Updated `mo_gramstain()` to reflect current taxonomy, fixes #83

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 1.8.2.9054
+Version: 1.8.2.9056
-Date: 2022-11-28
+Date: 2022-12-09
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)
   data analysis and to work with microbial and antimicrobial properties by

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 1.8.2.9054
+# AMR 1.8.2.9056
 
 This version will eventually become v2.0! We're happy to reach a new major milestone soon!
 

R/mo_property.R

@@ -45,9 +45,9 @@
 #'
 #' 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. According to Cavalier-Smith (2002, [PMID 11837318](https://pubmed.ncbi.nlm.nih.gov/11837318)), who defined subkingdoms Negibacteria and Posibacteria, only these phyla are Posibacteria: Actinobacteria, Chloroflexi, Firmicutes and Tenericutes. These bacteria are considered Gram-positive, except for members of the class Negativicutes which are Gram-negative. Members of other bacterial phyla are all 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` (except when the input is `NA` or the MO code is `UNKNOWN`), thus always return `FALSE` for species outside the taxonomic kingdom of Bacteria.
+#' 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 yeasts - [mo_is_yeast()] - will be based on the taxonomic kingdom and class. *Budding yeasts* are fungi of the phylum Ascomycetes, class Saccharomycetes (also called Hemiascomycetes). *True yeasts* are aggregated into the underlying order Saccharomycetales. Thus, for all microorganisms that are fungi and member of the taxonomic class Saccharomycetes, the function will return `TRUE`. It returns `FALSE` otherwise (except when the input is `NA` or the MO code is `UNKNOWN`).
+#' 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).
 #'
@@ -400,13 +400,17 @@ mo_gramstain <- function(x, language = get_AMR_locale(), keep_synonyms = getOpti
   # overwrite these 4 phyla with Gram-positives
   # Source: https://itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=956097 (Cavalier-Smith, 2002)
   x[(mo_phylum(x.mo, language = NULL, keep_synonyms = keep_synonyms) %in% c(
+    # no longer in use, does not hurt to keep here:
     "Actinobacteria",
     "Chloroflexi",
     "Firmicutes",
     "Tenericutes",
-    "Bacillota" # this one is new! It was renamed from Firmicutes by Gibbons et al., 2021
+    "Actinomycetota", # since 2021, old name was Actinobacteria
+    "Chloroflexota", # since 2021, old name was Chloroflexi
+    "Bacillota", # since 2021, old name was Firmicutes
+    "Mycoplasmatota" # since 2021, old name was Tenericutes
   ) &
-    # but class Negativicutes (of phylum Firmicutes) are Gram-negative!
+    # but class Negativicutes (of phylum Bacillota) are Gram-negative!
     mo_class(x.mo, language = NULL, keep_synonyms = keep_synonyms) != "Negativicutes")
   # and of course our own ID for Gram-positives
   | x.mo == "B_GRAMP"] <- "Gram-positive"

inst/tinytest/test-mo_property.R

@@ -44,6 +44,43 @@ expect_equal(mo_shortname("Staphylococcus aureus", Becker = "all", language = "e
 expect_equal(mo_shortname("Streptococcus agalactiae"), "S. agalactiae")
 expect_equal(mo_shortname("Streptococcus agalactiae", Lancefield = TRUE), "GBS")
 
+# check gram stain determination, to prevent we lag after a taxonomic renaming
+current_grampos_phyla <- c(
+  "Actinomycetota", # since 2021, old name was Actinobacteria
+  "Chloroflexota", # since 2021, old name was Chloroflexi
+  "Bacillota", # since 2021, old name was Firmicutes
+  "Mycoplasmatota" # since 2021, old name was Tenericutes
+)
+expect_true(all(current_grampos_phyla %in% microorganisms$phylum, na.rm = TRUE))
+current_grampos_classes <- c(
+  "",
+  "Acidimicrobiia",
+  "Actinomycetes",
+  "Anaerolineae",
+  "Ardenticatenia",
+  "Bacilli",
+  "Caldilineae",
+  "Chloroflexia",
+  "Clostridia",
+  "Coriobacteriia",
+  "Culicoidibacteria",
+  "Dehalococcoidia",
+  "Erysipelotrichia",
+  "Ktedonobacteria",
+  "Limnochordia",
+  "Mollicutes",
+  "Negativicutes",
+  "Nitriliruptoria",
+  "Rubrobacteria",
+  "Tepidiformia",
+  "Thermoflexia",
+  "Thermoleophilia",
+  "Thermolithobacteria",
+  "Tissierellia"
+)
+expect_identical(sort(unique(microorganisms[which(microorganisms$phylum %in% current_grampos_phyla), "class", drop = TRUE])),
+                 current_grampos_classes)
+
 expect_equal(mo_species("Escherichia coli"), "coli")
 expect_equal(mo_subspecies("Escherichia coli"), "")
 expect_equal(mo_type("Escherichia coli", language = "en"), "Bacteria")
@@ -72,8 +109,7 @@ expect_true(mo_url("Candida albicans") %like% "gbif.org")
 expect_true(mo_url("Escherichia coli") %like% "lpsn.dsmz.de")
 
 # test integrity
-MOs <- microorganisms
+expect_identical(microorganisms$fullname, mo_fullname(microorganisms$fullname, language = "en", keep_synonyms = TRUE))
-expect_identical(MOs$fullname, mo_fullname(MOs$fullname, language = "en", keep_synonyms = TRUE))
 
 # check languages
 expect_equal(mo_type("Escherichia coli", language = "de"), "Bakterien")

man/mo_property.Rd

@@ -296,9 +296,9 @@ The short name - \code{\link[=mo_shortname]{mo_shortname()}} - almost always ret
 
 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. According to Cavalier-Smith (2002, \href{https://pubmed.ncbi.nlm.nih.gov/11837318}{PMID 11837318}), who defined subkingdoms Negibacteria and Posibacteria, only these phyla are Posibacteria: Actinobacteria, Chloroflexi, Firmicutes and Tenericutes. These bacteria are considered Gram-positive, except for members of the class Negativicutes which are Gram-negative. Members of other bacterial phyla are all 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} (except 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.
+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 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 Ascomycetes, class Saccharomycetes (also called Hemiascomycetes). \emph{True yeasts} are aggregated into the underlying order Saccharomycetales. Thus, for all microorganisms that are fungi and member of the taxonomic class Saccharomycetes, the function will return \code{TRUE}. It returns \code{FALSE} otherwise (except when the input is \code{NA} or the MO code is \code{UNKNOWN}).
+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).