P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-08 18:01:50 +02:00
Code Releases Activity

(v1.0.1.9004) Support dplyr 1.0.0

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2020-03-14 14:05:43 +01:00
parent 3760bcb11e
commit 219cff403f
62 changed files with 616 additions and 213 deletions
Download Patch File Download Diff File Expand all files Collapse all files

48
R/mo.R
View File

@ -78,9 +78,9 @@
#' - Uncertainty level 3: allow all of level 1 and 2, strip off text elements from the end, allow any part of a taxonomic name.
#'
#' This leads to e.g.:
#' - `"Streptococcus group B (known as S. agalactiae)"`. The text between brackets will be removed and a warning will be thrown that the result *Streptococcus group B* (`B_STRPT_GRPB`) needs review.
#' - `"S. aureus - please mind: MRSA"`. The last word will be stripped, after which the function will try to find a match. If it does not, the second last word will be stripped, etc. Again, a warning will be thrown that the result *Staphylococcus aureus* (`B_STPHY_AURS`) needs review.
#' - `"Fluoroquinolone-resistant Neisseria gonorrhoeae"`. The first word will be stripped, after which the function will try to find a match. A warning will be thrown that the result *Neisseria gonorrhoeae* (`B_NESSR_GNRR`) needs review.
#' - `"Streptococcus group B (known as S. agalactiae)"`. The text between brackets will be removed and a warning will be thrown that the result *Streptococcus group B* (``r as.mo("Streptococcus group B")``) needs review.
#' - `"S. aureus - please mind: MRSA"`. The last word will be stripped, after which the function will try to find a match. If it does not, the second last word will be stripped, etc. Again, a warning will be thrown that the result *Staphylococcus aureus* (``r as.mo("Staphylococcus aureus")``) needs review.
#' - `"Fluoroquinolone-resistant Neisseria gonorrhoeae"`. The first word will be stripped, after which the function will try to find a match. A warning will be thrown that the result *Neisseria gonorrhoeae* (``r as.mo("Neisseria gonorrhoeae")``) needs review.
#'
#' The level of uncertainty can be set using the argument `allow_uncertain`. The default is `allow_uncertain = TRUE`, which is equal to uncertainty level 2. Using `allow_uncertain = FALSE` is equal to uncertainty level 0 and will skip all rules. You can also use e.g. `as.mo(..., allow_uncertain = 1)` to only allow up to level 1 uncertainty.
#'
@ -234,7 +234,7 @@ is.mo <- function(x) {
inherits(x, "mo")
}
#' @importFrom dplyr %>% pull left_join n_distinct progress_estimated filter distinct
#' @importFrom dplyr %>% pull left_join n_distinct filter distinct
#' @importFrom data.table data.table as.data.table setkey
#' @importFrom crayon magenta red blue silver italic
#' @importFrom cleaner percentage
@ -1675,12 +1675,48 @@ print.mo <- function(x, ...) {
print.default(x, quote = FALSE)
}
#' @importFrom pillar type_sum
#' @importFrom vctrs vec_ptype_abbr
#' @export
type_sum.mo <- function(x) {
vec_ptype_abbr.mo <- function(x, ...) {
"mo"
}
#' @importFrom vctrs vec_ptype_full
#' @export
vec_ptype_full.mo <- function(x, ...) {
"mo"
}
#' @importFrom vctrs vec_ptype2
#' @export
vec_ptype2.mo <- function(x, y, ...) {
vctrs::vec_ptype2(x = as.character(x), y = as.character(y), ...)
}
#' @importFrom vctrs vec_cast
#' @export
vec_cast.mo <- function(x, to, ...) {
as.mo(vctrs::vec_cast(x = as.character(x), to = as.character(to), ...))
}
#' @importFrom vctrs vec_cast
#' @export
vec_cast.mo.mo <- function(x, to, ...) {
as.mo(vctrs::vec_cast(x = as.character(x), to = as.character(to), ...))
}
#' @importFrom vctrs vec_cast
#' @export
vec_cast.mo.character <- function(x, to, ...) {
vctrs::vec_cast(x = as.character(x), to = as.character(to), ...)
}
#' @importFrom vctrs vec_cast
#' @export
vec_cast.character.mo <- function(x, to, ...) {
as.mo(vctrs::vec_cast(x = as.character(x), to = as.character(to), ...))
}
#' @importFrom pillar pillar_shaft
#' @export
pillar_shaft.mo <- function(x, ...) {