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incorporate Bartlett et al (2022)

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dr. M.S. (Matthijs) Berends
2022-12-19 15:32:41 +01:00
parent 23fe427cbc
commit b1b7534c78
24 changed files with 36375 additions and 36304 deletions
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R/mo.R
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@ -97,6 +97,7 @@
#' 7. `r TAXONOMY_VERSION$LPSN$citation` Accessed from <`r TAXONOMY_VERSION$LPSN$url`> on `r documentation_date(TAXONOMY_VERSION$LPSN$accessed_date)`.
#' 8. `r TAXONOMY_VERSION$GBIF$citation` Accessed from <`r TAXONOMY_VERSION$GBIF$url`> on `r documentation_date(TAXONOMY_VERSION$GBIF$accessed_date)`.
#' 9. `r TAXONOMY_VERSION$SNOMED$citation` URL: <`r TAXONOMY_VERSION$SNOMED$url`>
#' 10. Bartlett A *et al.* (2022). **A comprehensive list of bacterial pathogens infecting humans** *Microbiology* 168:001269; \doi{10.1099/mic.0.001269}
#' @export
#' @return A [character] [vector] with additional class [`mo`]
#' @seealso [microorganisms] for the [data.frame] that is being used to determine ID's.
@ -782,7 +783,7 @@ print.mo_uncertainties <- function(x, ...) {
return(invisible(NULL))
}
cat(word_wrap("Matching scores are based on the resemblance between the input and the full taxonomic name, and the pathogenicity in humans. See `?mo_matching_score`.\n\n", add_fn = font_blue))
cat(word_wrap("Matching scores are based on the resemblance between the input and the full taxonomic name, and the pathogenicity in humans according to Bartlett ", font_italic("et al."), " (2022). See `?mo_matching_score`.\n\n", add_fn = font_blue))
if (has_colour()) {
cat(word_wrap("Colour keys: ",
font_red_bg(" 0.000-0.499 "),