Saccharomyces}, \emph{Sarcoptes}, \emph{Scolecobasidium}, \emph{Scopulariopsis}, \emph{Scytalidium}, \emph{Sphingobacterium}, \emph{Spirometra}, \emph{Spiroplasma}, \emph{Sporobolomyces}, \emph{Stachybotrys}, \emph{Streptobacillus}, \emph{Strongyloides}, \emph{Syngamus}, \emph{Taenia}, \emph{Tannerella}, \emph{Tenacibaculum}, \emph{Terrimonas}, \emph{Toxocara}, \emph{Treponema}, \emph{Trichinella}, \emph{Trichobilharzia}, \emph{Trichoderma}, \emph{Trichomonas}, \emph{Trichophyton}, \emph{Trichosporon}, \emph{Trichostrongylus}, \emph{Trichuris}, \emph{Tritirachium}, \emph{Trombicula}, \emph{Trypanosoma}, \emph{Tunga}, \emph{Ureaplasma}, \emph{Victivallis}, \emph{Wautersiella}, \emph{Weeksella} or \emph{Wuchereria}.
\strong{Group 2} consists of all microorganisms where the taxonomic phylum is Proteobacteria, Firmicutes, Actinobacteria or Sarcomastigophora, or where the taxonomic genus is \emph{Absidia}, \emph{Acanthamoeba}, \emph{Acholeplasma}, \emph{Acremonium}, \emph{Actinotignum}, \emph{Aedes}, \emph{Alistipes}, \emph{Alloprevotella}, \emph{Alternaria}, \emph{Amoeba}, \emph{Anaerosalibacter}, \emph{Ancylostoma}, \emph{Angiostrongylus}, \emph{Anisakis}, \emph{Anopheles}, \emph{Apophysomyces}, \emph{Arachnia}, \emph{Aspergillus}, \emph{Aureobasidium}, \emph{Bacteroides}, \emph{Basidiobolus}, \emph{Beauveria}, \emph{Bergeyella}, \emph{Blastocystis}, \emph{Blastomyces}, \emph{Borrelia}, \emph{Brachyspira}, \emph{Branhamella}, \emph{Butyricimonas}, \emph{Candida}, \emph{Capillaria}, \emph{Capnocytophaga}, \emph{Catabacter}, \emph{Cetobacterium}, \emph{Chaetomium}, \emph{Chlamydia}, \emph{Chlamydophila}, \emph{Chryseobacterium}, \emph{Chrysonilia}, \emph{Cladophialophora}, \emph{Cladosporium}, \emph{Conidiobolus}, \emph{Contracaecum}, \emph{Cordylobia}, \emph{Cryptococcus}, \emph{Curvularia}, \emph{Deinococcus}, \emph{Demodex}, \emph{Dermatobia}, \emph{Dientamoeba}, \emph{Diphyllobothrium}, \emph{Dirofilaria}, \emph{Dysgonomonas}, \emph{Echinostoma}, \emph{Elizabethkingia}, \emph{Empedobacter}, \emph{Entamoeba}, \emph{Enterobius}, \emph{Exophiala}, \emph{Exserohilum}, \emph{Fasciola}, \emph{Flavobacterium}, \emph{Fonsecaea}, \emph{Fusarium}, \emph{Fusobacterium}, \emph{Giardia}, \emph{Haloarcula}, \emph{Halobacterium}, \emph{Halococcus}, \emph{Hendersonula}, \emph{Heterophyes}, \emph{Histomonas}, \emph{Histoplasma}, \emph{Hymenolepis}, \emph{Hypomyces}, \emph{Hysterothylacium}, \emph{Leishmania}, \emph{Lelliottia}, \emph{Leptosphaeria}, \emph{Leptotrichia}, \emph{Lucilia}, \emph{Lumbricus}, \emph{Malassezia}, \emph{Malbranchea}, \emph{Metagonimus}, \emph{Microsporidium}, \emph{Microsporum}, \emph{Mortierella}, \emph{Mucor}, \emph{Mycocentrospora}, \emph{Mycoplasma}, \emph{Myroides}, \emph{Necator}, \emph{Nectria}, \emph{Ochroconis}, \emph{Odoribacter}, \emph{Oesophagostomum}, \emph{Oidiodendron}, \emph{Opisthorchis}, \emph{Ornithobacterium}, \emph{Parabacteroides}, \emph{Pediculus}, \emph{Pedobacter}, \emph{Phlebotomus}, \emph{Phocaeicola}, \emph{Phocanema}, \emph{Phoma}, \emph{Piedraia}, \emph{Pithomyces}, \emph{Pityrosporum}, \emph{Pneumocystis}, \emph{Porphyromonas}, \emph{Prevotella}, \emph{Pseudallescheria}, \emph{Pseudoterranova}, \emph{Pulex}, \emph{Rhizomucor}, \emph{Rhizopus}, \emph{Rhodotorula}, \emph{Riemerella}, \emph{Saccharomyces}, \emph{Sarcoptes}, \emph{Scolecobasidium}, \emph{Scopulariopsis}, \emph{Scytalidium}, \emph{Sphingobacterium}, \emph{Spirometra}, \emph{Spiroplasma}, \emph{Sporobolomyces}, \emph{Stachybotrys}, \emph{Streptobacillus}, \emph{Strongyloides}, \emph{Syngamus}, \emph{Taenia}, \emph{Tannerella}, \emph{Tenacibaculum}, \emph{Terrimonas}, \emph{Toxocara}, \emph{Treponema}, \emph{Trichinella}, \emph{Trichobilharzia}, \emph{Trichoderma}, \emph{Trichomonas}, \emph{Trichophyton}, \emph{Trichosporon}, \emph{Trichostrongylus}, \emph{Trichuris}, \emph{Tritirachium}, \emph{Trombicula}, \emph{Trypanosoma}, \emph{Tunga}, \emph{Ureaplasma}, \emph{Victivallis}, \emph{Wautersiella}, \emph{Weeksella} or \emph{Wuchereria}.
\strong{Group 3} consists of all other microorganisms.

2
man/mo_property.Rd
View File

@ -317,7 +317,7 @@ The grouping into human pathogenic prevalence (\eqn{p}) is based on experience f
\strong{Group 1} (most prevalent microorganisms) consists of all microorganisms where the taxonomic class is Gammaproteobacteria or where the taxonomic genus is \emph{Enterococcus}, \emph{Staphylococcus} or \emph{Streptococcus}. This group consequently contains all common Gram-negative bacteria, such as \emph{Pseudomonas} and \emph{Legionella} and all species within the order Enterobacterales.
\strong{Group 2} consists of all microorganisms where the taxonomic phylum is Proteobacteria, Firmicutes, Actinobacteria or Sarcomastigophora, or where the taxonomic genus is \emph{Absidia}, \emph{Acanthamoeba}, \emph{Acholeplasma}, \emph{Acremonium}, \emph{Actinotignum}, \emph{Aedes}, \emph{Alistipes}, \emph{Alloprevotella}, \emph{Alternaria}, \emph{Amoeba}, \emph{Anaerosalibacter}, \emph{Ancylostoma}, \emph{Angiostrongylus}, \emph{Anisakis}, \emph{Anopheles}, \emph{Apophysomyces}, \emph{Arachnia}, \emph{Aspergillus}, \emph{Aureobasidium}, \emph{Bacteroides}, \emph{Basidiobolus}, \emph{Beauveria}, \emph{Bergeyella}, \emph{Blastocystis}, \emph{Blastomyces}, \emph{Borrelia}, \emph{Brachyspira}, \emph{Branhamella}, \emph{Butyricimonas}, \emph{Candida}, \emph{Capillaria}, \emph{Capnocytophaga}, \emph{Catabacter}, \emph{Cetobacterium}, \emph{Chaetomium}, \emph{Chlamydia}, \emph{Chlamydophila}, \emph{Chryseobacterium}, \emph{Chrysonilia}, \emph{Cladophialophora}, \emph{Cladosporium}, \emph{Conidiobolus}, \emph{Contracaecum}, \emph{Cordylobia}, \emph{Cryptococcus}, \emph{Curvularia}, \emph{Deinococcus}, \emph{Demodex}, \emph{Dermatobia}, \emph{Dientamoeba}, \emph{Diphyllobothrium}, \emph{Dirofilaria}, \emph{Dysgonomonas}, \emph{Echinostoma}, \emph{Elizabethkingia}, \emph{Empedobacter}, \emph{Entamoeba}, \emph{Enterobius}, \emph{Exophiala}, \emph{Exserohilum}, \emph{Fasciola}, \emph{Flavobacterium}, \emph{Fonsecaea}, \emph{Fusarium}, \emph{Fusobacterium}, \emph{Giardia}, \emph{Haloarcula}, \emph{Halobacterium}, \emph{Halococcus}, \emph{Hendersonula}, \emph{Heterophyes}, \emph{Histomonas}, \emph{Histoplasma}, \emph{Hymenolepis}, \emph{Hypomyces}, \emph{Hysterothylacium}, \emph{Leishmania}, \emph{Lelliottia}, \emph{Leptosphaeria}, \emph{Leptotrichia}, \emph{Lucilia}, \emph{Lumbricus}, \emph{Malassezia}, \emph{Malbranchea}, \emph{Metagonimus}, \emph{Microsporidium}, \emph{Microsporum}, \emph{Mortierella}, \emph{Mucor}, \emph{Mycocentrospora}, \emph{Mycoplasma}, \emph{Myroides}, \emph{Necator}, \emph{Nectria}, \emph{Ochroconis}, \emph{Odoribacter}, \emph{Oesophagostomum}, \emph{Oidiodendron}, \emph{Opisthorchis}, \emph{Ornithobacterium}, \emph{Parabacteroides}, \emph{Pediculus}, \emph{Pedobacter}, \emph{Phlebotomus}, \emph{Phocaeicola}, \emph{Phocanema}, \emph{Phoma}, \emph{Piedraia}, \emph{Pithomyces}, \emph{Pityrosporum}, \emph{Porphyromonas}, \emph{Prevotella}, \emph{Pseudallescheria}, \emph{Pseudoterranova}, \emph{Pulex}, \emph{Rhizomucor}, \emph{Rhizopus}, \emph{Rhodotorula}, \emph{Riemerella}, \emph{Saccharomyces}, \emph{Sarcoptes}, \emph{Scolecobasidium}, \emph{Scopulariopsis}, \emph{Scytalidium}, \emph{Sphingobacterium}, \emph{Spirometra}, \emph{Spiroplasma}, \emph{Sporobolomyces}, \emph{Stachybotrys}, \emph{Streptobacillus}, \emph{Strongyloides}, \emph{Syngamus}, \emph{Taenia}, \emph{Tannerella}, \emph{Tenacibaculum}, \emph{Terrimonas}, \emph{Toxocara}, \emph{Treponema}, \emph{Trichinella}, \emph{Trichobilharzia}, \emph{Trichoderma}, \emph{Trichomonas}, \emph{Trichophyton}, \emph{Trichosporon}, \emph{Trichostrongylus}, \emph{Trichuris}, \emph{Tritirachium}, \emph{Trombicula}, \emph{Trypanosoma}, \emph{Tunga}, \emph{Ureaplasma}, \emph{Victivallis}, \emph{Wautersiella}, \emph{Weeksella} or \emph{Wuchereria}.
\strong{Group 2} consists of all microorganisms where the taxonomic phylum is Proteobacteria, Firmicutes, Actinobacteria or Sarcomastigophora, or where the taxonomic genus is \emph{Absidia}, \emph{Acanthamoeba}, \emph{Acholeplasma}, \emph{Acremonium}, \emph{Actinotignum}, \emph{Aedes}, \emph{Alistipes}, \emph{Alloprevotella}, \emph{Alternaria}, \emph{Amoeba}, \emph{Anaerosalibacter}, \emph{Ancylostoma}, \emph{Angiostrongylus}, \emph{Anisakis}, \emph{Anopheles}, \emph{Apophysomyces}, \emph{Arachnia}, \emph{Aspergillus}, \emph{Aureobasidium}, \emph{Bacteroides}, \emph{Basidiobolus}, \emph{Beauveria}, \emph{Bergeyella}, \emph{Blastocystis}, \emph{Blastomyces}, \emph{Borrelia}, \emph{Brachyspira}, \emph{Branhamella}, \emph{Butyricimonas}, \emph{Candida}, \emph{Capillaria}, \emph{Capnocytophaga}, \emph{Catabacter}, \emph{Cetobacterium}, \emph{Chaetomium}, \emph{Chlamydia}, \emph{Chlamydophila}, \emph{Chryseobacterium}, \emph{Chrysonilia}, \emph{Cladophialophora}, \emph{Cladosporium}, \emph{Conidiobolus}, \emph{Contracaecum}, \emph{Cordylobia}, \emph{Cryptococcus}, \emph{Curvularia}, \emph{Deinococcus}, \emph{Demodex}, \emph{Dermatobia}, \emph{Dientamoeba}, \emph{Diphyllobothrium}, \emph{Dirofilaria}, \emph{Dysgonomonas}, \emph{Echinostoma}, \emph{Elizabethkingia}, \emph{Empedobacter}, \emph{Entamoeba}, \emph{Enterobius}, \emph{Exophiala}, \emph{Exserohilum}, \emph{Fasciola}, \emph{Flavobacterium}, \emph{Fonsecaea}, \emph{Fusarium}, \emph{Fusobacterium}, \emph{Giardia}, \emph{Haloarcula}, \emph{Halobacterium}, \emph{Halococcus}, \emph{Hendersonula}, \emph{Heterophyes}, \emph{Histomonas}, \emph{Histoplasma}, \emph{Hymenolepis}, \emph{Hypomyces}, \emph{Hysterothylacium}, \emph{Leishmania}, \emph{Lelliottia}, \emph{Leptosphaeria}, \emph{Leptotrichia}, \emph{Lucilia}, \emph{Lumbricus}, \emph{Malassezia}, \emph{Malbranchea}, \emph{Metagonimus}, \emph{Microsporidium}, \emph{Microsporum}, \emph{Mortierella}, \emph{Mucor}, \emph{Mycocentrospora}, \emph{Mycoplasma}, \emph{Myroides}, \emph{Necator}, \emph{Nectria}, \emph{Ochroconis}, \emph{Odoribacter}, \emph{Oesophagostomum}, \emph{Oidiodendron}, \emph{Opisthorchis}, \emph{Ornithobacterium}, \emph{Parabacteroides}, \emph{Pediculus}, \emph{Pedobacter}, \emph{Phlebotomus}, \emph{Phocaeicola}, \emph{Phocanema}, \emph{Phoma}, \emph{Piedraia}, \emph{Pithomyces}, \emph{Pityrosporum}, \emph{Pneumocystis}, \emph{Porphyromonas}, \emph{Prevotella}, \emph{Pseudallescheria}, \emph{Pseudoterranova}, \emph{Pulex}, \emph{Rhizomucor}, \emph{Rhizopus}, \emph{Rhodotorula}, \emph{Riemerella}, \emph{Saccharomyces}, \emph{Sarcoptes}, \emph{Scolecobasidium}, \emph{Scopulariopsis}, \emph{Scytalidium}, \emph{Sphingobacterium}, \emph{Spirometra}, \emph{Spiroplasma}, \emph{Sporobolomyces}, \emph{Stachybotrys}, \emph{Streptobacillus}, \emph{Strongyloides}, \emph{Syngamus}, \emph{Taenia}, \emph{Tannerella}, \emph{Tenacibaculum}, \emph{Terrimonas}, \emph{Toxocara}, \emph{Treponema}, \emph{Trichinella}, \emph{Trichobilharzia}, \emph{Trichoderma}, \emph{Trichomonas}, \emph{Trichophyton}, \emph{Trichosporon}, \emph{Trichostrongylus}, \emph{Trichuris}, \emph{Tritirachium}, \emph{Trombicula}, \emph{Trypanosoma}, \emph{Tunga}, \emph{Ureaplasma}, \emph{Victivallis}, \emph{Wautersiella}, \emph{Weeksella} or \emph{Wuchereria}.
\strong{Group 3} consists of all other microorganisms.