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guess_mo deprecation

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2019-01-06 16:40:55 +01:00
parent 5c6ff1bbda
commit 0205b6178d
6 changed files with 46 additions and 107 deletions
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7
R/deprecated.R
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@ -46,3 +46,10 @@ ratio <- function(x, ratio) {
}
sum(x, na.rm = TRUE) * (ratio / sum(ratio, na.rm = TRUE))
}
#' @rdname AMR-deprecated
#' @exported
guess_mo <- function(...) {
.Deprecated(new = "as.mo", package = "AMR")
as.mo(...)
}

14
R/mo.R
View File

@ -76,7 +76,6 @@
#' \item{\code{"D. spartina"}. This is the abbreviation of an old taxonomic name: \emph{Didymosphaeria spartinae} (the last "e" was missing from the input). This fungus was renamed to \emph{Leptosphaeria obiones}, so a warning will be thrown that this result (\code{F_LPTSP_OBI}) needs review.}
#' }
#'
#' \code{guess_mo} is an alias of \code{as.mo}.
#' @inheritSection itis ITIS
# (source as a section, so it can be inherited by other man pages)
#' @section Source:
@ -109,12 +108,11 @@
#' as.mo("GAS") # Group A Streptococci
#' as.mo("GBS") # Group B Streptococci
#'
#' # guess_mo is an alias of as.mo and works the same
#' guess_mo("S. epidermidis") # will remain species: B_STPHY_EPI
#' guess_mo("S. epidermidis", Becker = TRUE) # will not remain species: B_STPHY_CNS
#' as.mo("S. epidermidis") # will remain species: B_STPHY_EPI
#' as.mo("S. epidermidis", Becker = TRUE) # will not remain species: B_STPHY_CNS
#'
#' guess_mo("S. pyogenes") # will remain species: B_STRPTC_PYO
#' guess_mo("S. pyogenes", Lancefield = TRUE) # will not remain species: B_STRPTC_GRA
#' as.mo("S. pyogenes") # will remain species: B_STRPTC_PYO
#' as.mo("S. pyogenes", Lancefield = TRUE) # will not remain species: B_STRPTC_GRA
#'
#' # Use mo_* functions to get a specific property based on `mo`
#' Ecoli <- as.mo("E. coli") # returns `B_ESCHR_COL`
@ -154,10 +152,6 @@ is.mo <- function(x) {
identical(class(x), "mo")
}
#' @rdname as.mo
#' @export
guess_mo <- as.mo
#' @importFrom dplyr %>% pull left_join n_distinct progress_estimated
#' @importFrom data.table data.table as.data.table setkey
#' @importFrom crayon magenta red italic