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microorganisms update, added Salmonella groups

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dr. M.S. (Matthijs) Berends
2022-12-16 16:10:43 +01:00
parent 8da2467209
commit 5f3a7694aa
43 changed files with 38933 additions and 105358 deletions
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R/data.R
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@ -120,6 +120,7 @@
#' ### Manual additions
#' For convenience, some entries were added manually:
#'
#' - `r format_included_data_number(which(microorganisms$genus == "Salmonella" & microorganisms$species == "enterica" & microorganisms$source == "manually added"))` entries for the city-like serovars of *Salmonellae*
#' - 11 entries of *Streptococcus* (beta-haemolytic: groups A, B, C, D, F, G, H, K and unspecified; other: viridans, milleri)
#' - 2 entries of *Staphylococcus* (coagulase-negative (CoNS) and coagulase-positive (CoPS))
#' - 1 entry of *Blastocystis* (*B. hominis*), although it officially does not exist (Noel *et al.* 2005, PMID 15634993)
@ -140,6 +141,8 @@
#' * `r TAXONOMY_VERSION$GBIF$citation` Accessed from <`r TAXONOMY_VERSION$GBIF$url`> on `r documentation_date(TAXONOMY_VERSION$GBIF$accessed_date)`.
#'
#' * `r TAXONOMY_VERSION$SNOMED$citation` URL: <`r TAXONOMY_VERSION$SNOMED$url`>
#'
#' * Grimont *et al.*. Antigenic Formulae of the Salmonella Serovars, 2007, 9th Edition. WHO Collaborating Centre for Reference and Research on *Salmonella* (WHOCC-SALM).
#' @seealso [as.mo()], [mo_property()], [microorganisms.codes], [intrinsic_resistant]
#' @examples
#' microorganisms