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(v1.4.0.9003) CoNS update

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dr. M.S. (Matthijs) Berends 2020-10-20 21:00:57 +02:00
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commit 2ef7dfc8a3
21 changed files with 112 additions and 86 deletions
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4
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR Package: AMR
Version: 1.4.0.9002 Version: 1.4.0.9003
Date: 2020-10-19 Date: 2020-10-20
Title: Antimicrobial Resistance Analysis Title: Antimicrobial Resistance Analysis
Authors@R: c( Authors@R: c(
person(role = c("aut", "cre"), person(role = c("aut", "cre"),

6
NEWS.md
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@ -1,5 +1,5 @@
# AMR 1.4.0.9002 # AMR 1.4.0.9003
## <small>Last updated: 19 October 2020</small> ## <small>Last updated: 20 October 2020</small>
### New ### New
* Functions `is_gram_negative()` and `is_gram_positive()` as wrappers around `mo_gramstain()`. They always return `TRUE` or `FALSE`, thus always return `FALSE` for species outside the taxonomic kingdom of Bacteria. * Functions `is_gram_negative()` and `is_gram_positive()` as wrappers around `mo_gramstain()`. They always return `TRUE` or `FALSE`, thus always return `FALSE` for species outside the taxonomic kingdom of Bacteria.
@ -7,6 +7,8 @@
### Changed ### Changed
* For all function parameters in the code, it is now defined what the exact type of user input should be (inspired by the [`typed`](https://github.com/moodymudskipper/typed) package). If the user input for a certain function does not meet the requirements for a specific parameter (such as the class or length), an informative error will be thrown. This makes the package more robust and the use of it more reproducible and reliable. In total, more than 400 arguments were defined. * For all function parameters in the code, it is now defined what the exact type of user input should be (inspired by the [`typed`](https://github.com/moodymudskipper/typed) package). If the user input for a certain function does not meet the requirements for a specific parameter (such as the class or length), an informative error will be thrown. This makes the package more robust and the use of it more reproducible and reliable. In total, more than 400 arguments were defined.
* Deprecated function `p_symbol()` that not really fits the scope of this package. It will be removed in a future version. See [here](https://github.com/msberends/AMR/blob/v1.4.0/R/p_symbol.R) for the source code to preserve it. * Deprecated function `p_symbol()` that not really fits the scope of this package. It will be removed in a future version. See [here](https://github.com/msberends/AMR/blob/v1.4.0/R/p_symbol.R) for the source code to preserve it.
* Better determination of disk zones and MIC values when running `as.rsi()` on a data.frame
* Updated coagulase-negative staphylococci with Becker *et al.* 2020 (PMID 32056452), meaning that the species *S. argensis*, *S. caeli*, *S. debuckii*, *S. edaphicus* and *S. pseudoxylosus* are now all considered CoNS
### Other ### Other
* More extensive unit tests * More extensive unit tests

26
R/ab_property.R
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@ -89,7 +89,7 @@
#' ab_atc("cephthriaxone") #' ab_atc("cephthriaxone")
#' ab_atc("seephthriaaksone") #' ab_atc("seephthriaaksone")
ab_name <- function(x, language = get_locale(), tolower = FALSE, ...) { ab_name <- function(x, language = get_locale(), tolower = FALSE, ...) {
meet_criteria(x, allow_class = c("character", "numeric", "integer")) meet_criteria(x, allow_NA = TRUE)
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE) meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
meet_criteria(tolower, allow_class = "logical", has_length = 1) meet_criteria(tolower, allow_class = "logical", has_length = 1)
@ -106,21 +106,21 @@ ab_name <- function(x, language = get_locale(), tolower = FALSE, ...) {
#' @aliases ATC #' @aliases ATC
#' @export #' @export
ab_atc <- function(x, ...) { ab_atc <- function(x, ...) {
meet_criteria(x, allow_class = c("character", "numeric", "integer")) meet_criteria(x, allow_NA = TRUE)
ab_validate(x = x, property = "atc", ...) ab_validate(x = x, property = "atc", ...)
} }
#' @rdname ab_property #' @rdname ab_property
#' @export #' @export
ab_cid <- function(x, ...) { ab_cid <- function(x, ...) {
meet_criteria(x, allow_class = c("character", "numeric", "integer")) meet_criteria(x, allow_NA = TRUE)
ab_validate(x = x, property = "cid", ...) ab_validate(x = x, property = "cid", ...)
} }
#' @rdname ab_property #' @rdname ab_property
#' @export #' @export
ab_synonyms <- function(x, ...) { ab_synonyms <- function(x, ...) {
meet_criteria(x, allow_class = c("character", "numeric", "integer")) meet_criteria(x, allow_NA = TRUE)
syns <- ab_validate(x = x, property = "synonyms", ...) syns <- ab_validate(x = x, property = "synonyms", ...)
names(syns) <- x names(syns) <- x
if (length(syns) == 1) { if (length(syns) == 1) {
@ -133,14 +133,14 @@ ab_synonyms <- function(x, ...) {
#' @rdname ab_property #' @rdname ab_property
#' @export #' @export
ab_tradenames <- function(x, ...) { ab_tradenames <- function(x, ...) {
meet_criteria(x, allow_class = c("character", "numeric", "integer")) meet_criteria(x, allow_NA = TRUE)
ab_synonyms(x, ...) ab_synonyms(x, ...)
} }
#' @rdname ab_property #' @rdname ab_property
#' @export #' @export
ab_group <- function(x, language = get_locale(), ...) { ab_group <- function(x, language = get_locale(), ...) {
meet_criteria(x, allow_class = c("character", "numeric", "integer")) meet_criteria(x, allow_NA = TRUE)
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE) meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
translate_AMR(ab_validate(x = x, property = "group", ...), language = language) translate_AMR(ab_validate(x = x, property = "group", ...), language = language)
} }
@ -148,7 +148,7 @@ ab_group <- function(x, language = get_locale(), ...) {
#' @rdname ab_property #' @rdname ab_property
#' @export #' @export
ab_atc_group1 <- function(x, language = get_locale(), ...) { ab_atc_group1 <- function(x, language = get_locale(), ...) {
meet_criteria(x, allow_class = c("character", "numeric", "integer")) meet_criteria(x, allow_NA = TRUE)
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE) meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
translate_AMR(ab_validate(x = x, property = "atc_group1", ...), language = language) translate_AMR(ab_validate(x = x, property = "atc_group1", ...), language = language)
} }
@ -156,7 +156,7 @@ ab_atc_group1 <- function(x, language = get_locale(), ...) {
#' @rdname ab_property #' @rdname ab_property
#' @export #' @export
ab_atc_group2 <- function(x, language = get_locale(), ...) { ab_atc_group2 <- function(x, language = get_locale(), ...) {
meet_criteria(x, allow_class = c("character", "numeric", "integer")) meet_criteria(x, allow_NA = TRUE)
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE) meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
translate_AMR(ab_validate(x = x, property = "atc_group2", ...), language = language) translate_AMR(ab_validate(x = x, property = "atc_group2", ...), language = language)
} }
@ -164,7 +164,7 @@ ab_atc_group2 <- function(x, language = get_locale(), ...) {
#' @rdname ab_property #' @rdname ab_property
#' @export #' @export
ab_loinc <- function(x, ...) { ab_loinc <- function(x, ...) {
meet_criteria(x, allow_class = c("character", "numeric", "integer")) meet_criteria(x, allow_NA = TRUE)
loincs <- ab_validate(x = x, property = "loinc", ...) loincs <- ab_validate(x = x, property = "loinc", ...)
names(loincs) <- x names(loincs) <- x
if (length(loincs) == 1) { if (length(loincs) == 1) {
@ -177,7 +177,7 @@ ab_loinc <- function(x, ...) {
#' @rdname ab_property #' @rdname ab_property
#' @export #' @export
ab_ddd <- function(x, administration = "oral", units = FALSE, ...) { ab_ddd <- function(x, administration = "oral", units = FALSE, ...) {
meet_criteria(x, allow_class = c("character", "numeric", "integer")) meet_criteria(x, allow_NA = TRUE)
meet_criteria(administration, is_in = c("oral", "iv"), has_length = 1) meet_criteria(administration, is_in = c("oral", "iv"), has_length = 1)
meet_criteria(units, allow_class = "logical", has_length = 1) meet_criteria(units, allow_class = "logical", has_length = 1)
@ -193,7 +193,7 @@ ab_ddd <- function(x, administration = "oral", units = FALSE, ...) {
#' @rdname ab_property #' @rdname ab_property
#' @export #' @export
ab_info <- function(x, language = get_locale(), ...) { ab_info <- function(x, language = get_locale(), ...) {
meet_criteria(x, allow_class = c("character", "numeric", "integer")) meet_criteria(x, allow_NA = TRUE)
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE) meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
x <- as.ab(x, ...) x <- as.ab(x, ...)
@ -215,7 +215,7 @@ ab_info <- function(x, language = get_locale(), ...) {
#' @rdname ab_property #' @rdname ab_property
#' @export #' @export
ab_url <- function(x, open = FALSE, ...) { ab_url <- function(x, open = FALSE, ...) {
meet_criteria(x, allow_class = c("character", "numeric", "integer")) meet_criteria(x, allow_NA = TRUE)
meet_criteria(open, allow_class = "logical", has_length = 1) meet_criteria(open, allow_class = "logical", has_length = 1)
ab <- as.ab(x = x, ... = ...) ab <- as.ab(x = x, ... = ...)
@ -242,7 +242,7 @@ ab_url <- function(x, open = FALSE, ...) {
#' @rdname ab_property #' @rdname ab_property
#' @export #' @export
ab_property <- function(x, property = "name", language = get_locale(), ...) { ab_property <- function(x, property = "name", language = get_locale(), ...) {
meet_criteria(x, allow_class = c("character", "numeric", "integer")) meet_criteria(x, allow_NA = TRUE)
meet_criteria(property, is_in = colnames(antibiotics), has_length = 1) meet_criteria(property, is_in = colnames(antibiotics), has_length = 1)
meet_criteria(language, is_in = c(LANGUAGES_SUPPORTED, ""), has_length = 1, allow_NULL = TRUE, allow_NA = TRUE) meet_criteria(language, is_in = c(LANGUAGES_SUPPORTED, ""), has_length = 1, allow_NULL = TRUE, allow_NA = TRUE)
translate_AMR(ab_validate(x = x, property = property, ...), language = language) translate_AMR(ab_validate(x = x, property = property, ...), language = language)

2
R/deprecated.R
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@ -32,7 +32,7 @@
#' @name AMR-deprecated #' @name AMR-deprecated
#' @export #' @export
p_symbol <- function(p, emptychar = " ") { p_symbol <- function(p, emptychar = " ") {
.Deprecated(package = "AMR") .Deprecated(package = "AMR", new = "cleaner::p_symbol")
p <- as.double(p) p <- as.double(p)
s <- rep(NA_character_, length(p)) s <- rep(NA_character_, length(p))

2
R/mic.R
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@ -323,7 +323,7 @@ get_skimmers.mic <- function(column) {
inline_hist <- import_fn("inline_hist", "skimr", error_on_fail = FALSE) inline_hist <- import_fn("inline_hist", "skimr", error_on_fail = FALSE)
sfl( sfl(
skim_type = "mic", skim_type = "mic",
min = ~as.character(sort(na.omit(.))[1]), min = ~as.character(sort(stats::na.omit(.))[1]),
max = ~as.character(sort(stats::na.omit(.))[length(stats::na.omit(.))]), max = ~as.character(sort(stats::na.omit(.))[length(stats::na.omit(.))]),
median = ~as.character(stats::na.omit(.)[as.double(stats::na.omit(.)) == median(as.double(stats::na.omit(.)))])[1], median = ~as.character(stats::na.omit(.)[as.double(stats::na.omit(.)) == median(as.double(stats::na.omit(.)))])[1],
n_unique = ~pm_n_distinct(., na.rm = TRUE), n_unique = ~pm_n_distinct(., na.rm = TRUE),

24
R/mo.R
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@ -28,10 +28,10 @@
#' Use this function to determine a valid microorganism ID ([`mo`]). Determination is done using intelligent rules and the complete taxonomic kingdoms Bacteria, Chromista, Protozoa, Archaea and most microbial species from the kingdom Fungi (see Source). The input can be almost anything: a full name (like `"Staphylococcus aureus"`), an abbreviated name (like `"S. aureus"`), an abbreviation known in the field (like `"MRSA"`), or just a genus. Please see *Examples*. #' Use this function to determine a valid microorganism ID ([`mo`]). Determination is done using intelligent rules and the complete taxonomic kingdoms Bacteria, Chromista, Protozoa, Archaea and most microbial species from the kingdom Fungi (see Source). The input can be almost anything: a full name (like `"Staphylococcus aureus"`), an abbreviated name (like `"S. aureus"`), an abbreviation known in the field (like `"MRSA"`), or just a genus. Please see *Examples*.
#' @inheritSection lifecycle Stable lifecycle #' @inheritSection lifecycle Stable lifecycle
#' @param x a character vector or a [data.frame] with one or two columns #' @param x a character vector or a [data.frame] with one or two columns
#' @param Becker a logical to indicate whether *Staphylococci* should be categorised into coagulase-negative *Staphylococci* ("CoNS") and coagulase-positive *Staphylococci* ("CoPS") instead of their own species, according to Karsten Becker *et al.* (1,2). Note that this does not include species that were newly named after these publications, like *S. caeli*. #' @param Becker a logical to indicate whether *Staphylococci* should be categorised into coagulase-negative *Staphylococci* ("CoNS") and coagulase-positive *Staphylococci* ("CoPS") instead of their own species, according to Karsten Becker *et al.* (1,2,3).
#' #'
#' This excludes *Staphylococcus aureus* at default, use `Becker = "all"` to also categorise *S. aureus* as "CoPS". #' This excludes *Staphylococcus aureus* at default, use `Becker = "all"` to also categorise *S. aureus* as "CoPS".
#' @param Lancefield a logical to indicate whether beta-haemolytic *Streptococci* should be categorised into Lancefield groups instead of their own species, according to Rebecca C. Lancefield (3). These *Streptococci* will be categorised in their first group, e.g. *Streptococcus dysgalactiae* will be group C, although officially it was also categorised into groups G and L. #' @param Lancefield a logical to indicate whether beta-haemolytic *Streptococci* should be categorised into Lancefield groups instead of their own species, according to Rebecca C. Lancefield (4). These *Streptococci* will be categorised in their first group, e.g. *Streptococcus dysgalactiae* will be group C, although officially it was also categorised into groups G and L.
#' #'
#' This excludes *Enterococci* at default (who are in group D), use `Lancefield = "all"` to also categorise all *Enterococci* as group D. #' This excludes *Enterococci* at default (who are in group D), use `Lancefield = "all"` to also categorise all *Enterococci* as group D.
#' @param allow_uncertain a number between `0` (or `"none"`) and `3` (or `"all"`), or `TRUE` (= `2`) or `FALSE` (= `0`) to indicate whether the input should be checked for less probable results, please see *Details* #' @param allow_uncertain a number between `0` (or `"none"`) and `3` (or `"all"`), or `TRUE` (= `2`) or `FALSE` (= `0`) to indicate whether the input should be checked for less probable results, please see *Details*
@ -104,8 +104,9 @@
#' @section Source: #' @section Source:
#' 1. Becker K *et al.* **Coagulase-Negative Staphylococci**. 2014. Clin Microbiol Rev. 27(4): 870–926. <https://dx.doi.org/10.1128/CMR.00109-13> #' 1. Becker K *et al.* **Coagulase-Negative Staphylococci**. 2014. Clin Microbiol Rev. 27(4): 870–926. <https://dx.doi.org/10.1128/CMR.00109-13>
#' 2. Becker K *et al.* **Implications of identifying the recently defined members of the *S. aureus* complex, *S. argenteus* and *S. schweitzeri*: A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS).** 2019. Clin Microbiol Infect. <https://doi.org/10.1016/j.cmi.2019.02.028> #' 2. Becker K *et al.* **Implications of identifying the recently defined members of the *S. aureus* complex, *S. argenteus* and *S. schweitzeri*: A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS).** 2019. Clin Microbiol Infect. <https://doi.org/10.1016/j.cmi.2019.02.028>
#' 3. Lancefield RC **A serological differentiation of human and other groups of hemolytic streptococci**. 1933. J Exp Med. 57(4): 571–95. <https://dx.doi.org/10.1084/jem.57.4.571> #' 3. Becker K *et al.* **Emergence of coagulase-negative staphylococci** 2020. Expert Rev Anti Infect Ther. 18(4):349-366. <https://dx.doi.org/10.1080/14787210.2020.1730813>
#' 4. Catalogue of Life: Annual Checklist (public online taxonomic database), <http://www.catalogueoflife.org> (check included annual version with [catalogue_of_life_version()]). #' 4. Lancefield RC **A serological differentiation of human and other groups of hemolytic streptococci**. 1933. J Exp Med. 57(4): 571–95. <https://dx.doi.org/10.1084/jem.57.4.571>
#' 5. Catalogue of Life: Annual Checklist (public online taxonomic database), <http://www.catalogueoflife.org> (check included annual version with [catalogue_of_life_version()]).
#' @export #' @export
#' @return A [character] [vector] with additional class [`mo`] #' @return A [character] [vector] with additional class [`mo`]
#' @seealso [microorganisms] for the [data.frame] that is being used to determine ID's. #' @seealso [microorganisms] for the [data.frame] that is being used to determine ID's.
@ -158,7 +159,7 @@ as.mo <- function(x,
ignore_pattern = getOption("AMR_ignore_pattern"), ignore_pattern = getOption("AMR_ignore_pattern"),
language = get_locale(), language = get_locale(),
...) { ...) {
meet_criteria(x, allow_NA = TRUE) meet_criteria(x, allow_class = c("mo", "data.frame", "list", "character", "numeric", "integer", "factor"), allow_NA = TRUE)
meet_criteria(Becker, allow_class = c("logical", "character"), has_length = 1) meet_criteria(Becker, allow_class = c("logical", "character"), has_length = 1)
meet_criteria(Lancefield, allow_class = c("logical", "character"), has_length = 1) meet_criteria(Lancefield, allow_class = c("logical", "character"), has_length = 1)
meet_criteria(allow_uncertain, allow_class = c("logical", "numeric", "integer"), has_length = 1) meet_criteria(allow_uncertain, allow_class = c("logical", "numeric", "integer"), has_length = 1)
@ -275,7 +276,7 @@ exec_as.mo <- function(x,
actual_uncertainty = 1, actual_uncertainty = 1,
actual_input = NULL, actual_input = NULL,
language = get_locale()) { language = get_locale()) {
meet_criteria(x, allow_NA = TRUE) meet_criteria(x, allow_class = c("mo", "data.frame", "list", "character", "numeric", "integer", "factor"), allow_NA = TRUE)
meet_criteria(Becker, allow_class = c("logical", "character"), has_length = 1) meet_criteria(Becker, allow_class = c("logical", "character"), has_length = 1)
meet_criteria(Lancefield, allow_class = c("logical", "character"), has_length = 1) meet_criteria(Lancefield, allow_class = c("logical", "character"), has_length = 1)
meet_criteria(allow_uncertain, allow_class = c("logical", "numeric", "integer"), has_length = 1) meet_criteria(allow_uncertain, allow_class = c("logical", "numeric", "integer"), has_length = 1)
@ -1431,15 +1432,18 @@ exec_as.mo <- function(x,
if (length(uncertainties$input) > 1) { if (length(uncertainties$input) > 1) {
plural <- c("s", "them", "were") plural <- c("s", "them", "were")
} }
msg <- paste0("Result", plural[1], " of ", nr2char(length(uncertainties$input)), " value", plural[1], msg <- paste0("Translation to ", nr2char(length(uncertainties$input)), " microorganism", plural[1],
" ", plural[3], " guessed with uncertainty. Use mo_uncertainties() to review ", plural[2], ".") " ", plural[3], " guessed with uncertainty. Use mo_uncertainties() to review ", plural[2], ".")
message(font_blue(msg)) message(font_red(msg))
} }
# Becker ---- # Becker ----
if (Becker == TRUE | Becker == "all") { if (Becker == TRUE | Becker == "all") {
# warn when species found that are not in Becker (2014, PMID 25278577) and Becker (2019, PMID 30872103) # warn when species found that are not in:
post_Becker <- c("argensis", "caeli", "cornubiensis", "edaphicus") # - Becker et al. 2014, PMID 25278577
# - Becker et al. 2019, PMID 30872103
# - Becker et al. 2020, PMID 32056452
post_Becker <- c("") # 2020-10-20 currently all are mentioned in above papers
if (any(x %in% MO_lookup[which(MO_lookup$species %in% post_Becker), property])) { if (any(x %in% MO_lookup[which(MO_lookup$species %in% post_Becker), property])) {
warning("Becker ", font_italic("et al."), " (2014, 2019) does not contain these species named after their publication: ", warning("Becker ", font_italic("et al."), " (2014, 2019) does not contain these species named after their publication: ",

62
R/rsi.R
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@ -461,6 +461,12 @@ as.rsi.data.frame <- function(x,
meet_criteria(conserve_capped_values, allow_class = "logical", has_length = 1) meet_criteria(conserve_capped_values, allow_class = "logical", has_length = 1)
meet_criteria(add_intrinsic_resistance, allow_class = "logical", has_length = 1) meet_criteria(add_intrinsic_resistance, allow_class = "logical", has_length = 1)
# -- MO
col_mo.bak <- col_mo
if (is.null(col_mo)) {
col_mo <- search_type_in_df(x = x, type = "mo", info = FALSE)
}
# -- UTIs # -- UTIs
col_uti <- uti col_uti <- uti
if (is.null(col_uti)) { if (is.null(col_uti)) {
@ -501,29 +507,25 @@ as.rsi.data.frame <- function(x,
i <- 0 i <- 0
sel <- colnames(pm_select(x, ...)) sel <- colnames(pm_select(x, ...))
if (!is.null(col_mo)) {
sel <- sel[sel != col_mo]
}
ab_cols <- colnames(x)[sapply(x, function(y) { ab_cols <- colnames(x)[sapply(x, function(y) {
i <<- i + 1 i <<- i + 1
check <- is.mic(y) | is.disk(y) check <- is.mic(y) | is.disk(y)
ab <- colnames(x)[i] ab <- colnames(x)[i]
if (!is.null(col_mo) && ab == col_mo) {
return(FALSE)
}
if (!is.null(col_uti) && ab == col_uti) {
return(FALSE)
}
if (length(sel) == 0 || (length(sel) > 0 && ab %in% sel)) { if (length(sel) == 0 || (length(sel) > 0 && ab %in% sel)) {
ab_coerced <- suppressWarnings(as.ab(ab)) ab_coerced <- suppressWarnings(as.ab(ab))
if (is.na(ab_coerced) || (length(sel) > 0 & !ab %in% sel)) { if (is.na(ab_coerced) || (length(sel) > 0 & !ab %in% sel)) {
# not even a valid AB code # not even a valid AB code
return(FALSE) return(FALSE)
} else { } else {
if (!check & all_valid_mics(y)) {
message(font_blue(paste0("NOTE: Assuming column `", ab, "` (",
ifelse(ab_coerced != ab, paste0(ab_coerced, ", "), ""),
ab_name(ab_coerced, tolower = TRUE), ") contains MIC values.")))
} else if (!check & all_valid_disks(y)) {
message(font_blue(paste0("NOTE: Assuming column `", ab, "` (",
ifelse(ab_coerced != ab, paste0(ab_coerced, ", "), ""),
ab_name(ab_coerced, tolower = TRUE), ") contains disk zones.")))
} else if (!check & !is.rsi(y)) {
message(font_blue(paste0("NOTE: Assuming column `", ab, "` (",
ifelse(ab_coerced != ab, paste0(ab_coerced, ", "), ""),
ab_name(ab_coerced, tolower = TRUE), ") must be cleaned to valid R/SI values.")))
}
return(TRUE) return(TRUE)
} }
} else { } else {
@ -535,36 +537,46 @@ as.rsi.data.frame <- function(x,
"no columns with MIC values, disk zones or antibiotic column names found in this data set. Use as.mic() or as.disk() to transform antimicrobial columns.") "no columns with MIC values, disk zones or antibiotic column names found in this data set. Use as.mic() or as.disk() to transform antimicrobial columns.")
# set type per column # set type per column
types <- character(length(ab_cols)) types <- character(length(ab_cols))
types[sapply(x[, ab_cols], is.mic)] <- "mic"
types[types == "" & sapply(x[, ab_cols], all_valid_mics)] <- "mic"
types[sapply(x[, ab_cols], is.disk)] <- "disk" types[sapply(x[, ab_cols], is.disk)] <- "disk"
types[types == "" & sapply(x[, ab_cols], all_valid_disks)] <- "disk" types[types == "" & sapply(x[, ab_cols], all_valid_disks)] <- "disk"
types[sapply(x[, ab_cols], is.mic)] <- "mic"
types[types == "" & sapply(x[, ab_cols], all_valid_mics)] <- "mic"
types[types == "" & !sapply(x[, ab_cols], is.rsi)] <- "rsi" types[types == "" & !sapply(x[, ab_cols], is.rsi)] <- "rsi"
if (any(types %in% c("mic", "disk"), na.rm = TRUE)) { if (any(types %in% c("mic", "disk"), na.rm = TRUE)) {
# now we need an mo column - try to find columns based on type # now we need an mo column
if (is.null(col_mo)) { stop_if(is.null(col_mo), "`col_mo` must be set")
# if not null, we already found it, now find again so a message will show
if (is.null(col_mo.bak)) {
col_mo <- search_type_in_df(x = x, type = "mo") col_mo <- search_type_in_df(x = x, type = "mo")
stop_if(is.null(col_mo), "`col_mo` must be set")
} }
} }
x_mo <- as.mo(x %pm>% pm_pull(col_mo))
for (i in seq_len(length(ab_cols))) { for (i in seq_len(length(ab_cols))) {
if (types[i] == "mic") { if (types[i] == "mic") {
x[, ab_cols[i]] <- as.rsi.mic(x = x %pm>% pm_pull(ab_cols[i]), x[, ab_cols[i]] <- as.rsi.mic(x = x %pm>% pm_pull(ab_cols[i]),
mo = x %pm>% pm_pull(col_mo), mo = x_mo,
ab = ab_cols[i], ab = ab_cols[i],
guideline = guideline, guideline = guideline,
uti = uti, uti = uti,
conserve_capped_values = conserve_capped_values) conserve_capped_values = conserve_capped_values)
} else if (types[i] == "disk") { } else if (types[i] == "disk") {
x[, ab_cols[i]] <- as.rsi.disk(x = x %pm>% pm_pull(ab_cols[i]), x[, ab_cols[i]] <- as.rsi.disk(x = x %pm>% pm_pull(ab_cols[i]),
mo = x %pm>% pm_pull(col_mo), mo = x_mo,
ab = ab_cols[i], ab = ab_cols[i],
guideline = guideline, guideline = guideline,
uti = uti) uti = uti)
} else if (types[i] == "rsi") { } else if (types[i] == "rsi") {
ab <- ab_cols[i]
ab_coerced <- suppressWarnings(as.ab(ab))
message(font_blue(paste0("=> Cleaning values in column `", font_bold(ab), "` (",
ifelse(ab_coerced != ab, paste0(ab_coerced, ", "), ""),
ab_name(ab_coerced, tolower = TRUE), ")... ")),
appendLF = FALSE)
x[, ab_cols[i]] <- as.rsi.default(x = x %pm>% pm_pull(ab_cols[i])) x[, ab_cols[i]] <- as.rsi.default(x = x %pm>% pm_pull(ab_cols[i]))
message(font_green("OK."))
} }
} }
@ -760,11 +772,11 @@ freq.rsi <- function(x, ...) {
x_name <- gsub(".*[$]", "", x_name) x_name <- gsub(".*[$]", "", x_name)
if (x_name %in% c("x", ".")) { if (x_name %in% c("x", ".")) {
# try again going through system calls # try again going through system calls
x_name <- na.omit(sapply(sys.calls(), x_name <- stats::na.omit(sapply(sys.calls(),
function(call) { function(call) {
call_txt <- as.character(call) call_txt <- as.character(call)
ifelse(call_txt[1] %like% "freq$", call_txt[length(call_txt)], character(0)) ifelse(call_txt[1] %like% "freq$", call_txt[length(call_txt)], character(0))
}))[1L] }))[1L]
} }
ab <- suppressMessages(suppressWarnings(as.ab(x_name))) ab <- suppressMessages(suppressWarnings(as.ab(x_name)))
freq.default <- import_fn("freq.default", "cleaner", error_on_fail = FALSE) freq.default <- import_fn("freq.default", "cleaner", error_on_fail = FALSE)

26
R/zzz.R
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@ -84,23 +84,25 @@
} }
create_species_cons_cops <- function(type = c("CoNS", "CoPS")) { create_species_cons_cops <- function(type = c("CoNS", "CoPS")) {
# Determination of which staphylococcal species are CoNS/CoPS according to Becker et al.: # Determination of which staphylococcal species are CoNS/CoPS according to:
# https://cmr.asm.org/content/cmr/27/4/870/F6.large.jpg # - Becker et al. 2014, PMID 25278577
# - Becker et al. 2019, PMID 30872103
# - Becker et al. 2020, PMID 32056452
# this function returns class <mo> # this function returns class <mo>
MO_staph <- AMR::microorganisms MO_staph <- AMR::microorganisms
MO_staph <- MO_staph[which(MO_staph$genus == "Staphylococcus"), , drop = FALSE] MO_staph <- MO_staph[which(MO_staph$genus == "Staphylococcus"), , drop = FALSE]
if (type == "CoNS") { if (type == "CoNS") {
MO_staph[which(MO_staph$species %in% c("coagulase-negative", MO_staph[which(MO_staph$species %in% c("coagulase-negative", "argensis", "arlettae",
"arlettae", "auricularis", "capitis", "auricularis", "caeli", "capitis", "caprae",
"caprae", "carnosus", "chromogenes", "cohnii", "condimenti", "carnosus", "chromogenes", "cohnii", "condimenti",
"devriesei", "epidermidis", "equorum", "felis", "debuckii", "devriesei", "edaphicus", "epidermidis",
"fleurettii", "gallinarum", "haemolyticus", "equorum", "felis", "fleurettii", "gallinarum",
"hominis", "jettensis", "kloosii", "lentus", "haemolyticus", "hominis", "jettensis", "kloosii",
"lugdunensis", "massiliensis", "microti", "lentus", "lugdunensis", "massiliensis", "microti",
"muscae", "nepalensis", "pasteuri", "petrasii", "muscae", "nepalensis", "pasteuri", "petrasii",
"pettenkoferi", "piscifermentans", "rostri", "pettenkoferi", "piscifermentans", "pseudoxylosus",
"saccharolyticus", "saprophyticus", "sciuri", "rostri", "saccharolyticus", "saprophyticus",
"stepanovicii", "simulans", "succinus", "sciuri", "simulans", "stepanovicii", "succinus",
"vitulinus", "warneri", "xylosus") "vitulinus", "warneri", "xylosus")
| (MO_staph$species == "schleiferi" & MO_staph$subspecies %in% c("schleiferi", ""))), | (MO_staph$species == "schleiferi" & MO_staph$subspecies %in% c("schleiferi", ""))),
"mo", drop = TRUE] "mo", drop = TRUE]

2
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a> <a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9002</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9003</span>
</span> </span>
</div> </div>

2
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9002</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9003</span>
</span> </span>
</div> </div>

2
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9002</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9003</span>
</span> </span>
</div> </div>

2
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9002</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9003</span>
</span> </span>
</div> </div>

2
docs/index.html
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@ -43,7 +43,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9002</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9003</span>
</span> </span>
</div> </div>

14
docs/news/index.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9002</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9003</span>
</span> </span>
</div> </div>
@ -236,13 +236,13 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small> <small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div> </div>
<div id="amr-1409002" class="section level1"> <div id="amr-1409003" class="section level1">
<h1 class="page-header" data-toc-text="1.4.0.9002"> <h1 class="page-header" data-toc-text="1.4.0.9003">
<a href="#amr-1409002" class="anchor"></a>AMR 1.4.0.9002<small> Unreleased </small> <a href="#amr-1409003" class="anchor"></a>AMR 1.4.0.9003<small> Unreleased </small>
</h1> </h1>
<div id="last-updated-19-october-2020" class="section level2"> <div id="last-updated-20-october-2020" class="section level2">
<h2 class="hasAnchor"> <h2 class="hasAnchor">
<a href="#last-updated-19-october-2020" class="anchor"></a><small>Last updated: 19 October 2020</small> <a href="#last-updated-20-october-2020" class="anchor"></a><small>Last updated: 20 October 2020</small>
</h2> </h2>
<div id="new" class="section level3"> <div id="new" class="section level3">
<h3 class="hasAnchor"> <h3 class="hasAnchor">
@ -257,6 +257,8 @@
<ul> <ul>
<li>For all function parameters in the code, it is now defined what the exact type of user input should be (inspired by the <a href="https://github.com/moodymudskipper/typed"><code>typed</code></a> package). If the user input for a certain function does not meet the requirements for a specific parameter (such as the class or length), an informative error will be thrown. This makes the package more robust and the use of it more reproducible and reliable. In total, more than 400 arguments were defined.</li> <li>For all function parameters in the code, it is now defined what the exact type of user input should be (inspired by the <a href="https://github.com/moodymudskipper/typed"><code>typed</code></a> package). If the user input for a certain function does not meet the requirements for a specific parameter (such as the class or length), an informative error will be thrown. This makes the package more robust and the use of it more reproducible and reliable. In total, more than 400 arguments were defined.</li>
<li>Deprecated function <code><a href="../reference/AMR-deprecated.html">p_symbol()</a></code> that not really fits the scope of this package. It will be removed in a future version. See <a href="https://github.com/msberends/AMR/blob/v1.4.0/R/p_symbol.R">here</a> for the source code to preserve it.</li> <li>Deprecated function <code><a href="../reference/AMR-deprecated.html">p_symbol()</a></code> that not really fits the scope of this package. It will be removed in a future version. See <a href="https://github.com/msberends/AMR/blob/v1.4.0/R/p_symbol.R">here</a> for the source code to preserve it.</li>
<li>Better determination of disk zones and MIC values when running <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on a data.frame</li>
<li>Updated coagulase-negative staphylococci with Becker <em>et al.</em> 2020 (PMID 32056452), meaning that the species <em>S. argensis</em>, <em>S. caeli</em>, <em>S. debuckii</em>, <em>S. edaphicus</em> and <em>S. pseudoxylosus</em> are now all considered CoNS</li>
</ul> </ul>
</div> </div>
<div id="other" class="section level3"> <div id="other" class="section level3">

2
docs/pkgdown.yml
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@ -12,7 +12,7 @@ articles:
datasets: datasets.html datasets: datasets.html
resistance_predict: resistance_predict.html resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html welcome_to_AMR: welcome_to_AMR.html
last_built: 2020-10-19T18:44Z last_built: 2020-10-20T18:59Z
urls: urls:
reference: https://msberends.github.io/AMR//reference reference: https://msberends.github.io/AMR//reference
article: https://msberends.github.io/AMR//articles article: https://msberends.github.io/AMR//articles

7
docs/reference/as.mo.html
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@ -82,7 +82,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9000</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9003</span>
</span> </span>
</div> </div>
@ -270,12 +270,12 @@
</tr> </tr>
<tr> <tr>
<th>Becker</th> <th>Becker</th>
<td><p>a logical to indicate whether <em>Staphylococci</em> should be categorised into coagulase-negative <em>Staphylococci</em> ("CoNS") and coagulase-positive <em>Staphylococci</em> ("CoPS") instead of their own species, according to Karsten Becker <em>et al.</em> (1,2). Note that this does not include species that were newly named after these publications, like <em>S. caeli</em>.</p> <td><p>a logical to indicate whether <em>Staphylococci</em> should be categorised into coagulase-negative <em>Staphylococci</em> ("CoNS") and coagulase-positive <em>Staphylococci</em> ("CoPS") instead of their own species, according to Karsten Becker <em>et al.</em> (1,2,3).</p>
<p>This excludes <em>Staphylococcus aureus</em> at default, use <code>Becker = "all"</code> to also categorise <em>S. aureus</em> as "CoPS".</p></td> <p>This excludes <em>Staphylococcus aureus</em> at default, use <code>Becker = "all"</code> to also categorise <em>S. aureus</em> as "CoPS".</p></td>
</tr> </tr>
<tr> <tr>
<th>Lancefield</th> <th>Lancefield</th>
<td><p>a logical to indicate whether beta-haemolytic <em>Streptococci</em> should be categorised into Lancefield groups instead of their own species, according to Rebecca C. Lancefield (3). These <em>Streptococci</em> will be categorised in their first group, e.g. <em>Streptococcus dysgalactiae</em> will be group C, although officially it was also categorised into groups G and L.</p> <td><p>a logical to indicate whether beta-haemolytic <em>Streptococci</em> should be categorised into Lancefield groups instead of their own species, according to Rebecca C. Lancefield (4). These <em>Streptococci</em> will be categorised in their first group, e.g. <em>Streptococcus dysgalactiae</em> will be group C, although officially it was also categorised into groups G and L.</p>
<p>This excludes <em>Enterococci</em> at default (who are in group D), use <code>Lancefield = "all"</code> to also categorise all <em>Enterococci</em> as group D.</p></td> <p>This excludes <em>Enterococci</em> at default (who are in group D), use <code>Lancefield = "all"</code> to also categorise all <em>Enterococci</em> as group D.</p></td>
</tr> </tr>
<tr> <tr>
@ -370,6 +370,7 @@
<ol> <ol>
<li><p>Becker K <em>et al.</em> <strong>Coagulase-Negative Staphylococci</strong>. 2014. Clin Microbiol Rev. 27(4): 870–926. <a href='https://dx.doi.org/10.1128/CMR.00109-13'>https://dx.doi.org/10.1128/CMR.00109-13</a></p></li> <li><p>Becker K <em>et al.</em> <strong>Coagulase-Negative Staphylococci</strong>. 2014. Clin Microbiol Rev. 27(4): 870–926. <a href='https://dx.doi.org/10.1128/CMR.00109-13'>https://dx.doi.org/10.1128/CMR.00109-13</a></p></li>
<li><p>Becker K <em>et al.</em> <strong>Implications of identifying the recently defined members of the <em>S. aureus</em> complex, <em>S. argenteus</em> and <em>S. schweitzeri</em>: A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS).</strong> 2019. Clin Microbiol Infect. <a href='https://doi.org/10.1016/j.cmi.2019.02.028'>https://doi.org/10.1016/j.cmi.2019.02.028</a></p></li> <li><p>Becker K <em>et al.</em> <strong>Implications of identifying the recently defined members of the <em>S. aureus</em> complex, <em>S. argenteus</em> and <em>S. schweitzeri</em>: A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS).</strong> 2019. Clin Microbiol Infect. <a href='https://doi.org/10.1016/j.cmi.2019.02.028'>https://doi.org/10.1016/j.cmi.2019.02.028</a></p></li>
<li><p>Becker K <em>et al.</em> <strong>Emergence of coagulase-negative staphylococci</strong> 2020. Expert Rev Anti Infect Ther. 18(4):349-366. <a href='https://dx.doi.org/10.1080/14787210.2020.1730813'>https://dx.doi.org/10.1080/14787210.2020.1730813</a></p></li>
<li><p>Lancefield RC <strong>A serological differentiation of human and other groups of hemolytic streptococci</strong>. 1933. J Exp Med. 57(4): 571–95. <a href='https://dx.doi.org/10.1084/jem.57.4.571'>https://dx.doi.org/10.1084/jem.57.4.571</a></p></li> <li><p>Lancefield RC <strong>A serological differentiation of human and other groups of hemolytic streptococci</strong>. 1933. J Exp Med. 57(4): 571–95. <a href='https://dx.doi.org/10.1084/jem.57.4.571'>https://dx.doi.org/10.1084/jem.57.4.571</a></p></li>
<li><p>Catalogue of Life: Annual Checklist (public online taxonomic database), <a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a> (check included annual version with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version()</a></code>).</p></li> <li><p>Catalogue of Life: Annual Checklist (public online taxonomic database), <a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a> (check included annual version with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version()</a></code>).</p></li>
</ol> </ol>

2
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9002</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9003</span>
</span> </span>
</div> </div>

3
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@ -82,7 +82,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9001</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9003</span>
</span> </span>
</div> </div>
@ -381,6 +381,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<ol> <ol>
<li><p>Becker K <em>et al.</em> <strong>Coagulase-Negative Staphylococci</strong>. 2014. Clin Microbiol Rev. 27(4): 870–926. <a href='https://dx.doi.org/10.1128/CMR.00109-13'>https://dx.doi.org/10.1128/CMR.00109-13</a></p></li> <li><p>Becker K <em>et al.</em> <strong>Coagulase-Negative Staphylococci</strong>. 2014. Clin Microbiol Rev. 27(4): 870–926. <a href='https://dx.doi.org/10.1128/CMR.00109-13'>https://dx.doi.org/10.1128/CMR.00109-13</a></p></li>
<li><p>Becker K <em>et al.</em> <strong>Implications of identifying the recently defined members of the <em>S. aureus</em> complex, <em>S. argenteus</em> and <em>S. schweitzeri</em>: A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS).</strong> 2019. Clin Microbiol Infect. <a href='https://doi.org/10.1016/j.cmi.2019.02.028'>https://doi.org/10.1016/j.cmi.2019.02.028</a></p></li> <li><p>Becker K <em>et al.</em> <strong>Implications of identifying the recently defined members of the <em>S. aureus</em> complex, <em>S. argenteus</em> and <em>S. schweitzeri</em>: A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS).</strong> 2019. Clin Microbiol Infect. <a href='https://doi.org/10.1016/j.cmi.2019.02.028'>https://doi.org/10.1016/j.cmi.2019.02.028</a></p></li>
<li><p>Becker K <em>et al.</em> <strong>Emergence of coagulase-negative staphylococci</strong> 2020. Expert Rev Anti Infect Ther. 18(4):349-366. <a href='https://dx.doi.org/10.1080/14787210.2020.1730813'>https://dx.doi.org/10.1080/14787210.2020.1730813</a></p></li>
<li><p>Lancefield RC <strong>A serological differentiation of human and other groups of hemolytic streptococci</strong>. 1933. J Exp Med. 57(4): 571–95. <a href='https://dx.doi.org/10.1084/jem.57.4.571'>https://dx.doi.org/10.1084/jem.57.4.571</a></p></li> <li><p>Lancefield RC <strong>A serological differentiation of human and other groups of hemolytic streptococci</strong>. 1933. J Exp Med. 57(4): 571–95. <a href='https://dx.doi.org/10.1084/jem.57.4.571'>https://dx.doi.org/10.1084/jem.57.4.571</a></p></li>
<li><p>Catalogue of Life: Annual Checklist (public online taxonomic database), <a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a> (check included annual version with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version()</a></code>).</p></li> <li><p>Catalogue of Life: Annual Checklist (public online taxonomic database), <a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a> (check included annual version with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version()</a></code>).</p></li>
</ol> </ol>

2
docs/survey.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9002</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9003</span>
</span> </span>
</div> </div>

5
man/as.mo.Rd
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@ -31,11 +31,11 @@ mo_renamed()
\arguments{ \arguments{
\item{x}{a character vector or a \link{data.frame} with one or two columns} \item{x}{a character vector or a \link{data.frame} with one or two columns}
\item{Becker}{a logical to indicate whether \emph{Staphylococci} should be categorised into coagulase-negative \emph{Staphylococci} ("CoNS") and coagulase-positive \emph{Staphylococci} ("CoPS") instead of their own species, according to Karsten Becker \emph{et al.} (1,2). Note that this does not include species that were newly named after these publications, like \emph{S. caeli}. \item{Becker}{a logical to indicate whether \emph{Staphylococci} should be categorised into coagulase-negative \emph{Staphylococci} ("CoNS") and coagulase-positive \emph{Staphylococci} ("CoPS") instead of their own species, according to Karsten Becker \emph{et al.} (1,2,3).
This excludes \emph{Staphylococcus aureus} at default, use \code{Becker = "all"} to also categorise \emph{S. aureus} as "CoPS".} This excludes \emph{Staphylococcus aureus} at default, use \code{Becker = "all"} to also categorise \emph{S. aureus} as "CoPS".}
\item{Lancefield}{a logical to indicate whether beta-haemolytic \emph{Streptococci} should be categorised into Lancefield groups instead of their own species, according to Rebecca C. Lancefield (3). These \emph{Streptococci} will be categorised in their first group, e.g. \emph{Streptococcus dysgalactiae} will be group C, although officially it was also categorised into groups G and L. \item{Lancefield}{a logical to indicate whether beta-haemolytic \emph{Streptococci} should be categorised into Lancefield groups instead of their own species, according to Rebecca C. Lancefield (4). These \emph{Streptococci} will be categorised in their first group, e.g. \emph{Streptococcus dysgalactiae} will be group C, although officially it was also categorised into groups G and L.
This excludes \emph{Enterococci} at default (who are in group D), use \code{Lancefield = "all"} to also categorise all \emph{Enterococci} as group D.} This excludes \emph{Enterococci} at default (who are in group D), use \code{Lancefield = "all"} to also categorise all \emph{Enterococci} as group D.}
@ -125,6 +125,7 @@ The intelligent rules consider the prevalence of microorganisms in humans groupe
\enumerate{ \enumerate{
\item Becker K \emph{et al.} \strong{Coagulase-Negative Staphylococci}. 2014. Clin Microbiol Rev. 27(4): 870–926. \url{https://dx.doi.org/10.1128/CMR.00109-13} \item Becker K \emph{et al.} \strong{Coagulase-Negative Staphylococci}. 2014. Clin Microbiol Rev. 27(4): 870–926. \url{https://dx.doi.org/10.1128/CMR.00109-13}
\item Becker K \emph{et al.} \strong{Implications of identifying the recently defined members of the \emph{S. aureus} complex, \emph{S. argenteus} and \emph{S. schweitzeri}: A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS).} 2019. Clin Microbiol Infect. \url{https://doi.org/10.1016/j.cmi.2019.02.028} \item Becker K \emph{et al.} \strong{Implications of identifying the recently defined members of the \emph{S. aureus} complex, \emph{S. argenteus} and \emph{S. schweitzeri}: A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS).} 2019. Clin Microbiol Infect. \url{https://doi.org/10.1016/j.cmi.2019.02.028}
\item Becker K \emph{et al.} \strong{Emergence of coagulase-negative staphylococci} 2020. Expert Rev Anti Infect Ther. 18(4):349-366. \url{https://dx.doi.org/10.1080/14787210.2020.1730813}
\item Lancefield RC \strong{A serological differentiation of human and other groups of hemolytic streptococci}. 1933. J Exp Med. 57(4): 571–95. \url{https://dx.doi.org/10.1084/jem.57.4.571} \item Lancefield RC \strong{A serological differentiation of human and other groups of hemolytic streptococci}. 1933. J Exp Med. 57(4): 571–95. \url{https://dx.doi.org/10.1084/jem.57.4.571}
\item Catalogue of Life: Annual Checklist (public online taxonomic database), \url{http://www.catalogueoflife.org} (check included annual version with \code{\link[=catalogue_of_life_version]{catalogue_of_life_version()}}). \item Catalogue of Life: Annual Checklist (public online taxonomic database), \url{http://www.catalogueoflife.org} (check included annual version with \code{\link[=catalogue_of_life_version]{catalogue_of_life_version()}}).
} }

1
man/mo_property.Rd
View File

@ -164,6 +164,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
\enumerate{ \enumerate{
\item Becker K \emph{et al.} \strong{Coagulase-Negative Staphylococci}. 2014. Clin Microbiol Rev. 27(4): 870–926. \url{https://dx.doi.org/10.1128/CMR.00109-13} \item Becker K \emph{et al.} \strong{Coagulase-Negative Staphylococci}. 2014. Clin Microbiol Rev. 27(4): 870–926. \url{https://dx.doi.org/10.1128/CMR.00109-13}
\item Becker K \emph{et al.} \strong{Implications of identifying the recently defined members of the \emph{S. aureus} complex, \emph{S. argenteus} and \emph{S. schweitzeri}: A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS).} 2019. Clin Microbiol Infect. \url{https://doi.org/10.1016/j.cmi.2019.02.028} \item Becker K \emph{et al.} \strong{Implications of identifying the recently defined members of the \emph{S. aureus} complex, \emph{S. argenteus} and \emph{S. schweitzeri}: A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS).} 2019. Clin Microbiol Infect. \url{https://doi.org/10.1016/j.cmi.2019.02.028}
\item Becker K \emph{et al.} \strong{Emergence of coagulase-negative staphylococci} 2020. Expert Rev Anti Infect Ther. 18(4):349-366. \url{https://dx.doi.org/10.1080/14787210.2020.1730813}
\item Lancefield RC \strong{A serological differentiation of human and other groups of hemolytic streptococci}. 1933. J Exp Med. 57(4): 571–95. \url{https://dx.doi.org/10.1084/jem.57.4.571} \item Lancefield RC \strong{A serological differentiation of human and other groups of hemolytic streptococci}. 1933. J Exp Med. 57(4): 571–95. \url{https://dx.doi.org/10.1084/jem.57.4.571}
\item Catalogue of Life: Annual Checklist (public online taxonomic database), \url{http://www.catalogueoflife.org} (check included annual version with \code{\link[=catalogue_of_life_version]{catalogue_of_life_version()}}). \item Catalogue of Life: Annual Checklist (public online taxonomic database), \url{http://www.catalogueoflife.org} (check included annual version with \code{\link[=catalogue_of_life_version]{catalogue_of_life_version()}}).
} }