update prevalence with new phyla

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 1.8.2.9057
+Version: 1.8.2.9058
 Date: 2022-12-09
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 1.8.2.9057
+# AMR 1.8.2.9058
 
 This version will eventually become v2.0! We're happy to reach a new major milestone soon!
 

R/mo_property.R

@@ -37,19 +37,19 @@
 #' @param ab any (vector of) text that can be coerced to a valid antibiotic drug code with [as.ab()]
 #' @param open browse the URL using [`browseURL()`][utils::browseURL()]
 #' @details All functions will, at default, keep old taxonomic properties. Please refer to this example, knowing that *Escherichia blattae* was renamed to *Shimwellia blattae* in 2010:
-#' - `mo_name("Escherichia blattae")` will return `"Shimwellia blattae"` (with a message about the renaming)
+#' - `mo_name("Escherichia blattae")` will return `"Shimwellia blattae"` (with a note about the renaming)
-#' - `mo_ref("Escherichia blattae", keep_synonyms = TRUE)` will return `"Burgess et al., 1973"` (with a warning about the renaming)
+#' - `mo_ref("Escherichia blattae", keep_synonyms = TRUE)` will return `"Burgess et al., 1973"` (without a note)
-#' - `mo_ref("Shimwellia blattae", keep_synonyms = FALSE)` will return `"Priest et al., 2010"` (without a message)
+#' - `mo_ref("Shimwellia blattae", keep_synonyms = FALSE)` will return `"Priest et al., 2010"` (without a note)
 #'
 #' The short name - [mo_shortname()] - almost always returns the first character of the genus and the full species, like `"E. coli"`. Exceptions are abbreviations of staphylococci (such as *"CoNS"*, Coagulase-Negative Staphylococci) and beta-haemolytic streptococci (such as *"GBS"*, Group B Streptococci). Please bear in mind that e.g. *E. coli* could mean *Escherichia coli* (kingdom of Bacteria) as well as *Entamoeba coli* (kingdom of Protozoa). Returning to the full name will be done using [as.mo()] internally, giving priority to bacteria and human pathogens, i.e. `"E. coli"` will be considered *Escherichia coli*. In other words, `mo_fullname(mo_shortname("Entamoeba coli"))` returns `"Escherichia coli"`.
 #'
 #' Since the top-level of the taxonomy is sometimes referred to as 'kingdom' and sometimes as 'domain', the functions [mo_kingdom()] and [mo_domain()] return the exact same results.
 #'
-#' The Gram stain - [mo_gramstain()] - will be determined based on the taxonomic kingdom and phylum. Originally, Cavalier-Smith defined the so-called subkingdoms Negibacteria and Posibacteria (2002, [PMID 11837318](https://pubmed.ncbi.nlm.nih.gov/11837318/)), and only considered these phyla as Posibacteria: Actinobacteria, Chloroflexi, Firmicutes, and Tenericutes. All of these phyla were renamed to Actinomycetota, Chloroflexota, Bacillota, and Mycoplasmatota (2021, [PMID 34694987](https://pubmed.ncbi.nlm.nih.gov/34694987/)). Bacteria in these phyla are considered Gram-positive in this `AMR` package, except for members of the class Negativicutes (within phylum Bacillota) which are Gram-negative. All other bacteria are considered Gram-negative. Species outside the kingdom of Bacteria will return a value `NA`. Functions [mo_is_gram_negative()] and [mo_is_gram_positive()] always return `TRUE` or `FALSE` (or `NA` when the input is `NA` or the MO code is `UNKNOWN`), thus always return `FALSE` for species outside the taxonomic kingdom of Bacteria.
+#' Determination of the Gram stain - [mo_gramstain()] - will be based on the taxonomic kingdom and phylum. Originally, Cavalier-Smith defined the so-called subkingdoms Negibacteria and Posibacteria (2002, [PMID 11837318](https://pubmed.ncbi.nlm.nih.gov/11837318/)), and only considered these phyla as Posibacteria: Actinobacteria, Chloroflexi, Firmicutes, and Tenericutes. These phyla were renamed to Actinomycetota, Chloroflexota, Bacillota, and Mycoplasmatota (2021, [PMID 34694987](https://pubmed.ncbi.nlm.nih.gov/34694987/)). Bacteria in these phyla are considered Gram-positive in this `AMR` package, except for members of the class Negativicutes (within phylum Bacillota) which are Gram-negative. All other bacteria are considered Gram-negative. Species outside the kingdom of Bacteria will return a value `NA`. Functions [mo_is_gram_negative()] and [mo_is_gram_positive()] always return `TRUE` or `FALSE` (or `NA` when the input is `NA` or the MO code is `UNKNOWN`), thus always return `FALSE` for species outside the taxonomic kingdom of Bacteria.
 #'
 #' Determination of yeasts - [mo_is_yeast()] - will be based on the taxonomic kingdom and class. *Budding yeasts* are fungi of the phylum Ascomycota, class Saccharomycetes (also called Hemiascomycetes). *True yeasts* are aggregated into the underlying order Saccharomycetales. Thus, for all microorganisms that are member of the taxonomic class Saccharomycetes, the function will return `TRUE`. It returns `FALSE` otherwise (or `NA` when the input is `NA` or the MO code is `UNKNOWN`).
 #'
-#' Intrinsic resistance - [mo_is_intrinsic_resistant()] - will be determined based on the [intrinsic_resistant] data set, which is based on `r format_eucast_version_nr(3.3)`. The [mo_is_intrinsic_resistant()] functions can be vectorised over arguments `x` (input for microorganisms) and over `ab` (input for antibiotics).
+#' Determination of intrinsic resistance - [mo_is_intrinsic_resistant()] - will be based on the [intrinsic_resistant] data set, which is based on `r format_eucast_version_nr(3.3)`. The [mo_is_intrinsic_resistant()] function can be vectorised over both argument `x` (input for microorganisms) and `ab` (input for antibiotics).
 #'
 #' All output [will be translated][translate] where possible.
 #'
@@ -347,7 +347,13 @@ mo_kingdom <- function(x, language = get_AMR_locale(), keep_synonyms = getOption
 
 #' @rdname mo_property
 #' @export
-mo_domain <- mo_kingdom
+mo_domain <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) {
+  if (missing(x)) {
+    # this tries to find the data and an 'mo' column
+    x <- find_mo_col(fn = "mo_domain")
+  }
+  mo_kingdom(x = x, language = language, keep_synonyms = keep_synonyms, ...)
+}
 
 #' @rdname mo_property
 #' @export

R/translate.R

@@ -84,9 +84,11 @@
 #' set_AMR_locale("Deutsch")
 #' set_AMR_locale("German")
 #' set_AMR_locale("de")
+#' ab_name("amoxi/clav")
 #'
 #' # reset to system default
 #' reset_AMR_locale()
+#' ab_name("amoxi/clav")
 get_AMR_locale <- function() {
   if (!is.null(getOption("AMR_locale", default = NULL))) {
     return(validate_language(getOption("AMR_locale"), extra_txt = "set with `options(AMR_locale = ...)`"))

data-raw/microorganisms.md5

@@ -1 +1 @@
-4cb5e83062897061b17ddac6d5cd31d7
+0a4241916334341aa70923aac880997d

data-raw/reproduction_of_microorganisms.R

@@ -733,11 +733,14 @@ taxonomy <- taxonomy %>%
     ~ 1,
     kingdom %in% c("Archaea", "Bacteria", "Chromista", "Fungi") &
       (phylum %in% c(
-        "Proteobacteria",
+        "Sarcomastigophora",
-        "Firmicutes",
+        "Firmicutes", # old, now Bacillota
-        "Bacillota", # this one is new - this was renamed from Firmicutes by Gibbons et al., 2021
+        "Bacillota",
-        "Actinobacteria",
+        "Proteobacteria", # old, now Pseudomonadota
-        "Sarcomastigophora"
+        "Pseudomonadota",
+        "Actinobacteria", # old, now Actinomycetota
+        "Actinomycetota"
+        
       ) |
         genus %in% MO_PREVALENT_GENERA)
     ~ 2,

man/as.mo.Rd

@@ -152,7 +152,7 @@ The grouping into human pathogenic prevalence (\eqn{p}) is based on experience f
 
 All characters in \eqn{x} and \eqn{n} are ignored that are other than A-Z, a-z, 0-9, spaces and parentheses.
 
-All matches are sorted descending on their matching score and for all user input values, the top match will be returned. This will lead to the effect that e.g., \code{"E. coli"} will return the microbial ID of \emph{Escherichia coli} (\eqn{m = 0.688}, a highly prevalent microorganism found in humans) and not \emph{Entamoeba coli} (\eqn{m = 0.119}, a less prevalent microorganism in humans), although the latter would alphabetically come first.
+All matches are sorted descending on their matching score and for all user input values, the top match will be returned. This will lead to the effect that e.g., \code{"E. coli"} will return the microbial ID of \emph{Escherichia coli} (\eqn{m = 0.688}, a highly prevalent microorganism found in humans) and not \emph{Entamoeba coli} (\eqn{m = 0.079}, a less prevalent microorganism in humans), although the latter would alphabetically come first.
 }
 
 \section{Reference Data Publicly Available}{

man/mo_matching_score.Rd

@@ -43,7 +43,7 @@ The grouping into human pathogenic prevalence (\eqn{p}) is based on experience f
 
 All characters in \eqn{x} and \eqn{n} are ignored that are other than A-Z, a-z, 0-9, spaces and parentheses.
 
-All matches are sorted descending on their matching score and for all user input values, the top match will be returned. This will lead to the effect that e.g., \code{"E. coli"} will return the microbial ID of \emph{Escherichia coli} (\eqn{m = 0.688}, a highly prevalent microorganism found in humans) and not \emph{Entamoeba coli} (\eqn{m = 0.119}, a less prevalent microorganism in humans), although the latter would alphabetically come first.
+All matches are sorted descending on their matching score and for all user input values, the top match will be returned. This will lead to the effect that e.g., \code{"E. coli"} will return the microbial ID of \emph{Escherichia coli} (\eqn{m = 0.688}, a highly prevalent microorganism found in humans) and not \emph{Entamoeba coli} (\eqn{m = 0.079}, a less prevalent microorganism in humans), although the latter would alphabetically come first.
 }
 
 \section{Reference Data Publicly Available}{

man/mo_property.Rd

@@ -287,20 +287,20 @@ Use these functions to return a specific property of a microorganism based on th
 \details{
 All functions will, at default, keep old taxonomic properties. Please refer to this example, knowing that \emph{Escherichia blattae} was renamed to \emph{Shimwellia blattae} in 2010:
 \itemize{
-\item \code{mo_name("Escherichia blattae")} will return \code{"Shimwellia blattae"} (with a message about the renaming)
+\item \code{mo_name("Escherichia blattae")} will return \code{"Shimwellia blattae"} (with a note about the renaming)
-\item \code{mo_ref("Escherichia blattae", keep_synonyms = TRUE)} will return \code{"Burgess et al., 1973"} (with a warning about the renaming)
+\item \code{mo_ref("Escherichia blattae", keep_synonyms = TRUE)} will return \code{"Burgess et al., 1973"} (without a note)
-\item \code{mo_ref("Shimwellia blattae", keep_synonyms = FALSE)} will return \code{"Priest et al., 2010"} (without a message)
+\item \code{mo_ref("Shimwellia blattae", keep_synonyms = FALSE)} will return \code{"Priest et al., 2010"} (without a note)
 }
 
 The short name - \code{\link[=mo_shortname]{mo_shortname()}} - almost always returns the first character of the genus and the full species, like \code{"E. coli"}. Exceptions are abbreviations of staphylococci (such as \emph{"CoNS"}, Coagulase-Negative Staphylococci) and beta-haemolytic streptococci (such as \emph{"GBS"}, Group B Streptococci). Please bear in mind that e.g. \emph{E. coli} could mean \emph{Escherichia coli} (kingdom of Bacteria) as well as \emph{Entamoeba coli} (kingdom of Protozoa). Returning to the full name will be done using \code{\link[=as.mo]{as.mo()}} internally, giving priority to bacteria and human pathogens, i.e. \code{"E. coli"} will be considered \emph{Escherichia coli}. In other words, \code{mo_fullname(mo_shortname("Entamoeba coli"))} returns \code{"Escherichia coli"}.
 
 Since the top-level of the taxonomy is sometimes referred to as 'kingdom' and sometimes as 'domain', the functions \code{\link[=mo_kingdom]{mo_kingdom()}} and \code{\link[=mo_domain]{mo_domain()}} return the exact same results.
 
-The Gram stain - \code{\link[=mo_gramstain]{mo_gramstain()}} - will be determined based on the taxonomic kingdom and phylum. Originally, Cavalier-Smith defined the so-called subkingdoms Negibacteria and Posibacteria (2002, \href{https://pubmed.ncbi.nlm.nih.gov/11837318/}{PMID 11837318}), and only considered these phyla as Posibacteria: Actinobacteria, Chloroflexi, Firmicutes, and Tenericutes. All of these phyla were renamed to Actinomycetota, Chloroflexota, Bacillota, and Mycoplasmatota (2021, \href{https://pubmed.ncbi.nlm.nih.gov/34694987/}{PMID 34694987}). Bacteria in these phyla are considered Gram-positive in this \code{AMR} package, except for members of the class Negativicutes (within phylum Bacillota) which are Gram-negative. All other bacteria are considered Gram-negative. Species outside the kingdom of Bacteria will return a value \code{NA}. Functions \code{\link[=mo_is_gram_negative]{mo_is_gram_negative()}} and \code{\link[=mo_is_gram_positive]{mo_is_gram_positive()}} always return \code{TRUE} or \code{FALSE} (or \code{NA} when the input is \code{NA} or the MO code is \code{UNKNOWN}), thus always return \code{FALSE} for species outside the taxonomic kingdom of Bacteria.
+Determination of the Gram stain - \code{\link[=mo_gramstain]{mo_gramstain()}} - will be based on the taxonomic kingdom and phylum. Originally, Cavalier-Smith defined the so-called subkingdoms Negibacteria and Posibacteria (2002, \href{https://pubmed.ncbi.nlm.nih.gov/11837318/}{PMID 11837318}), and only considered these phyla as Posibacteria: Actinobacteria, Chloroflexi, Firmicutes, and Tenericutes. These phyla were renamed to Actinomycetota, Chloroflexota, Bacillota, and Mycoplasmatota (2021, \href{https://pubmed.ncbi.nlm.nih.gov/34694987/}{PMID 34694987}). Bacteria in these phyla are considered Gram-positive in this \code{AMR} package, except for members of the class Negativicutes (within phylum Bacillota) which are Gram-negative. All other bacteria are considered Gram-negative. Species outside the kingdom of Bacteria will return a value \code{NA}. Functions \code{\link[=mo_is_gram_negative]{mo_is_gram_negative()}} and \code{\link[=mo_is_gram_positive]{mo_is_gram_positive()}} always return \code{TRUE} or \code{FALSE} (or \code{NA} when the input is \code{NA} or the MO code is \code{UNKNOWN}), thus always return \code{FALSE} for species outside the taxonomic kingdom of Bacteria.
 
 Determination of yeasts - \code{\link[=mo_is_yeast]{mo_is_yeast()}} - will be based on the taxonomic kingdom and class. \emph{Budding yeasts} are fungi of the phylum Ascomycota, class Saccharomycetes (also called Hemiascomycetes). \emph{True yeasts} are aggregated into the underlying order Saccharomycetales. Thus, for all microorganisms that are member of the taxonomic class Saccharomycetes, the function will return \code{TRUE}. It returns \code{FALSE} otherwise (or \code{NA} when the input is \code{NA} or the MO code is \code{UNKNOWN}).
 
-Intrinsic resistance - \code{\link[=mo_is_intrinsic_resistant]{mo_is_intrinsic_resistant()}} - will be determined based on the \link{intrinsic_resistant} data set, which is based on \href{https://www.eucast.org/expert_rules_and_expected_phenotypes/}{'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3} (2021). The \code{\link[=mo_is_intrinsic_resistant]{mo_is_intrinsic_resistant()}} functions can be vectorised over arguments \code{x} (input for microorganisms) and over \code{ab} (input for antibiotics).
+Determination of intrinsic resistance - \code{\link[=mo_is_intrinsic_resistant]{mo_is_intrinsic_resistant()}} - will be based on the \link{intrinsic_resistant} data set, which is based on \href{https://www.eucast.org/expert_rules_and_expected_phenotypes/}{'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3} (2021). The \code{\link[=mo_is_intrinsic_resistant]{mo_is_intrinsic_resistant()}} function can be vectorised over both argument \code{x} (input for microorganisms) and \code{ab} (input for antibiotics).
 
 All output \link[=translate]{will be translated} where possible.
 
@@ -336,7 +336,7 @@ The grouping into human pathogenic prevalence (\eqn{p}) is based on experience f
 
 All characters in \eqn{x} and \eqn{n} are ignored that are other than A-Z, a-z, 0-9, spaces and parentheses.
 
-All matches are sorted descending on their matching score and for all user input values, the top match will be returned. This will lead to the effect that e.g., \code{"E. coli"} will return the microbial ID of \emph{Escherichia coli} (\eqn{m = 0.688}, a highly prevalent microorganism found in humans) and not \emph{Entamoeba coli} (\eqn{m = 0.119}, a less prevalent microorganism in humans), although the latter would alphabetically come first.
+All matches are sorted descending on their matching score and for all user input values, the top match will be returned. This will lead to the effect that e.g., \code{"E. coli"} will return the microbial ID of \emph{Escherichia coli} (\eqn{m = 0.688}, a highly prevalent microorganism found in humans) and not \emph{Entamoeba coli} (\eqn{m = 0.079}, a less prevalent microorganism in humans), although the latter would alphabetically come first.
 }
 
 \section{Source}{

man/translate.Rd

@@ -76,7 +76,9 @@ mo_name("Coagulase-negative Staphylococcus (CoNS)")
 set_AMR_locale("Deutsch")
 set_AMR_locale("German")
 set_AMR_locale("de")
+ab_name("amoxi/clav")
 
 # reset to system default
 reset_AMR_locale()
+ab_name("amoxi/clav")
 }