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update mo algorithm
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@ -52,14 +52,16 @@
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#'
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#' The grouping into human pathogenic prevalence (\eqn{p}) is based on recent work from Bartlett *et al.* (2022, \doi{10.1099/mic.0.001269}) who extensively studied medical-scientific literature to categorise all bacterial species into these groups:
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#'
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#' - **Established**, if a taxonomic species has infected at least three persons in three or more references. These records have `prevalence = 1.0` in the [microorganisms] data set.
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#' - **Putative**, if a taxonomic species has fewer than three known cases. These records have `prevalence = 2.0` in the [microorganisms] data set.
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#' - **Established**, if a taxonomic species has infected at least three persons in three or more references. These records have `prevalence = 1.0` in the [microorganisms] data set;
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#' - **Putative**, if a taxonomic species has fewer than three known cases. These records have `prevalence = 1.25` in the [microorganisms] data set.
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#'
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#' Furthermore,
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#'
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#' - Any *other* bacterial genus, species or subspecies of which the genus is present in the two aforementioned groups, has `prevalence = 2.5` in the [microorganisms] data set.
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#' - Any *non-bacterial* genus, species or subspecies of which the genus is present in the following list, also has `prevalence = 2.5` in the [microorganisms] data set: `r vector_or(MO_PREVALENT_GENERA, quotes = "*")`.
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#' - All other records have `prevalence = 3.0` in the [microorganisms] data set.
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#' - Any genus present in the **established** list also has `prevalence = 1.0` in the [microorganisms] data set;
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#' - Any other genus present in the **putative** list has `prevalence = 1.25` in the [microorganisms] data set;
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#' - Any other species or subspecies of which the genus is present in the two aforementioned groups, has `prevalence = 1.5` in the [microorganisms] data set;
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#' - Any *non-bacterial* genus, species or subspecies of which the genus is present in the following list, has `prevalence = 1.5` in the [microorganisms] data set: `r vector_or(MO_PREVALENT_GENERA, quotes = "*")`;
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#' - All other records have `prevalence = 2.0` in the [microorganisms] data set.
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#'
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#' When calculating the matching score, all characters in \eqn{x} and \eqn{n} are ignored that are other than A-Z, a-z, 0-9, spaces and parentheses.
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#'
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@ -840,7 +840,7 @@ mo_validate <- function(x, property, language, keep_synonyms = keep_synonyms, ..
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} else if (property == "snomed") {
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return(sort(as.character(eval(parse(text = x)))))
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} else {
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# everything else is character
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# everything else as character
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return(as.character(x))
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}
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}
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