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@@ -184,135 +184,116 @@ mo_property(x, property = "fullname", language = get_AMR_locale(),
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## Value
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- An [integer](https://rdrr.io/r/base/integer.html) in case of
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`mo_year()`
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- An [ordered factor](https://rdrr.io/pkg/data.table/man/fctr.html) in
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case of `mo_pathogenicity()`
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- A [list](https://rdrr.io/r/base/list.html) in case of `mo_taxonomy()`,
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`mo_synonyms()`, `mo_snomed()`, and `mo_info()`
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- A [logical](https://rdrr.io/r/base/logical.html) in case of
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`mo_is_anaerobic()`, `mo_is_gram_negative()`, `mo_is_gram_positive()`,
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`mo_is_intrinsic_resistant()`, and `mo_is_yeast()`
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- A named [character](https://rdrr.io/r/base/character.html) in case of
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`mo_synonyms()` and `mo_url()`
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- A [character](https://rdrr.io/r/base/character.html) in all other
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cases
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\- An \[integer\] in case of \[mo_year()\] - An \[ordered
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factor\]\[factor\] in case of \[mo_pathogenicity()\] - A \[list\] in
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case of \[mo_taxonomy()\], \[mo_synonyms()\], \[mo_snomed()\], and
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\[mo_info()\] - A \[logical\] in case of \[mo_is_anaerobic()\],
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\[mo_is_gram_negative()\], \[mo_is_gram_positive()\],
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\[mo_is_intrinsic_resistant()\], and \[mo_is_yeast()\] - A named
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\[character\] in case of \[mo_synonyms()\] and \[mo_url()\] - A
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\[character\] in all other cases
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## Details
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All functions will, at default, **not** keep old taxonomic properties,
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as synonyms are automatically replaced with the current taxonomy. Take
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for example *Enterobacter aerogenes*, which was initially named in 1960
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but renamed to *Klebsiella aerogenes* in 2017:
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All functions will, at default, \*\*not\*\* keep old taxonomic
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properties, as synonyms are automatically replaced with the current
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taxonomy. Take for example \*Enterobacter aerogenes\*, which was
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initially named in 1960 but renamed to \*Klebsiella aerogenes\* in
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2017: - \`mo_genus("Enterobacter aerogenes")\` will return
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\`"Klebsiella"\` (with a note about the renaming) -
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\`mo_genus("Enterobacter aerogenes", keep_synonyms = TRUE)\` will return
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\`"Enterobacter"\` (with a once-per-session warning that the name is
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outdated) - \`mo_ref("Enterobacter aerogenes")\` will return \`"Tindall
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et al., 2017"\` (with a note about the renaming) -
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\`mo_ref("Enterobacter aerogenes", keep_synonyms = TRUE)\` will return
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\`"Hormaeche et al., 1960"\` (with a once-per-session warning that the
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name is outdated)
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- `mo_genus("Enterobacter aerogenes")` will return `"Klebsiella"` (with
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a note about the renaming)
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- `mo_genus("Enterobacter aerogenes", keep_synonyms = TRUE)` will return
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`"Enterobacter"` (with a once-per-session warning that the name is
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outdated)
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- `mo_ref("Enterobacter aerogenes")` will return
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`"Tindall et al., 2017"` (with a note about the renaming)
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- `mo_ref("Enterobacter aerogenes", keep_synonyms = TRUE)` will return
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`"Hormaeche et al., 1960"` (with a once-per-session warning that the
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name is outdated)
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The short name (`mo_shortname()`) returns the first character of the
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genus and the full species, such as `"E. coli"`, for species and
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The short name (\[mo_shortname()\]) returns the first character of the
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genus and the full species, such as \`"E. coli"\`, for species and
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subspecies. Exceptions are abbreviations of staphylococci (such as
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*"CoNS"*, Coagulase-Negative Staphylococci) and beta-haemolytic
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streptococci (such as *"GBS"*, Group B Streptococci). Please bear in
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mind that e.g. *E. coli* could mean *Escherichia coli* (kingdom of
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Bacteria) as well as *Entamoeba coli* (kingdom of Protozoa). Returning
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to the full name will be done using
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[`as.mo()`](https://amr-for-r.org/reference/as.mo.md) internally, giving
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priority to bacteria and human pathogens, i.e. `"E. coli"` will be
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considered *Escherichia coli*. As a result,
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`mo_fullname(mo_shortname("Entamoeba coli"))` returns
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`"Escherichia coli"`.
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\*"CoNS"\*, Coagulase-Negative Staphylococci) and beta-haemolytic
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streptococci (such as \*"GBS"\*, Group B Streptococci). Please bear in
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mind that e.g. \*E. coli\* could mean \*Escherichia coli\* (kingdom of
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Bacteria) as well as \*Entamoeba coli\* (kingdom of Protozoa). Returning
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to the full name will be done using \[as.mo()\] internally, giving
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priority to bacteria and human pathogens, i.e. \`"E. coli"\` will be
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considered \*Escherichia coli\*. As a result,
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\`mo_fullname(mo_shortname("Entamoeba coli"))\` returns \`"Escherichia
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coli"\`.
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Since the top-level of the taxonomy is sometimes referred to as
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'kingdom' and sometimes as 'domain', the functions `mo_kingdom()` and
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`mo_domain()` return the exact same results.
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'kingdom' and sometimes as 'domain', the functions \[mo_kingdom()\] and
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\[mo_domain()\] return the exact same results.
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Determination of human pathogenicity (`mo_pathogenicity()`) is strongly
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based on Bartlett *et al.* (2022,
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Determination of human pathogenicity (\[mo_pathogenicity()\]) is
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strongly based on Bartlett \*et al.\* (2022,
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[doi:10.1099/mic.0.001269](https://doi.org/10.1099/mic.0.001269) ). This
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function returns a
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[factor](https://rdrr.io/pkg/data.table/man/fctr.html) with the levels
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*Pathogenic*, *Potentially pathogenic*, *Non-pathogenic*, and *Unknown*.
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function returns a \[factor\] with the levels \*Pathogenic\*,
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\*Potentially pathogenic\*, \*Non-pathogenic\*, and \*Unknown\*.
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Determination of the Gram stain (`mo_gramstain()`) will be based on the
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taxonomic kingdom and phylum. Originally, Cavalier-Smith defined the
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so-called subkingdoms Negibacteria and Posibacteria (2002, [PMID
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11837318](https://pubmed.ncbi.nlm.nih.gov/11837318/)), and only
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Determination of the Gram stain (\[mo_gramstain()\]) will be based on
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the taxonomic kingdom and phylum. Originally, Cavalier-Smith defined the
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so-called subkingdoms Negibacteria and Posibacteria (2002, \[PMID
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11837318\](https://pubmed.ncbi.nlm.nih.gov/11837318/)), and only
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considered these phyla as Posibacteria: Actinobacteria, Chloroflexi,
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Firmicutes, and Tenericutes. These phyla were later renamed to
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Actinomycetota, Chloroflexota, Bacillota, and Mycoplasmatota (2021,
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[PMID 34694987](https://pubmed.ncbi.nlm.nih.gov/34694987/)). Bacteria in
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these phyla are considered Gram-positive in this `AMR` package, except
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for members of the class Negativicutes (within phylum Bacillota) which
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are Gram-negative. All other bacteria are considered Gram-negative.
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Species outside the kingdom of Bacteria will return a value `NA`.
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Functions `mo_is_gram_negative()` and `mo_is_gram_positive()` always
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return `TRUE` or `FALSE` (or `NA` when the input is `NA` or the MO code
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is `UNKNOWN`), thus always return `FALSE` for species outside the
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taxonomic kingdom of Bacteria.
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\[PMID 34694987\](https://pubmed.ncbi.nlm.nih.gov/34694987/)). Bacteria
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in these phyla are considered Gram-positive in this \`AMR\` package,
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except for members of the class Negativicutes (within phylum Bacillota)
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which are Gram-negative. All other bacteria are considered
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Gram-negative. Species outside the kingdom of Bacteria will return a
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value \`NA\`. Functions \[mo_is_gram_negative()\] and
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\[mo_is_gram_positive()\] always return \`TRUE\` or \`FALSE\` (or \`NA\`
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when the input is \`NA\` or the MO code is \`UNKNOWN\`), thus always
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return \`FALSE\` for species outside the taxonomic kingdom of Bacteria.
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Determination of yeasts (`mo_is_yeast()`) will be based on the taxonomic
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kingdom and class. *Budding yeasts* are yeasts that reproduce asexually
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through a process called budding, where a new cell develops from a small
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protrusion on the parent cell. Taxonomically, these are members of the
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phylum Ascomycota, class Saccharomycetes (also called Hemiascomycetes)
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or Pichiomycetes. *True yeasts* quite specifically refers to yeasts in
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the underlying order Saccharomycetales (such as *Saccharomyces
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cerevisiae*). Thus, for all microorganisms that are member of the
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taxonomic class Saccharomycetes or Pichiomycetes, the function will
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return `TRUE`. It returns `FALSE` otherwise (or `NA` when the input is
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`NA` or the MO code is `UNKNOWN`).
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Determination of yeasts (\[mo_is_yeast()\]) will be based on the
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taxonomic kingdom and class. \*Budding yeasts\* are yeasts that
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reproduce asexually through a process called budding, where a new cell
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develops from a small protrusion on the parent cell. Taxonomically,
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these are members of the phylum Ascomycota, class Saccharomycetes (also
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called Hemiascomycetes) or Pichiomycetes. \*True yeasts\* quite
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specifically refers to yeasts in the underlying order Saccharomycetales
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(such as \*Saccharomyces cerevisiae\*). Thus, for all microorganisms
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that are member of the taxonomic class Saccharomycetes or Pichiomycetes,
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the function will return \`TRUE\`. It returns \`FALSE\` otherwise (or
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\`NA\` when the input is \`NA\` or the MO code is \`UNKNOWN\`).
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Determination of intrinsic resistance (`mo_is_intrinsic_resistant()`)
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will be based on the
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[intrinsic_resistant](https://amr-for-r.org/reference/intrinsic_resistant.md)
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data set, which is based on ['EUCAST Expected Resistant Phenotypes'
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v1.2](https://www.eucast.org/bacteria/important-additional-information/expert-rules/)
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(2023). The `mo_is_intrinsic_resistant()` function can be vectorised
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over both argument `x` (input for microorganisms) and `ab` (input for
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Determination of intrinsic resistance (\[mo_is_intrinsic_resistant()\])
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will be based on the \[intrinsic_resistant\] data set, which is based on
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\`r
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format_eucast_version_nr(names(EUCAST_VERSION_EXPECTED_PHENOTYPES\[1\]))\`.
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The \[mo_is_intrinsic_resistant()\] function can be vectorised over both
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argument \`x\` (input for microorganisms) and \`ab\` (input for
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antimicrobials).
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Determination of bacterial oxygen tolerance (`mo_oxygen_tolerance()`)
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will be based on BacDive, see *Source*. The function `mo_is_anaerobic()`
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only returns `TRUE` if the oxygen tolerance is `"anaerobe"`, indicting
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an obligate anaerobic species or genus. It always returns `FALSE` for
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species outside the taxonomic kingdom of Bacteria.
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Determination of bacterial oxygen tolerance (\[mo_oxygen_tolerance()\])
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will be based on BacDive, see \*Source\*. The function
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\[mo_is_anaerobic()\] only returns \`TRUE\` if the oxygen tolerance is
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\`"anaerobe"\`, indicting an obligate anaerobic species or genus. It
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always returns \`FALSE\` for species outside the taxonomic kingdom of
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Bacteria.
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The function `mo_url()` will return the direct URL to the online
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The function \[mo_url()\] will return the direct URL to the online
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database entry, which also shows the scientific reference of the
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concerned species. [This MycoBank URL](https://www.mycobank.org) will be
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used for fungi wherever available , [this LPSN
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URL](https://www.mycobank.org) for bacteria wherever available, and
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[this GBIF link](https://www.gbif.org) otherwise.
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concerned species. \[This MycoBank URL\](\`r
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TAXONOMY_VERSION\$MycoBank\$url\`) will be used for fungi wherever
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available , \[this LPSN URL\](\`r TAXONOMY_VERSION\$MycoBank\$url\`) for
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bacteria wherever available, and \[this GBIF link\](\`r
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TAXONOMY_VERSION\$GBIF\$url\`) otherwise.
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SNOMED codes (`mo_snomed()`) was last updated on July 16th, 2024. See
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*Source* and the
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[microorganisms](https://amr-for-r.org/reference/microorganisms.md) data
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set for more info.
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SNOMED codes (\[mo_snomed()\]) was last updated on \`r
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documentation_date(TAXONOMY_VERSION\$SNOMED\$accessed_date)\`. See
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\*Source\* and the \[microorganisms\] data set for more info.
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Old taxonomic names (so-called 'synonyms') can be retrieved with
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`mo_synonyms()` (which will have the scientific reference as
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[name](https://rdrr.io/r/base/names.html)), the current taxonomic name
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can be retrieved with `mo_current()`. Both functions return full names.
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\[mo_synonyms()\] (which will have the scientific reference as
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\[name\]\[base::names()\]), the current taxonomic name can be retrieved
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with \[mo_current()\]. Both functions return full names.
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All output [will be
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translated](https://amr-for-r.org/reference/translate.md) where
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possible.
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All output \[will be translated\]\[translate\] where possible.
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## Matching Score for Microorganisms
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