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guess_ab_col, benchmarks
This commit is contained in:
2
R/age.R
2
R/age.R
@ -48,7 +48,7 @@ age <- function(x, reference = Sys.Date()) {
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as.integer(years_gap - 1),
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as.integer(years_gap))
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if (any(ages > 120)) {
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warning("Some ages are >120.")
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warning("Some ages are > 120.")
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}
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ages
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}
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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) }
|
||||
if (identical(pita, as.name("guess_ab_col"))) { pita <- guess_ab_col(tbl, "pita", verbose = verbose) }
|
||||
if (identical(poly, as.name("guess_ab_col"))) { poly <- guess_ab_col(tbl, "poly", verbose = verbose) }
|
||||
if (identical(pris, as.name("guess_ab_col"))) { pris <- guess_ab_col(tbl, "pris", verbose = verbose) }
|
||||
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,
|
||||
|
||||
@ -21,18 +21,28 @@
|
||||
|
||||
#' Guess antibiotic column
|
||||
#'
|
||||
#' This tries to find a column name in a data set based on information from the \code{\link{antibiotics}} data set.
|
||||
#' This tries to find a column name in a data set based on information from the \code{\link{antibiotics}} data set. You can look for an antibiotic (trade) of abbreviation and it will search the data for any column containing a name or ATC code of that antibiotic.
|
||||
#' @param tbl a \code{data.frame}
|
||||
#' @param col a character to look for
|
||||
#' @param verbose a logical to indicate whether additional info should be printed
|
||||
#' @importFrom dplyr %>% select filter_all any_vars
|
||||
#' @export
|
||||
#' @inheritSection AMR Read more on our website!
|
||||
# @examples
|
||||
#
|
||||
guess_ab <- function(tbl = NULL, col = NULL, verbose = FALSE) {
|
||||
#' @examples
|
||||
#' df <- data.frame(amox = "S",
|
||||
#' tetr = "R")
|
||||
#'
|
||||
#' guess_ab_col(df, "amoxicillin")
|
||||
#' # [1] "amox"
|
||||
#' guess_ab_col(df, "J01AA07") # ATC code of Tetracycline
|
||||
#' # [1] "tetr"
|
||||
#'
|
||||
#' guess_ab_col(df, "J01AA07", verbose = TRUE)
|
||||
#' # using column `tetr` for col "J01AA07"
|
||||
#' # [1] "tetr"
|
||||
guess_ab_col <- function(tbl = NULL, col = NULL, verbose = FALSE) {
|
||||
if (is.null(tbl) & is.null(col)) {
|
||||
return(as.name("guess_ab"))
|
||||
return(as.name("guess_ab_col"))
|
||||
}
|
||||
#stop("This function should not be called directly.")
|
||||
if (length(col) > 1) {
|
||||
@ -42,35 +52,58 @@ guess_ab <- function(tbl = NULL, col = NULL, verbose = FALSE) {
|
||||
if (!is.data.frame(tbl)) {
|
||||
stop("`tbl` must be a data.frame")
|
||||
}
|
||||
|
||||
tbl_names <- colnames(tbl)
|
||||
if (col %in% tbl_names) {
|
||||
return(col)
|
||||
}
|
||||
ab_result <- antibiotics %>%
|
||||
select(atc:trade_name) %>%
|
||||
filter_all(any_vars(tolower(.) == tolower(col)))
|
||||
if (nrow(ab_result) > 1) {
|
||||
# get most likely one
|
||||
if (col %in% ab_result$atc) {
|
||||
ab_result <- ab_result %>% filter(atc == col)
|
||||
} else if (col %in% ab_result$certe) {
|
||||
ab_result <- ab_result %>% filter(certe == col)
|
||||
} else if (col %in% ab_result$umcg) {
|
||||
ab_result <- ab_result %>% filter(umcg == col)
|
||||
} else if (col %in% ab_result$umcg) {
|
||||
ab_result <- ab_result %>% filter(official == col)
|
||||
} else {
|
||||
ab_result <- ab_result[1,]
|
||||
}
|
||||
filter_all(any_vars(tolower(.) == tolower(col))) %>%
|
||||
filter_all(any_vars(. %in% tbl_names))
|
||||
|
||||
if (nrow(ab_result) == 0 & nchar(col) > 4) {
|
||||
# use like when col >= 5 characters
|
||||
ab_result <- antibiotics %>%
|
||||
select(atc:trade_name) %>%
|
||||
filter_all(any_vars(tolower(.) %like% tolower(col))) %>%
|
||||
filter_all(any_vars(. %in% tbl_names))
|
||||
}
|
||||
tbl_result <- tbl_names[tbl_names %in% ab_result]
|
||||
if (length(tbl_result) > 1) {
|
||||
tbl_result <- tbl_result[1]
|
||||
warning('using column `', tbl_result, '` for col "', col, '"', call. = FALSE)
|
||||
} else if (length(tbl_result) == 0) {
|
||||
|
||||
if (nrow(ab_result) > 1) {
|
||||
# looking more and more for reliable hit
|
||||
ab_result_1 <- ab_result %>% filter(tolower(atc) == tolower(col))
|
||||
if (nrow(ab_result_1) == 0) {
|
||||
ab_result_1 <- ab_result %>% filter(tolower(certe) == tolower(col))
|
||||
}
|
||||
if (nrow(ab_result_1) == 0) {
|
||||
ab_result_1 <- ab_result %>% filter(tolower(umcg) == tolower(col))
|
||||
}
|
||||
if (nrow(ab_result_1) == 0) {
|
||||
ab_result_1 <- ab_result %>% filter(tolower(official) == tolower(col))
|
||||
}
|
||||
if (nrow(ab_result_1) == 0) {
|
||||
ab_result_1 <- ab_result[1, ]
|
||||
}
|
||||
ab_result <- ab_result_1
|
||||
}
|
||||
|
||||
if (length(ab_result) == 0) {
|
||||
if (verbose == TRUE) {
|
||||
message('no result found for col "', col, '"')
|
||||
}
|
||||
return(NULL)
|
||||
} else if (verbose == TRUE) {
|
||||
message('using column `', tbl_result, '` for col "', col, '"')
|
||||
} else {
|
||||
result <- tbl_names[tbl_names %in% ab_result]
|
||||
if (length(result) == 0) {
|
||||
if (verbose == TRUE) {
|
||||
message('no result found for col "', col, '"')
|
||||
}
|
||||
return(NULL)
|
||||
}
|
||||
if (verbose == TRUE) {
|
||||
message('using column `', result, '` for col "', col, '"')
|
||||
}
|
||||
return(result)
|
||||
}
|
||||
tbl_result
|
||||
}
|
||||
@ -25,12 +25,12 @@
|
||||
#' @param tbl table with antibiotics coloms, like \code{amox} and \code{amcl}.
|
||||
#' @param x,y characters to compare
|
||||
#' @inheritParams first_isolate
|
||||
#' @param universal_1,universal_2,universal_3,universal_4,universal_5,universal_6 column names of \strong{broad-spectrum} antibiotics, case-insensitive
|
||||
#' @param GramPos_1,GramPos_2,GramPos_3,GramPos_4,GramPos_5,GramPos_6 column names of antibiotics for \strong{Gram positives}, case-insensitive
|
||||
#' @param GramNeg_1,GramNeg_2,GramNeg_3,GramNeg_4,GramNeg_5,GramNeg_6 column names of antibiotics for \strong{Gram negatives}, case-insensitive
|
||||
#' @param universal_1,universal_2,universal_3,universal_4,universal_5,universal_6 column names of \strong{broad-spectrum} antibiotics, case-insensitive. At default, the columns containing these antibiotics will be guessed with \code{\link{guess_ab_col}}.
|
||||
#' @param GramPos_1,GramPos_2,GramPos_3,GramPos_4,GramPos_5,GramPos_6 column names of antibiotics for \strong{Gram positives}, case-insensitive. At default, the columns containing these antibiotics will be guessed with \code{\link{guess_ab_col}}.
|
||||
#' @param GramNeg_1,GramNeg_2,GramNeg_3,GramNeg_4,GramNeg_5,GramNeg_6 column names of antibiotics for \strong{Gram negatives}, case-insensitive. At default, the columns containing these antibiotics will be guessed with \code{\link{guess_ab_col}}.
|
||||
#' @param warnings give warning about missing antibiotic columns, they will anyway be ignored
|
||||
#' @param ... other parameters passed on to function
|
||||
#' @details The function \code{key_antibiotics} returns a character vector with 12 antibiotic results for every isolate. These isolates can then be compared using \code{key_antibiotics_equal}, to check if two isolates have generally the same antibiogram. Missing and invalid values are replaced with a dot (\code{"."}). The \code{\link{first_isolate}} function only uses this function on the same microbial species from the same patient. Using this, an MRSA will be included after a susceptible \emph{S. aureus} (MSSA) found within the same episode (see \code{episode} parameter of \code{\link{first_isolate}}). Without key antibiotic comparison it wouldn't.
|
||||
#' @details The function \code{key_antibiotics} returns a character vector with 12 antibiotic results for every isolate. These isolates can then be compared using \code{key_antibiotics_equal}, to check if two isolates have generally the same antibiogram. Missing and invalid values are replaced with a dot (\code{"."}). The \code{\link{first_isolate}} function only uses this function on the same microbial species from the same patient. Using this, an MRSA will be included after a susceptible \emph{S. aureus} (MSSA) found within the same episode (see \code{episode} parameter of \code{\link{first_isolate}}). Without key antibiotic comparison it would not.
|
||||
#'
|
||||
#' At default, the antibiotics that are used for \strong{Gram positive bacteria} are (colum names): \cr
|
||||
#' \code{"amox"}, \code{"amcl"}, \code{"cfur"}, \code{"pita"}, \code{"cipr"}, \code{"trsu"} (until here is universal), \code{"vanc"}, \code{"teic"}, \code{"tetr"}, \code{"eryt"}, \code{"oxac"}, \code{"rifa"}.
|
||||
@ -78,24 +78,24 @@
|
||||
#' # FALSE, because I is not ignored and so the 4th value differs
|
||||
key_antibiotics <- function(tbl,
|
||||
col_mo = NULL,
|
||||
universal_1 = guess_ab(tbl, "amox"),
|
||||
universal_2 = guess_ab(tbl, "amcl"),
|
||||
universal_3 = guess_ab(tbl, "cfur"),
|
||||
universal_4 = guess_ab(tbl, "pita"),
|
||||
universal_5 = guess_ab(tbl, "cipr"),
|
||||
universal_6 = guess_ab(tbl, "trsu"),
|
||||
GramPos_1 = guess_ab(tbl, "vanc"),
|
||||
GramPos_2 = guess_ab(tbl, "teic"),
|
||||
GramPos_3 = guess_ab(tbl, "tetr"),
|
||||
GramPos_4 = guess_ab(tbl, "eryt"),
|
||||
GramPos_5 = guess_ab(tbl, "oxac"),
|
||||
GramPos_6 = guess_ab(tbl, "rifa"),
|
||||
GramNeg_1 = guess_ab(tbl, "gent"),
|
||||
GramNeg_2 = guess_ab(tbl, "tobr"),
|
||||
GramNeg_3 = guess_ab(tbl, "coli"),
|
||||
GramNeg_4 = guess_ab(tbl, "cfot"),
|
||||
GramNeg_5 = guess_ab(tbl, "cfta"),
|
||||
GramNeg_6 = guess_ab(tbl, "mero"),
|
||||
universal_1 = guess_ab_col(tbl, "amox"),
|
||||
universal_2 = guess_ab_col(tbl, "amcl"),
|
||||
universal_3 = guess_ab_col(tbl, "cfur"),
|
||||
universal_4 = guess_ab_col(tbl, "pita"),
|
||||
universal_5 = guess_ab_col(tbl, "cipr"),
|
||||
universal_6 = guess_ab_col(tbl, "trsu"),
|
||||
GramPos_1 = guess_ab_col(tbl, "vanc"),
|
||||
GramPos_2 = guess_ab_col(tbl, "teic"),
|
||||
GramPos_3 = guess_ab_col(tbl, "tetr"),
|
||||
GramPos_4 = guess_ab_col(tbl, "eryt"),
|
||||
GramPos_5 = guess_ab_col(tbl, "oxac"),
|
||||
GramPos_6 = guess_ab_col(tbl, "rifa"),
|
||||
GramNeg_1 = guess_ab_col(tbl, "gent"),
|
||||
GramNeg_2 = guess_ab_col(tbl, "tobr"),
|
||||
GramNeg_3 = guess_ab_col(tbl, "coli"),
|
||||
GramNeg_4 = guess_ab_col(tbl, "cfot"),
|
||||
GramNeg_5 = guess_ab_col(tbl, "cfta"),
|
||||
GramNeg_6 = guess_ab_col(tbl, "mero"),
|
||||
warnings = TRUE,
|
||||
...) {
|
||||
|
||||
@ -153,9 +153,6 @@ key_antibiotics <- function(tbl,
|
||||
left_join_microorganisms(by = col_mo) %>%
|
||||
mutate(key_ab = NA_character_)
|
||||
|
||||
print(as.character(gram_positive))
|
||||
print(gram_negative)
|
||||
|
||||
# Gram +
|
||||
tbl <- tbl %>% mutate(key_ab =
|
||||
if_else(gramstain == "Gram positive",
|
||||
|
||||
240
R/mdro.R
240
R/mdro.R
@ -46,66 +46,66 @@ mdro <- function(tbl,
|
||||
country = NULL,
|
||||
col_mo = NULL,
|
||||
info = TRUE,
|
||||
amcl = guess_ab(),
|
||||
amik = guess_ab(),
|
||||
amox = guess_ab(),
|
||||
ampi = guess_ab(),
|
||||
azit = guess_ab(),
|
||||
aztr = guess_ab(),
|
||||
cefa = guess_ab(),
|
||||
cfra = guess_ab(),
|
||||
cfep = guess_ab(),
|
||||
cfot = guess_ab(),
|
||||
cfox = guess_ab(),
|
||||
cfta = guess_ab(),
|
||||
cftr = guess_ab(),
|
||||
cfur = guess_ab(),
|
||||
chlo = guess_ab(),
|
||||
cipr = guess_ab(),
|
||||
clar = guess_ab(),
|
||||
clin = guess_ab(),
|
||||
clox = guess_ab(),
|
||||
coli = guess_ab(),
|
||||
czol = guess_ab(),
|
||||
dapt = guess_ab(),
|
||||
doxy = guess_ab(),
|
||||
erta = guess_ab(),
|
||||
eryt = guess_ab(),
|
||||
fosf = guess_ab(),
|
||||
fusi = guess_ab(),
|
||||
gent = guess_ab(),
|
||||
imip = guess_ab(),
|
||||
kana = guess_ab(),
|
||||
levo = guess_ab(),
|
||||
linc = guess_ab(),
|
||||
line = guess_ab(),
|
||||
mero = guess_ab(),
|
||||
metr = guess_ab(),
|
||||
mino = guess_ab(),
|
||||
moxi = guess_ab(),
|
||||
nali = guess_ab(),
|
||||
neom = guess_ab(),
|
||||
neti = guess_ab(),
|
||||
nitr = guess_ab(),
|
||||
novo = guess_ab(),
|
||||
norf = guess_ab(),
|
||||
oflo = guess_ab(),
|
||||
peni = guess_ab(),
|
||||
pipe = guess_ab(),
|
||||
pita = guess_ab(),
|
||||
poly = guess_ab(),
|
||||
qida = guess_ab(),
|
||||
rifa = guess_ab(),
|
||||
roxi = guess_ab(),
|
||||
siso = guess_ab(),
|
||||
teic = guess_ab(),
|
||||
tetr = guess_ab(),
|
||||
tica = guess_ab(),
|
||||
tige = guess_ab(),
|
||||
tobr = guess_ab(),
|
||||
trim = guess_ab(),
|
||||
trsu = guess_ab(),
|
||||
vanc = guess_ab()) {
|
||||
amcl = guess_ab_col(),
|
||||
amik = guess_ab_col(),
|
||||
amox = guess_ab_col(),
|
||||
ampi = guess_ab_col(),
|
||||
azit = guess_ab_col(),
|
||||
aztr = guess_ab_col(),
|
||||
cefa = guess_ab_col(),
|
||||
cfra = guess_ab_col(),
|
||||
cfep = guess_ab_col(),
|
||||
cfot = guess_ab_col(),
|
||||
cfox = guess_ab_col(),
|
||||
cfta = guess_ab_col(),
|
||||
cftr = guess_ab_col(),
|
||||
cfur = guess_ab_col(),
|
||||
chlo = guess_ab_col(),
|
||||
cipr = guess_ab_col(),
|
||||
clar = guess_ab_col(),
|
||||
clin = guess_ab_col(),
|
||||
clox = guess_ab_col(),
|
||||
coli = guess_ab_col(),
|
||||
czol = guess_ab_col(),
|
||||
dapt = guess_ab_col(),
|
||||
doxy = guess_ab_col(),
|
||||
erta = guess_ab_col(),
|
||||
eryt = guess_ab_col(),
|
||||
fosf = guess_ab_col(),
|
||||
fusi = guess_ab_col(),
|
||||
gent = guess_ab_col(),
|
||||
imip = guess_ab_col(),
|
||||
kana = guess_ab_col(),
|
||||
levo = guess_ab_col(),
|
||||
linc = guess_ab_col(),
|
||||
line = guess_ab_col(),
|
||||
mero = guess_ab_col(),
|
||||
metr = guess_ab_col(),
|
||||
mino = guess_ab_col(),
|
||||
moxi = guess_ab_col(),
|
||||
nali = guess_ab_col(),
|
||||
neom = guess_ab_col(),
|
||||
neti = guess_ab_col(),
|
||||
nitr = guess_ab_col(),
|
||||
novo = guess_ab_col(),
|
||||
norf = guess_ab_col(),
|
||||
oflo = guess_ab_col(),
|
||||
peni = guess_ab_col(),
|
||||
pipe = guess_ab_col(),
|
||||
pita = guess_ab_col(),
|
||||
poly = guess_ab_col(),
|
||||
qida = guess_ab_col(),
|
||||
rifa = guess_ab_col(),
|
||||
roxi = guess_ab_col(),
|
||||
siso = guess_ab_col(),
|
||||
teic = guess_ab_col(),
|
||||
tetr = guess_ab_col(),
|
||||
tica = guess_ab_col(),
|
||||
tige = guess_ab_col(),
|
||||
tobr = guess_ab_col(),
|
||||
trim = guess_ab_col(),
|
||||
trsu = guess_ab_col(),
|
||||
vanc = guess_ab_col()) {
|
||||
|
||||
if (!is.data.frame(tbl)) {
|
||||
stop("`tbl` must be a data frame.", call. = FALSE)
|
||||
@ -169,66 +169,66 @@ mdro <- function(tbl,
|
||||
}
|
||||
|
||||
# check columns
|
||||
if (identical(amcl, as.name("guess_ab"))) { amcl <- guess_ab(tbl, "amcl", verbose = info) }
|
||||
if (identical(amik, as.name("guess_ab"))) { amik <- guess_ab(tbl, "amik", verbose = info) }
|
||||
if (identical(amox, as.name("guess_ab"))) { amox <- guess_ab(tbl, "amox", verbose = info) }
|
||||
if (identical(ampi, as.name("guess_ab"))) { ampi <- guess_ab(tbl, "ampi", verbose = info) }
|
||||
if (identical(azit, as.name("guess_ab"))) { azit <- guess_ab(tbl, "azit", verbose = info) }
|
||||
if (identical(aztr, as.name("guess_ab"))) { aztr <- guess_ab(tbl, "aztr", verbose = info) }
|
||||
if (identical(cefa, as.name("guess_ab"))) { cefa <- guess_ab(tbl, "cefa", verbose = info) }
|
||||
if (identical(cfra, as.name("guess_ab"))) { cfra <- guess_ab(tbl, "cfra", verbose = info) }
|
||||
if (identical(cfep, as.name("guess_ab"))) { cfep <- guess_ab(tbl, "cfep", verbose = info) }
|
||||
if (identical(cfot, as.name("guess_ab"))) { cfot <- guess_ab(tbl, "cfot", verbose = info) }
|
||||
if (identical(cfox, as.name("guess_ab"))) { cfox <- guess_ab(tbl, "cfox", verbose = info) }
|
||||
if (identical(cfta, as.name("guess_ab"))) { cfta <- guess_ab(tbl, "cfta", verbose = info) }
|
||||
if (identical(cftr, as.name("guess_ab"))) { cftr <- guess_ab(tbl, "cftr", verbose = info) }
|
||||
if (identical(cfur, as.name("guess_ab"))) { cfur <- guess_ab(tbl, "cfur", verbose = info) }
|
||||
if (identical(chlo, as.name("guess_ab"))) { chlo <- guess_ab(tbl, "chlo", verbose = info) }
|
||||
if (identical(cipr, as.name("guess_ab"))) { cipr <- guess_ab(tbl, "cipr", verbose = info) }
|
||||
if (identical(clar, as.name("guess_ab"))) { clar <- guess_ab(tbl, "clar", verbose = info) }
|
||||
if (identical(clin, as.name("guess_ab"))) { clin <- guess_ab(tbl, "clin", verbose = info) }
|
||||
if (identical(clox, as.name("guess_ab"))) { clox <- guess_ab(tbl, "clox", verbose = info) }
|
||||
if (identical(coli, as.name("guess_ab"))) { coli <- guess_ab(tbl, "coli", verbose = info) }
|
||||
if (identical(czol, as.name("guess_ab"))) { czol <- guess_ab(tbl, "czol", verbose = info) }
|
||||
if (identical(dapt, as.name("guess_ab"))) { dapt <- guess_ab(tbl, "dapt", verbose = info) }
|
||||
if (identical(doxy, as.name("guess_ab"))) { doxy <- guess_ab(tbl, "doxy", verbose = info) }
|
||||
if (identical(erta, as.name("guess_ab"))) { erta <- guess_ab(tbl, "erta", verbose = info) }
|
||||
if (identical(eryt, as.name("guess_ab"))) { eryt <- guess_ab(tbl, "eryt", verbose = info) }
|
||||
if (identical(fosf, as.name("guess_ab"))) { fosf <- guess_ab(tbl, "fosf", verbose = info) }
|
||||
if (identical(fusi, as.name("guess_ab"))) { fusi <- guess_ab(tbl, "fusi", verbose = info) }
|
||||
if (identical(gent, as.name("guess_ab"))) { gent <- guess_ab(tbl, "gent", verbose = info) }
|
||||
if (identical(imip, as.name("guess_ab"))) { imip <- guess_ab(tbl, "imip", verbose = info) }
|
||||
if (identical(kana, as.name("guess_ab"))) { kana <- guess_ab(tbl, "kana", verbose = info) }
|
||||
if (identical(levo, as.name("guess_ab"))) { levo <- guess_ab(tbl, "levo", verbose = info) }
|
||||
if (identical(linc, as.name("guess_ab"))) { linc <- guess_ab(tbl, "linc", verbose = info) }
|
||||
if (identical(line, as.name("guess_ab"))) { line <- guess_ab(tbl, "line", verbose = info) }
|
||||
if (identical(mero, as.name("guess_ab"))) { mero <- guess_ab(tbl, "mero", verbose = info) }
|
||||
if (identical(metr, as.name("guess_ab"))) { metr <- guess_ab(tbl, "metr", verbose = info) }
|
||||
if (identical(mino, as.name("guess_ab"))) { mino <- guess_ab(tbl, "mino", verbose = info) }
|
||||
if (identical(moxi, as.name("guess_ab"))) { moxi <- guess_ab(tbl, "moxi", verbose = info) }
|
||||
if (identical(nali, as.name("guess_ab"))) { nali <- guess_ab(tbl, "nali", verbose = info) }
|
||||
if (identical(neom, as.name("guess_ab"))) { neom <- guess_ab(tbl, "neom", verbose = info) }
|
||||
if (identical(neti, as.name("guess_ab"))) { neti <- guess_ab(tbl, "neti", verbose = info) }
|
||||
if (identical(nitr, as.name("guess_ab"))) { nitr <- guess_ab(tbl, "nitr", verbose = info) }
|
||||
if (identical(novo, as.name("guess_ab"))) { novo <- guess_ab(tbl, "novo", verbose = info) }
|
||||
if (identical(norf, as.name("guess_ab"))) { norf <- guess_ab(tbl, "norf", verbose = info) }
|
||||
if (identical(oflo, as.name("guess_ab"))) { oflo <- guess_ab(tbl, "oflo", verbose = info) }
|
||||
if (identical(peni, as.name("guess_ab"))) { peni <- guess_ab(tbl, "peni", verbose = info) }
|
||||
if (identical(pipe, as.name("guess_ab"))) { pipe <- guess_ab(tbl, "pipe", verbose = info) }
|
||||
if (identical(pita, as.name("guess_ab"))) { pita <- guess_ab(tbl, "pita", verbose = info) }
|
||||
if (identical(poly, as.name("guess_ab"))) { poly <- guess_ab(tbl, "poly", verbose = info) }
|
||||
if (identical(qida, as.name("guess_ab"))) { qida <- guess_ab(tbl, "qida", verbose = info) }
|
||||
if (identical(rifa, as.name("guess_ab"))) { rifa <- guess_ab(tbl, "rifa", verbose = info) }
|
||||
if (identical(roxi, as.name("guess_ab"))) { roxi <- guess_ab(tbl, "roxi", verbose = info) }
|
||||
if (identical(siso, as.name("guess_ab"))) { siso <- guess_ab(tbl, "siso", verbose = info) }
|
||||
if (identical(teic, as.name("guess_ab"))) { teic <- guess_ab(tbl, "teic", verbose = info) }
|
||||
if (identical(tetr, as.name("guess_ab"))) { tetr <- guess_ab(tbl, "tetr", verbose = info) }
|
||||
if (identical(tica, as.name("guess_ab"))) { tica <- guess_ab(tbl, "tica", verbose = info) }
|
||||
if (identical(tige, as.name("guess_ab"))) { tige <- guess_ab(tbl, "tige", verbose = info) }
|
||||
if (identical(tobr, as.name("guess_ab"))) { tobr <- guess_ab(tbl, "tobr", verbose = info) }
|
||||
if (identical(trim, as.name("guess_ab"))) { trim <- guess_ab(tbl, "trim", verbose = info) }
|
||||
if (identical(trsu, as.name("guess_ab"))) { trsu <- guess_ab(tbl, "trsu", verbose = info) }
|
||||
if (identical(vanc, as.name("guess_ab"))) { vanc <- guess_ab(tbl, "vanc", verbose = info) }
|
||||
if (identical(amcl, as.name("guess_ab_col"))) { amcl <- guess_ab_col(tbl, "amcl", verbose = info) }
|
||||
if (identical(amik, as.name("guess_ab_col"))) { amik <- guess_ab_col(tbl, "amik", verbose = info) }
|
||||
if (identical(amox, as.name("guess_ab_col"))) { amox <- guess_ab_col(tbl, "amox", verbose = info) }
|
||||
if (identical(ampi, as.name("guess_ab_col"))) { ampi <- guess_ab_col(tbl, "ampi", verbose = info) }
|
||||
if (identical(azit, as.name("guess_ab_col"))) { azit <- guess_ab_col(tbl, "azit", verbose = info) }
|
||||
if (identical(aztr, as.name("guess_ab_col"))) { aztr <- guess_ab_col(tbl, "aztr", verbose = info) }
|
||||
if (identical(cefa, as.name("guess_ab_col"))) { cefa <- guess_ab_col(tbl, "cefa", verbose = info) }
|
||||
if (identical(cfra, as.name("guess_ab_col"))) { cfra <- guess_ab_col(tbl, "cfra", verbose = info) }
|
||||
if (identical(cfep, as.name("guess_ab_col"))) { cfep <- guess_ab_col(tbl, "cfep", verbose = info) }
|
||||
if (identical(cfot, as.name("guess_ab_col"))) { cfot <- guess_ab_col(tbl, "cfot", verbose = info) }
|
||||
if (identical(cfox, as.name("guess_ab_col"))) { cfox <- guess_ab_col(tbl, "cfox", verbose = info) }
|
||||
if (identical(cfta, as.name("guess_ab_col"))) { cfta <- guess_ab_col(tbl, "cfta", verbose = info) }
|
||||
if (identical(cftr, as.name("guess_ab_col"))) { cftr <- guess_ab_col(tbl, "cftr", verbose = info) }
|
||||
if (identical(cfur, as.name("guess_ab_col"))) { cfur <- guess_ab_col(tbl, "cfur", verbose = info) }
|
||||
if (identical(chlo, as.name("guess_ab_col"))) { chlo <- guess_ab_col(tbl, "chlo", verbose = info) }
|
||||
if (identical(cipr, as.name("guess_ab_col"))) { cipr <- guess_ab_col(tbl, "cipr", verbose = info) }
|
||||
if (identical(clar, as.name("guess_ab_col"))) { clar <- guess_ab_col(tbl, "clar", verbose = info) }
|
||||
if (identical(clin, as.name("guess_ab_col"))) { clin <- guess_ab_col(tbl, "clin", verbose = info) }
|
||||
if (identical(clox, as.name("guess_ab_col"))) { clox <- guess_ab_col(tbl, "clox", verbose = info) }
|
||||
if (identical(coli, as.name("guess_ab_col"))) { coli <- guess_ab_col(tbl, "coli", verbose = info) }
|
||||
if (identical(czol, as.name("guess_ab_col"))) { czol <- guess_ab_col(tbl, "czol", verbose = info) }
|
||||
if (identical(dapt, as.name("guess_ab_col"))) { dapt <- guess_ab_col(tbl, "dapt", verbose = info) }
|
||||
if (identical(doxy, as.name("guess_ab_col"))) { doxy <- guess_ab_col(tbl, "doxy", verbose = info) }
|
||||
if (identical(erta, as.name("guess_ab_col"))) { erta <- guess_ab_col(tbl, "erta", verbose = info) }
|
||||
if (identical(eryt, as.name("guess_ab_col"))) { eryt <- guess_ab_col(tbl, "eryt", verbose = info) }
|
||||
if (identical(fosf, as.name("guess_ab_col"))) { fosf <- guess_ab_col(tbl, "fosf", verbose = info) }
|
||||
if (identical(fusi, as.name("guess_ab_col"))) { fusi <- guess_ab_col(tbl, "fusi", verbose = info) }
|
||||
if (identical(gent, as.name("guess_ab_col"))) { gent <- guess_ab_col(tbl, "gent", verbose = info) }
|
||||
if (identical(imip, as.name("guess_ab_col"))) { imip <- guess_ab_col(tbl, "imip", verbose = info) }
|
||||
if (identical(kana, as.name("guess_ab_col"))) { kana <- guess_ab_col(tbl, "kana", verbose = info) }
|
||||
if (identical(levo, as.name("guess_ab_col"))) { levo <- guess_ab_col(tbl, "levo", verbose = info) }
|
||||
if (identical(linc, as.name("guess_ab_col"))) { linc <- guess_ab_col(tbl, "linc", verbose = info) }
|
||||
if (identical(line, as.name("guess_ab_col"))) { line <- guess_ab_col(tbl, "line", verbose = info) }
|
||||
if (identical(mero, as.name("guess_ab_col"))) { mero <- guess_ab_col(tbl, "mero", verbose = info) }
|
||||
if (identical(metr, as.name("guess_ab_col"))) { metr <- guess_ab_col(tbl, "metr", verbose = info) }
|
||||
if (identical(mino, as.name("guess_ab_col"))) { mino <- guess_ab_col(tbl, "mino", verbose = info) }
|
||||
if (identical(moxi, as.name("guess_ab_col"))) { moxi <- guess_ab_col(tbl, "moxi", verbose = info) }
|
||||
if (identical(nali, as.name("guess_ab_col"))) { nali <- guess_ab_col(tbl, "nali", verbose = info) }
|
||||
if (identical(neom, as.name("guess_ab_col"))) { neom <- guess_ab_col(tbl, "neom", verbose = info) }
|
||||
if (identical(neti, as.name("guess_ab_col"))) { neti <- guess_ab_col(tbl, "neti", verbose = info) }
|
||||
if (identical(nitr, as.name("guess_ab_col"))) { nitr <- guess_ab_col(tbl, "nitr", verbose = info) }
|
||||
if (identical(novo, as.name("guess_ab_col"))) { novo <- guess_ab_col(tbl, "novo", verbose = info) }
|
||||
if (identical(norf, as.name("guess_ab_col"))) { norf <- guess_ab_col(tbl, "norf", verbose = info) }
|
||||
if (identical(oflo, as.name("guess_ab_col"))) { oflo <- guess_ab_col(tbl, "oflo", verbose = info) }
|
||||
if (identical(peni, as.name("guess_ab_col"))) { peni <- guess_ab_col(tbl, "peni", verbose = info) }
|
||||
if (identical(pipe, as.name("guess_ab_col"))) { pipe <- guess_ab_col(tbl, "pipe", verbose = info) }
|
||||
if (identical(pita, as.name("guess_ab_col"))) { pita <- guess_ab_col(tbl, "pita", verbose = info) }
|
||||
if (identical(poly, as.name("guess_ab_col"))) { poly <- guess_ab_col(tbl, "poly", verbose = info) }
|
||||
if (identical(qida, as.name("guess_ab_col"))) { qida <- guess_ab_col(tbl, "qida", verbose = info) }
|
||||
if (identical(rifa, as.name("guess_ab_col"))) { rifa <- guess_ab_col(tbl, "rifa", verbose = info) }
|
||||
if (identical(roxi, as.name("guess_ab_col"))) { roxi <- guess_ab_col(tbl, "roxi", verbose = info) }
|
||||
if (identical(siso, as.name("guess_ab_col"))) { siso <- guess_ab_col(tbl, "siso", verbose = info) }
|
||||
if (identical(teic, as.name("guess_ab_col"))) { teic <- guess_ab_col(tbl, "teic", verbose = info) }
|
||||
if (identical(tetr, as.name("guess_ab_col"))) { tetr <- guess_ab_col(tbl, "tetr", verbose = info) }
|
||||
if (identical(tica, as.name("guess_ab_col"))) { tica <- guess_ab_col(tbl, "tica", verbose = info) }
|
||||
if (identical(tige, as.name("guess_ab_col"))) { tige <- guess_ab_col(tbl, "tige", verbose = info) }
|
||||
if (identical(tobr, as.name("guess_ab_col"))) { tobr <- guess_ab_col(tbl, "tobr", verbose = info) }
|
||||
if (identical(trim, as.name("guess_ab_col"))) { trim <- guess_ab_col(tbl, "trim", verbose = info) }
|
||||
if (identical(trsu, as.name("guess_ab_col"))) { trsu <- guess_ab_col(tbl, "trsu", verbose = info) }
|
||||
if (identical(vanc, as.name("guess_ab_col"))) { vanc <- guess_ab_col(tbl, "vanc", verbose = info) }
|
||||
col.list <- c(amcl, amik, amox, ampi, azit, 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