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dr. M.S. (Matthijs) Berends
2023-01-07 01:51:19 +01:00
parent 84ed8c32bb
commit 2375bfdcb5
8 changed files with 61 additions and 54 deletions
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R/mo.R
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@@ -83,7 +83,7 @@
#'
#' ### Microbial Prevalence of Pathogens in Humans
#'
#' The coercion rules consider the prevalence of microorganisms in humans grouped into three groups, which is available as the `prevalence` columns in the [microorganisms] data set. The grouping into human pathogenic prevalence is explained in the section *Matching Score for Microorganisms* below.
#' The coercion rules consider the prevalence of microorganisms in humans, which is available as the `prevalence` column in the [microorganisms] data set. The grouping into human pathogenic prevalence is explained in the section *Matching Score for Microorganisms* below.
#' @inheritSection mo_matching_score Matching Score for Microorganisms
#'
# (source as a section here, so it can be inherited by other man pages)
@@ -536,7 +536,7 @@ mo_cleaning_regex <- function() {
"|",
"([({]|\\[).+([})]|\\])",
"|",
"(^| )(e?spp|e?ssp|e?ss|e?sp|e?subsp|sube?species|biovar|biotype|serovar|serogr.?up|e?species|group|complex)[.]*( |$))"
"(^| )(e?spp|e?ssp|e?ss|e?sp|e?subsp|sube?species|biovar|biotype|serovar|serogr.?up|e?species)[.]*( |$|(complex|group)$))"
)
}
@@ -786,7 +786,7 @@ 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 according to Bartlett ", font_italic("et al."), " (2022). 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. 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 "),