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guess_ab_col, benchmarks
This commit is contained in:
254
R/eucast_rules.R
254
R/eucast_rules.R
@ -30,7 +30,7 @@
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#' @param ... parameters that are passed on to \code{eucast_rules}
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#' @inheritParams first_isolate
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#' @section Antibiotics:
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#' To define antibiotics column names, leave as it is to determine it automatically with \code{\link{guess_ab}} or input a text (case-insensitive) or use \code{NULL} to skip a column (e.g. \code{tica = NULL}). Non-existing columns will anyway be skipped with a warning.
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#' To define antibiotics column names, leave as it is to determine it automatically with \code{\link{guess_ab_col}} or input a text (case-insensitive) or use \code{NULL} to skip a column (e.g. \code{tica = NULL}). Non-existing columns will anyway be skipped with a warning.
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#'
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#' Abbrevations of the column containing antibiotics in the form: \strong{abbreviation}: generic name (\emph{ATC code})
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#'
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@ -158,69 +158,69 @@ eucast_rules <- function(tbl,
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info = TRUE,
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rules = c("breakpoints", "expert", "other", "all"),
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verbose = FALSE,
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amcl = guess_ab(),
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amik = guess_ab(),
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amox = guess_ab(),
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ampi = guess_ab(),
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azit = guess_ab(),
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azlo = guess_ab(),
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aztr = guess_ab(),
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cefa = guess_ab(),
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cfep = guess_ab(),
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cfot = guess_ab(),
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cfox = guess_ab(),
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cfra = guess_ab(),
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cfta = guess_ab(),
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cftr = guess_ab(),
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cfur = guess_ab(),
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chlo = guess_ab(),
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cipr = guess_ab(),
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clar = guess_ab(),
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clin = guess_ab(),
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clox = guess_ab(),
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coli = guess_ab(),
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czol = guess_ab(),
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dapt = guess_ab(),
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doxy = guess_ab(),
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erta = guess_ab(),
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eryt = guess_ab(),
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fosf = guess_ab(),
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fusi = guess_ab(),
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gent = guess_ab(),
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imip = guess_ab(),
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kana = guess_ab(),
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levo = guess_ab(),
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linc = guess_ab(),
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line = guess_ab(),
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mero = guess_ab(),
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mezl = guess_ab(),
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mino = guess_ab(),
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moxi = guess_ab(),
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nali = guess_ab(),
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neom = guess_ab(),
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neti = guess_ab(),
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nitr = guess_ab(),
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norf = guess_ab(),
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novo = guess_ab(),
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oflo = guess_ab(),
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oxac = guess_ab(),
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peni = guess_ab(),
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pipe = guess_ab(),
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pita = guess_ab(),
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poly = guess_ab(),
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pris = guess_ab(),
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qida = guess_ab(),
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rifa = guess_ab(),
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roxi = guess_ab(),
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siso = guess_ab(),
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teic = guess_ab(),
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tetr = guess_ab(),
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tica = guess_ab(),
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tige = guess_ab(),
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tobr = guess_ab(),
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trim = guess_ab(),
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trsu = guess_ab(),
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vanc = guess_ab()) {
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amcl = guess_ab_col(),
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amik = guess_ab_col(),
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amox = guess_ab_col(),
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ampi = guess_ab_col(),
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azit = guess_ab_col(),
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azlo = guess_ab_col(),
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aztr = guess_ab_col(),
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cefa = guess_ab_col(),
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cfep = guess_ab_col(),
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cfot = guess_ab_col(),
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cfox = guess_ab_col(),
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cfra = guess_ab_col(),
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cfta = guess_ab_col(),
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cftr = guess_ab_col(),
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cfur = guess_ab_col(),
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chlo = guess_ab_col(),
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cipr = guess_ab_col(),
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clar = guess_ab_col(),
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clin = guess_ab_col(),
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clox = guess_ab_col(),
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coli = guess_ab_col(),
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czol = guess_ab_col(),
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dapt = guess_ab_col(),
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doxy = guess_ab_col(),
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erta = guess_ab_col(),
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eryt = guess_ab_col(),
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fosf = guess_ab_col(),
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fusi = guess_ab_col(),
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gent = guess_ab_col(),
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imip = guess_ab_col(),
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kana = guess_ab_col(),
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levo = guess_ab_col(),
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linc = guess_ab_col(),
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line = guess_ab_col(),
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mero = guess_ab_col(),
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mezl = guess_ab_col(),
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mino = guess_ab_col(),
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moxi = guess_ab_col(),
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nali = guess_ab_col(),
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neom = guess_ab_col(),
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neti = guess_ab_col(),
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nitr = guess_ab_col(),
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norf = guess_ab_col(),
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novo = guess_ab_col(),
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oflo = guess_ab_col(),
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oxac = guess_ab_col(),
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peni = guess_ab_col(),
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pipe = guess_ab_col(),
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pita = guess_ab_col(),
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poly = guess_ab_col(),
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pris = guess_ab_col(),
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qida = guess_ab_col(),
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rifa = guess_ab_col(),
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roxi = guess_ab_col(),
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siso = guess_ab_col(),
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teic = guess_ab_col(),
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tetr = guess_ab_col(),
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tica = guess_ab_col(),
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tige = guess_ab_col(),
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tobr = guess_ab_col(),
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trim = guess_ab_col(),
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trsu = guess_ab_col(),
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vanc = guess_ab_col()) {
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EUCAST_VERSION_BREAKPOINTS <- "8.1, 2018"
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EUCAST_VERSION_EXPERT_RULES <- "3.1, 2016"
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@ -268,69 +268,69 @@ eucast_rules <- function(tbl,
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}
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# check columns
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if (identical(amcl, as.name("guess_ab"))) { amcl <- guess_ab(tbl, "amcl", verbose = verbose) }
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if (identical(amik, as.name("guess_ab"))) { amik <- guess_ab(tbl, "amik", verbose = verbose) }
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if (identical(amox, as.name("guess_ab"))) { amox <- guess_ab(tbl, "amox", verbose = verbose) }
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if (identical(ampi, as.name("guess_ab"))) { ampi <- guess_ab(tbl, "ampi", verbose = verbose) }
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if (identical(azit, as.name("guess_ab"))) { azit <- guess_ab(tbl, "azit", verbose = verbose) }
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if (identical(azlo, as.name("guess_ab"))) { azlo <- guess_ab(tbl, "azlo", verbose = verbose) }
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if (identical(aztr, as.name("guess_ab"))) { aztr <- guess_ab(tbl, "aztr", verbose = verbose) }
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if (identical(cefa, as.name("guess_ab"))) { cefa <- guess_ab(tbl, "cefa", verbose = verbose) }
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if (identical(cfep, as.name("guess_ab"))) { cfep <- guess_ab(tbl, "cfep", verbose = verbose) }
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if (identical(cfot, as.name("guess_ab"))) { cfot <- guess_ab(tbl, "cfot", verbose = verbose) }
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if (identical(cfox, as.name("guess_ab"))) { cfox <- guess_ab(tbl, "cfox", verbose = verbose) }
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if (identical(cfra, as.name("guess_ab"))) { cfra <- guess_ab(tbl, "cfra", verbose = verbose) }
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if (identical(cfta, as.name("guess_ab"))) { cfta <- guess_ab(tbl, "cfta", verbose = verbose) }
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if (identical(cftr, as.name("guess_ab"))) { cftr <- guess_ab(tbl, "cftr", verbose = verbose) }
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if (identical(cfur, as.name("guess_ab"))) { cfur <- guess_ab(tbl, "cfur", verbose = verbose) }
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if (identical(chlo, as.name("guess_ab"))) { chlo <- guess_ab(tbl, "chlo", verbose = verbose) }
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if (identical(cipr, as.name("guess_ab"))) { cipr <- guess_ab(tbl, "cipr", verbose = verbose) }
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if (identical(clar, as.name("guess_ab"))) { clar <- guess_ab(tbl, "clar", verbose = verbose) }
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if (identical(clin, as.name("guess_ab"))) { clin <- guess_ab(tbl, "clin", verbose = verbose) }
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if (identical(clox, as.name("guess_ab"))) { clox <- guess_ab(tbl, "clox", verbose = verbose) }
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if (identical(coli, as.name("guess_ab"))) { coli <- guess_ab(tbl, "coli", verbose = verbose) }
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if (identical(czol, as.name("guess_ab"))) { czol <- guess_ab(tbl, "czol", verbose = verbose) }
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if (identical(dapt, as.name("guess_ab"))) { dapt <- guess_ab(tbl, "dapt", verbose = verbose) }
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if (identical(doxy, as.name("guess_ab"))) { doxy <- guess_ab(tbl, "doxy", verbose = verbose) }
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if (identical(erta, as.name("guess_ab"))) { erta <- guess_ab(tbl, "erta", verbose = verbose) }
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if (identical(eryt, as.name("guess_ab"))) { eryt <- guess_ab(tbl, "eryt", verbose = verbose) }
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if (identical(fosf, as.name("guess_ab"))) { fosf <- guess_ab(tbl, "fosf", verbose = verbose) }
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if (identical(fusi, as.name("guess_ab"))) { fusi <- guess_ab(tbl, "fusi", verbose = verbose) }
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if (identical(gent, as.name("guess_ab"))) { gent <- guess_ab(tbl, "gent", verbose = verbose) }
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if (identical(imip, as.name("guess_ab"))) { imip <- guess_ab(tbl, "imip", verbose = verbose) }
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if (identical(kana, as.name("guess_ab"))) { kana <- guess_ab(tbl, "kana", verbose = verbose) }
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if (identical(levo, as.name("guess_ab"))) { levo <- guess_ab(tbl, "levo", verbose = verbose) }
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if (identical(linc, as.name("guess_ab"))) { linc <- guess_ab(tbl, "linc", verbose = verbose) }
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if (identical(line, as.name("guess_ab"))) { line <- guess_ab(tbl, "line", verbose = verbose) }
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if (identical(mero, as.name("guess_ab"))) { mero <- guess_ab(tbl, "mero", verbose = verbose) }
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if (identical(mezl, as.name("guess_ab"))) { mezl <- guess_ab(tbl, "mezl", verbose = verbose) }
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if (identical(mino, as.name("guess_ab"))) { mino <- guess_ab(tbl, "mino", verbose = verbose) }
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if (identical(moxi, as.name("guess_ab"))) { moxi <- guess_ab(tbl, "moxi", verbose = verbose) }
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if (identical(nali, as.name("guess_ab"))) { nali <- guess_ab(tbl, "nali", verbose = verbose) }
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if (identical(neom, as.name("guess_ab"))) { neom <- guess_ab(tbl, "neom", verbose = verbose) }
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if (identical(neti, as.name("guess_ab"))) { neti <- guess_ab(tbl, "neti", verbose = verbose) }
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if (identical(nitr, as.name("guess_ab"))) { nitr <- guess_ab(tbl, "nitr", verbose = verbose) }
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if (identical(norf, as.name("guess_ab"))) { norf <- guess_ab(tbl, "norf", verbose = verbose) }
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if (identical(novo, as.name("guess_ab"))) { novo <- guess_ab(tbl, "novo", verbose = verbose) }
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if (identical(oflo, as.name("guess_ab"))) { oflo <- guess_ab(tbl, "oflo", verbose = verbose) }
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if (identical(oxac, as.name("guess_ab"))) { oxac <- guess_ab(tbl, "oxac", verbose = verbose) }
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if (identical(peni, as.name("guess_ab"))) { peni <- guess_ab(tbl, "peni", verbose = verbose) }
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if (identical(pipe, as.name("guess_ab"))) { pipe <- guess_ab(tbl, "pipe", verbose = verbose) }
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if (identical(pita, as.name("guess_ab"))) { pita <- guess_ab(tbl, "pita", verbose = verbose) }
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if (identical(poly, as.name("guess_ab"))) { poly <- guess_ab(tbl, "poly", verbose = verbose) }
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if (identical(pris, as.name("guess_ab"))) { pris <- guess_ab(tbl, "pris", verbose = verbose) }
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if (identical(qida, as.name("guess_ab"))) { qida <- guess_ab(tbl, "qida", verbose = verbose) }
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if (identical(rifa, as.name("guess_ab"))) { rifa <- guess_ab(tbl, "rifa", verbose = verbose) }
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if (identical(roxi, as.name("guess_ab"))) { roxi <- guess_ab(tbl, "roxi", verbose = verbose) }
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if (identical(siso, as.name("guess_ab"))) { siso <- guess_ab(tbl, "siso", verbose = verbose) }
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if (identical(teic, as.name("guess_ab"))) { teic <- guess_ab(tbl, "teic", verbose = verbose) }
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if (identical(tetr, as.name("guess_ab"))) { tetr <- guess_ab(tbl, "tetr", verbose = verbose) }
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if (identical(tica, as.name("guess_ab"))) { tica <- guess_ab(tbl, "tica", verbose = verbose) }
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if (identical(tige, as.name("guess_ab"))) { tige <- guess_ab(tbl, "tige", verbose = verbose) }
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if (identical(tobr, as.name("guess_ab"))) { tobr <- guess_ab(tbl, "tobr", verbose = verbose) }
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if (identical(trim, as.name("guess_ab"))) { trim <- guess_ab(tbl, "trim", verbose = verbose) }
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if (identical(trsu, as.name("guess_ab"))) { trsu <- guess_ab(tbl, "trsu", verbose = verbose) }
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if (identical(vanc, as.name("guess_ab"))) { vanc <- guess_ab(tbl, "vanc", verbose = verbose) }
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if (identical(amcl, as.name("guess_ab_col"))) { amcl <- guess_ab_col(tbl, "amcl", verbose = verbose) }
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if (identical(amik, as.name("guess_ab_col"))) { amik <- guess_ab_col(tbl, "amik", verbose = verbose) }
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if (identical(amox, as.name("guess_ab_col"))) { amox <- guess_ab_col(tbl, "amox", verbose = verbose) }
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if (identical(ampi, as.name("guess_ab_col"))) { ampi <- guess_ab_col(tbl, "ampi", verbose = verbose) }
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if (identical(azit, as.name("guess_ab_col"))) { azit <- guess_ab_col(tbl, "azit", verbose = verbose) }
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if (identical(azlo, as.name("guess_ab_col"))) { azlo <- guess_ab_col(tbl, "azlo", verbose = verbose) }
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if (identical(aztr, as.name("guess_ab_col"))) { aztr <- guess_ab_col(tbl, "aztr", verbose = verbose) }
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if (identical(cefa, as.name("guess_ab_col"))) { cefa <- guess_ab_col(tbl, "cefa", verbose = verbose) }
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if (identical(cfep, as.name("guess_ab_col"))) { cfep <- guess_ab_col(tbl, "cfep", verbose = verbose) }
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if (identical(cfot, as.name("guess_ab_col"))) { cfot <- guess_ab_col(tbl, "cfot", verbose = verbose) }
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if (identical(cfox, as.name("guess_ab_col"))) { cfox <- guess_ab_col(tbl, "cfox", verbose = verbose) }
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if (identical(cfra, as.name("guess_ab_col"))) { cfra <- guess_ab_col(tbl, "cfra", verbose = verbose) }
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if (identical(cfta, as.name("guess_ab_col"))) { cfta <- guess_ab_col(tbl, "cfta", verbose = verbose) }
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if (identical(cftr, as.name("guess_ab_col"))) { cftr <- guess_ab_col(tbl, "cftr", verbose = verbose) }
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if (identical(cfur, as.name("guess_ab_col"))) { cfur <- guess_ab_col(tbl, "cfur", verbose = verbose) }
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if (identical(chlo, as.name("guess_ab_col"))) { chlo <- guess_ab_col(tbl, "chlo", verbose = verbose) }
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if (identical(cipr, as.name("guess_ab_col"))) { cipr <- guess_ab_col(tbl, "cipr", verbose = verbose) }
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if (identical(clar, as.name("guess_ab_col"))) { clar <- guess_ab_col(tbl, "clar", verbose = verbose) }
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if (identical(clin, as.name("guess_ab_col"))) { clin <- guess_ab_col(tbl, "clin", verbose = verbose) }
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if (identical(clox, as.name("guess_ab_col"))) { clox <- guess_ab_col(tbl, "clox", verbose = verbose) }
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if (identical(coli, as.name("guess_ab_col"))) { coli <- guess_ab_col(tbl, "coli", verbose = verbose) }
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if (identical(czol, as.name("guess_ab_col"))) { czol <- guess_ab_col(tbl, "czol", verbose = verbose) }
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if (identical(dapt, as.name("guess_ab_col"))) { dapt <- guess_ab_col(tbl, "dapt", verbose = verbose) }
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if (identical(doxy, as.name("guess_ab_col"))) { doxy <- guess_ab_col(tbl, "doxy", verbose = verbose) }
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if (identical(erta, as.name("guess_ab_col"))) { erta <- guess_ab_col(tbl, "erta", verbose = verbose) }
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if (identical(eryt, as.name("guess_ab_col"))) { eryt <- guess_ab_col(tbl, "eryt", verbose = verbose) }
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if (identical(fosf, as.name("guess_ab_col"))) { fosf <- guess_ab_col(tbl, "fosf", verbose = verbose) }
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if (identical(fusi, as.name("guess_ab_col"))) { fusi <- guess_ab_col(tbl, "fusi", verbose = verbose) }
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if (identical(gent, as.name("guess_ab_col"))) { gent <- guess_ab_col(tbl, "gent", verbose = verbose) }
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if (identical(imip, as.name("guess_ab_col"))) { imip <- guess_ab_col(tbl, "imip", verbose = verbose) }
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if (identical(kana, as.name("guess_ab_col"))) { kana <- guess_ab_col(tbl, "kana", verbose = verbose) }
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if (identical(levo, as.name("guess_ab_col"))) { levo <- guess_ab_col(tbl, "levo", verbose = verbose) }
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if (identical(linc, as.name("guess_ab_col"))) { linc <- guess_ab_col(tbl, "linc", verbose = verbose) }
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if (identical(line, as.name("guess_ab_col"))) { line <- guess_ab_col(tbl, "line", verbose = verbose) }
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if (identical(mero, as.name("guess_ab_col"))) { mero <- guess_ab_col(tbl, "mero", verbose = verbose) }
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if (identical(mezl, as.name("guess_ab_col"))) { mezl <- guess_ab_col(tbl, "mezl", verbose = verbose) }
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if (identical(mino, as.name("guess_ab_col"))) { mino <- guess_ab_col(tbl, "mino", verbose = verbose) }
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if (identical(moxi, as.name("guess_ab_col"))) { moxi <- guess_ab_col(tbl, "moxi", verbose = verbose) }
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if (identical(nali, as.name("guess_ab_col"))) { nali <- guess_ab_col(tbl, "nali", verbose = verbose) }
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if (identical(neom, as.name("guess_ab_col"))) { neom <- guess_ab_col(tbl, "neom", verbose = verbose) }
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if (identical(neti, as.name("guess_ab_col"))) { neti <- guess_ab_col(tbl, "neti", verbose = verbose) }
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if (identical(nitr, as.name("guess_ab_col"))) { nitr <- guess_ab_col(tbl, "nitr", verbose = verbose) }
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if (identical(norf, as.name("guess_ab_col"))) { norf <- guess_ab_col(tbl, "norf", verbose = verbose) }
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if (identical(novo, as.name("guess_ab_col"))) { novo <- guess_ab_col(tbl, "novo", verbose = verbose) }
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if (identical(oflo, as.name("guess_ab_col"))) { oflo <- guess_ab_col(tbl, "oflo", verbose = verbose) }
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if (identical(oxac, as.name("guess_ab_col"))) { oxac <- guess_ab_col(tbl, "oxac", verbose = verbose) }
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if (identical(peni, as.name("guess_ab_col"))) { peni <- guess_ab_col(tbl, "peni", verbose = verbose) }
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if (identical(pipe, as.name("guess_ab_col"))) { pipe <- guess_ab_col(tbl, "pipe", verbose = verbose) }
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if (identical(pita, as.name("guess_ab_col"))) { pita <- guess_ab_col(tbl, "pita", verbose = verbose) }
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if (identical(poly, as.name("guess_ab_col"))) { poly <- guess_ab_col(tbl, "poly", verbose = verbose) }
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if (identical(pris, as.name("guess_ab_col"))) { pris <- guess_ab_col(tbl, "pris", verbose = verbose) }
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if (identical(qida, as.name("guess_ab_col"))) { qida <- guess_ab_col(tbl, "qida", verbose = verbose) }
|
||||
if (identical(rifa, as.name("guess_ab_col"))) { rifa <- guess_ab_col(tbl, "rifa", verbose = verbose) }
|
||||
if (identical(roxi, as.name("guess_ab_col"))) { roxi <- guess_ab_col(tbl, "roxi", verbose = verbose) }
|
||||
if (identical(siso, as.name("guess_ab_col"))) { siso <- guess_ab_col(tbl, "siso", verbose = verbose) }
|
||||
if (identical(teic, as.name("guess_ab_col"))) { teic <- guess_ab_col(tbl, "teic", verbose = verbose) }
|
||||
if (identical(tetr, as.name("guess_ab_col"))) { tetr <- guess_ab_col(tbl, "tetr", verbose = verbose) }
|
||||
if (identical(tica, as.name("guess_ab_col"))) { tica <- guess_ab_col(tbl, "tica", verbose = verbose) }
|
||||
if (identical(tige, as.name("guess_ab_col"))) { tige <- guess_ab_col(tbl, "tige", verbose = verbose) }
|
||||
if (identical(tobr, as.name("guess_ab_col"))) { tobr <- guess_ab_col(tbl, "tobr", verbose = verbose) }
|
||||
if (identical(trim, as.name("guess_ab_col"))) { trim <- guess_ab_col(tbl, "trim", verbose = verbose) }
|
||||
if (identical(trsu, as.name("guess_ab_col"))) { trsu <- guess_ab_col(tbl, "trsu", verbose = verbose) }
|
||||
if (identical(vanc, as.name("guess_ab_col"))) { vanc <- guess_ab_col(tbl, "vanc", verbose = verbose) }
|
||||
col.list <- c(amcl, amik, amox, ampi, azit, azlo, aztr, cefa, cfra, cfep, cfot,
|
||||
cfox, cfta, cftr, cfur, chlo, cipr, clar, clin, clox, coli,
|
||||
czol, dapt, doxy, erta, eryt, fosf, fusi, gent, imip, kana,
|
||||
|
||||
Reference in New Issue
Block a user