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(v1.3.0.9022) mo_matching_score(), poorman update, as.rsi() fix

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dr. M.S. (Matthijs) Berends
2020-09-18 16:05:53 +02:00
parent 89401ede9f
commit 4e40e42011
138 changed files with 2923 additions and 1472 deletions
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14
R/mo_property.R
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@ -47,11 +47,11 @@
#' @rdname mo_property
#' @name mo_property
#' @return
#' - An [`integer`] in case of [mo_year()]
#' - A [`list`] in case of [mo_taxonomy()] and [mo_info()]
#' - A named [`character`] in case of [mo_url()]
#' - A [`double`] in case of [mo_snomed()]
#' - A [`character`] in all other cases
#' - An [integer] in case of [mo_year()]
#' - A [list] in case of [mo_taxonomy()] and [mo_info()]
#' - A named [character] in case of [mo_url()]
#' - A [double] in case of [mo_snomed()]
#' - A [character] in all other cases
#' @export
#' @seealso [microorganisms]
#' @inheritSection AMR Reference data publicly available
@ -378,8 +378,8 @@ mo_url <- function(x, open = FALSE, language = get_locale(), ...) {
mo_names <- mo_name(mo)
metadata <- get_mo_failures_uncertainties_renamed()
df <- data.frame(mo, stringsAsFactors = FALSE) %>%
left_join(select(microorganisms, mo, source, species_id), by = "mo")
df <- data.frame(mo, stringsAsFactors = FALSE) %pm>%
pm_left_join(pm_select(microorganisms, mo, source, species_id), by = "mo")
df$url <- ifelse(df$source == "CoL",
paste0(catalogue_of_life$url_CoL, "details/species/id/", df$species_id, "/"),
ifelse(df$source == "DSMZ",