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dplyr 0.8.0 support, fixes #7

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dr. M.S. (Matthijs) Berends
2018-12-22 22:39:34 +01:00
parent b937662a97
commit 0b8084871d
29 changed files with 555 additions and 479 deletions
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24
R/eucast_rules.R
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@ -24,7 +24,6 @@
#' @param rules a character vector that specifies which rules should be applied - one or more of \code{c("breakpoints", "expert", "other", "all")}
#' @param verbose a logical to indicate whether extensive info should be returned as a \code{data.frame} with info about which rows and columns are effected
#' @param amcl,amik,amox,ampi,azit,azlo,aztr,cefa,cfep,cfot,cfox,cfra,cfta,cftr,cfur,chlo,cipr,clar,clin,clox,coli,czol,dapt,doxy,erta,eryt,fosf,fusi,gent,imip,kana,levo,linc,line,mero,mezl,mino,moxi,nali,neom,neti,nitr,norf,novo,oflo,oxac,peni,pipe,pita,poly,pris,qida,rifa,roxi,siso,teic,tetr,tica,tige,tobr,trim,trsu,vanc column name of an antibiotic, see Antibiotics
#' @param col_bactid deprecated, use \code{col_mo} instead.
#' @param ... parameters that are passed on to \code{eucast_rules}
#' @inheritParams first_isolate
#' @section Antibiotics:
@ -217,8 +216,7 @@ eucast_rules <- function(tbl,
tobr = 'tobr',
trim = 'trim',
trsu = 'trsu',
vanc = 'vanc',
col_bactid = NULL) {
vanc = 'vanc') {
EUCAST_VERSION_BREAKPOINTS <- "8.1, 2018"
EUCAST_VERSION_EXPERT_RULES <- "3.1, 2016"
@ -229,12 +227,12 @@ eucast_rules <- function(tbl,
# try to find columns based on type
# -- mo
if (!is.null(col_bactid)) {
col_mo <- col_bactid
warning("Use of `col_bactid` is deprecated. Use `col_mo` instead.")
} else if (is.null(col_mo) & "mo" %in% lapply(tbl, class)) {
col_mo <- colnames(tbl)[lapply(tbl, class) == "mo"]
message("NOTE: Using column `", col_mo, "` as input for `col_mo`.")
if (is.null(col_mo) & "mo" %in% lapply(tbl, class)) {
col_mo <- colnames(tbl)[lapply(tbl, class) == "mo"][1]
message(blue(paste0("NOTE: Using column `", bold(col_mo), "` as input for `col_mo`.")))
}
if (is.null(col_mo)) {
stop("`col_mo` must be set.", call. = FALSE)
}
if (!all(rules %in% c("breakpoints", "expert", "other", "all"))) {
@ -1731,12 +1729,14 @@ eucast_rules <- function(tbl,
} else {
colour <- blue
}
decimal.mark <- getOption("OutDec")
big.mark <- ifelse(decimal.mark != ",", ",", ".")
cat(bold(paste('\n=> EUCAST rules', paste0(wouldve, 'affected'),
amount_affected_rows %>% length() %>% format(big.mark = ","),
'out of', nrow(tbl_original) %>% format(big.mark = ","),
amount_affected_rows %>% length() %>% format(big.mark = big.mark, decimal.mark = decimal.mark),
'out of', nrow(tbl_original) %>% format(big.mark = big.mark, decimal.mark = decimal.mark),
'rows ->',
colour(paste0(wouldve, 'changed'),
amount_changed %>% format(big.mark = ","), 'test results.\n\n'))))
amount_changed %>% format(big.mark = big.mark, decimal.mark = decimal.mark), 'test results.\n\n'))))
}
if (verbose == TRUE) {