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(v3.0.1.9059) Update taxonomy of microorganisms

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Matthijs Berends
2026-06-23 01:38:13 +02:00
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parent 0af3f84655
commit 3f9f931777
123 changed files with 121928 additions and 94162 deletions
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6
R/mo_matching_score.R
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@@ -47,7 +47,7 @@
#' * \eqn{l_n} is the length of \eqn{n};
#' * \eqn{lev} is the [Levenshtein distance function](https://en.wikipedia.org/wiki/Levenshtein_distance) (counting any insertion as 1, and any deletion or substitution as 2) that is needed to change \eqn{x} into \eqn{n};
#' * \eqn{p_n} is the human pathogenic prevalence group of \eqn{n}, as described below;
#' * \eqn{k_n} is the taxonomic kingdom of \eqn{n}, set as Bacteria = 1, Fungi = 1.25, Protozoa = 1.5, Chromista = 1.75, Archaea = 2, others = 3.
#' * \eqn{k_n} is the taxonomic domain ('kingdom' until taxonomic reclassification of 2024) of \eqn{n}, set as Bacteria = 1, Fungi = 1.25, Protozoa = 1.5, Chromista = 1.75, Archaea = 2, others = 3.
#'
#' 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:
#'
@@ -122,8 +122,8 @@ mo_matching_score <- function(x, n) {
# human pathogenic prevalence (1 to 3), see ?as.mo
p_n <- AMR_env$MO_lookup[match(n, AMR_env$MO_lookup$fullname), "prevalence", drop = TRUE]
# kingdom index (Bacteria = 1, Fungi = 2, Protozoa = 3, Archaea = 4, others = 5)
k_n <- AMR_env$MO_lookup[match(n, AMR_env$MO_lookup$fullname), "kingdom_index", drop = TRUE]
# domain index (Bacteria = 1, Fungi = 2, Protozoa = 3, Archaea = 4, others = 5)
k_n <- AMR_env$MO_lookup[match(n, AMR_env$MO_lookup$fullname), "domain_index", drop = TRUE]
# matching score:
(l_n - 0.5 * l_n.lev) / (l_n * p_n * k_n)