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guess_ab
This commit is contained in:
192
R/mdro.R
192
R/mdro.R
@ -46,66 +46,66 @@ mdro <- function(tbl,
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country = NULL,
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col_mo = NULL,
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info = TRUE,
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amcl = 'amcl',
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amik = 'amik',
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amox = 'amox',
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ampi = 'ampi',
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azit = 'azit',
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aztr = 'aztr',
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cefa = 'cefa',
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cfra = 'cfra',
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cfep = 'cfep',
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cfot = 'cfot',
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cfox = 'cfox',
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cfta = 'cfta',
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cftr = 'cftr',
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cfur = 'cfur',
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chlo = 'chlo',
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cipr = 'cipr',
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clar = 'clar',
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clin = 'clin',
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clox = 'clox',
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coli = 'coli',
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czol = 'czol',
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dapt = 'dapt',
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doxy = 'doxy',
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erta = 'erta',
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eryt = 'eryt',
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fosf = 'fosf',
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fusi = 'fusi',
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gent = 'gent',
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imip = 'imip',
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kana = 'kana',
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levo = 'levo',
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linc = 'linc',
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line = 'line',
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mero = 'mero',
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metr = 'metr',
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mino = 'mino',
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moxi = 'moxi',
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nali = 'nali',
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neom = 'neom',
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neti = 'neti',
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nitr = 'nitr',
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novo = 'novo',
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norf = 'norf',
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oflo = 'oflo',
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peni = 'peni',
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pipe = 'pipe',
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pita = 'pita',
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poly = 'poly',
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qida = 'qida',
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rifa = 'rifa',
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roxi = 'roxi',
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siso = 'siso',
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teic = 'teic',
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tetr = 'tetr',
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tica = 'tica',
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tige = 'tige',
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tobr = 'tobr',
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trim = 'trim',
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trsu = 'trsu',
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vanc = 'vanc') {
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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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aztr = guess_ab(),
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cefa = guess_ab(),
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cfra = 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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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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metr = 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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novo = guess_ab(),
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norf = guess_ab(),
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oflo = 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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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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if (!is.data.frame(tbl)) {
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stop("`tbl` must be a data frame.", call. = FALSE)
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@ -169,12 +169,77 @@ mdro <- 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 = info) }
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if (identical(amik, as.name("guess_ab"))) { amik <- guess_ab(tbl, "amik", verbose = info) }
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if (identical(amox, as.name("guess_ab"))) { amox <- guess_ab(tbl, "amox", verbose = info) }
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if (identical(ampi, as.name("guess_ab"))) { ampi <- guess_ab(tbl, "ampi", verbose = info) }
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if (identical(azit, as.name("guess_ab"))) { azit <- guess_ab(tbl, "azit", verbose = info) }
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if (identical(aztr, as.name("guess_ab"))) { aztr <- guess_ab(tbl, "aztr", verbose = info) }
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if (identical(cefa, as.name("guess_ab"))) { cefa <- guess_ab(tbl, "cefa", verbose = info) }
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if (identical(cfra, as.name("guess_ab"))) { cfra <- guess_ab(tbl, "cfra", verbose = info) }
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if (identical(cfep, as.name("guess_ab"))) { cfep <- guess_ab(tbl, "cfep", verbose = info) }
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if (identical(cfot, as.name("guess_ab"))) { cfot <- guess_ab(tbl, "cfot", verbose = info) }
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if (identical(cfox, as.name("guess_ab"))) { cfox <- guess_ab(tbl, "cfox", verbose = info) }
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if (identical(cfta, as.name("guess_ab"))) { cfta <- guess_ab(tbl, "cfta", verbose = info) }
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if (identical(cftr, as.name("guess_ab"))) { cftr <- guess_ab(tbl, "cftr", verbose = info) }
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if (identical(cfur, as.name("guess_ab"))) { cfur <- guess_ab(tbl, "cfur", verbose = info) }
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if (identical(chlo, as.name("guess_ab"))) { chlo <- guess_ab(tbl, "chlo", verbose = info) }
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if (identical(cipr, as.name("guess_ab"))) { cipr <- guess_ab(tbl, "cipr", verbose = info) }
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if (identical(clar, as.name("guess_ab"))) { clar <- guess_ab(tbl, "clar", verbose = info) }
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if (identical(clin, as.name("guess_ab"))) { clin <- guess_ab(tbl, "clin", verbose = info) }
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if (identical(clox, as.name("guess_ab"))) { clox <- guess_ab(tbl, "clox", verbose = info) }
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if (identical(coli, as.name("guess_ab"))) { coli <- guess_ab(tbl, "coli", verbose = info) }
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if (identical(czol, as.name("guess_ab"))) { czol <- guess_ab(tbl, "czol", verbose = info) }
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if (identical(dapt, as.name("guess_ab"))) { dapt <- guess_ab(tbl, "dapt", verbose = info) }
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if (identical(doxy, as.name("guess_ab"))) { doxy <- guess_ab(tbl, "doxy", verbose = info) }
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if (identical(erta, as.name("guess_ab"))) { erta <- guess_ab(tbl, "erta", verbose = info) }
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if (identical(eryt, as.name("guess_ab"))) { eryt <- guess_ab(tbl, "eryt", verbose = info) }
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if (identical(fosf, as.name("guess_ab"))) { fosf <- guess_ab(tbl, "fosf", verbose = info) }
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if (identical(fusi, as.name("guess_ab"))) { fusi <- guess_ab(tbl, "fusi", verbose = info) }
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if (identical(gent, as.name("guess_ab"))) { gent <- guess_ab(tbl, "gent", verbose = info) }
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if (identical(imip, as.name("guess_ab"))) { imip <- guess_ab(tbl, "imip", verbose = info) }
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if (identical(kana, as.name("guess_ab"))) { kana <- guess_ab(tbl, "kana", verbose = info) }
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if (identical(levo, as.name("guess_ab"))) { levo <- guess_ab(tbl, "levo", verbose = info) }
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if (identical(linc, as.name("guess_ab"))) { linc <- guess_ab(tbl, "linc", verbose = info) }
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if (identical(line, as.name("guess_ab"))) { line <- guess_ab(tbl, "line", verbose = info) }
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if (identical(mero, as.name("guess_ab"))) { mero <- guess_ab(tbl, "mero", verbose = info) }
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if (identical(metr, as.name("guess_ab"))) { metr <- guess_ab(tbl, "metr", verbose = info) }
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if (identical(mino, as.name("guess_ab"))) { mino <- guess_ab(tbl, "mino", verbose = info) }
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if (identical(moxi, as.name("guess_ab"))) { moxi <- guess_ab(tbl, "moxi", verbose = info) }
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if (identical(nali, as.name("guess_ab"))) { nali <- guess_ab(tbl, "nali", verbose = info) }
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if (identical(neom, as.name("guess_ab"))) { neom <- guess_ab(tbl, "neom", verbose = info) }
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if (identical(neti, as.name("guess_ab"))) { neti <- guess_ab(tbl, "neti", verbose = info) }
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if (identical(nitr, as.name("guess_ab"))) { nitr <- guess_ab(tbl, "nitr", verbose = info) }
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if (identical(novo, as.name("guess_ab"))) { novo <- guess_ab(tbl, "novo", verbose = info) }
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if (identical(norf, as.name("guess_ab"))) { norf <- guess_ab(tbl, "norf", verbose = info) }
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if (identical(oflo, as.name("guess_ab"))) { oflo <- guess_ab(tbl, "oflo", verbose = info) }
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if (identical(peni, as.name("guess_ab"))) { peni <- guess_ab(tbl, "peni", verbose = info) }
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if (identical(pipe, as.name("guess_ab"))) { pipe <- guess_ab(tbl, "pipe", verbose = info) }
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if (identical(pita, as.name("guess_ab"))) { pita <- guess_ab(tbl, "pita", verbose = info) }
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if (identical(poly, as.name("guess_ab"))) { poly <- guess_ab(tbl, "poly", verbose = info) }
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if (identical(qida, as.name("guess_ab"))) { qida <- guess_ab(tbl, "qida", verbose = info) }
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if (identical(rifa, as.name("guess_ab"))) { rifa <- guess_ab(tbl, "rifa", verbose = info) }
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if (identical(roxi, as.name("guess_ab"))) { roxi <- guess_ab(tbl, "roxi", verbose = info) }
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if (identical(siso, as.name("guess_ab"))) { siso <- guess_ab(tbl, "siso", verbose = info) }
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if (identical(teic, as.name("guess_ab"))) { teic <- guess_ab(tbl, "teic", verbose = info) }
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if (identical(tetr, as.name("guess_ab"))) { tetr <- guess_ab(tbl, "tetr", verbose = info) }
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if (identical(tica, as.name("guess_ab"))) { tica <- guess_ab(tbl, "tica", verbose = info) }
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if (identical(tige, as.name("guess_ab"))) { tige <- guess_ab(tbl, "tige", verbose = info) }
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if (identical(tobr, as.name("guess_ab"))) { tobr <- guess_ab(tbl, "tobr", verbose = info) }
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if (identical(trim, as.name("guess_ab"))) { trim <- guess_ab(tbl, "trim", verbose = info) }
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if (identical(trsu, as.name("guess_ab"))) { trsu <- guess_ab(tbl, "trsu", verbose = info) }
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if (identical(vanc, as.name("guess_ab"))) { vanc <- guess_ab(tbl, "vanc", verbose = info) }
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col.list <- c(amcl, amik, amox, ampi, azit, aztr, cefa, cfra, cfep, cfot,
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cfox, cfta, cftr, cfur, chlo, cipr, clar, clin, clox, coli,
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czol, dapt, doxy, erta, eryt, fosf, fusi, gent, imip, kana,
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levo, linc, line, mero, metr, mino, moxi, nali, neom, neti, nitr,
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novo, norf, oflo, peni, pita, poly, qida, rifa, roxi, siso,
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teic, tetr, tica, tige, tobr, trim, trsu, vanc)
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levo, linc, line, mero, metr, mino, moxi, nali, neom, neti,
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nitr, novo, norf, oflo, peni, pipe, pita, poly, qida, rifa,
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roxi, siso, teic, tetr, tica, tige, tobr, trim, trsu, vanc)
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if (length(col.list) < 60) {
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warning('Some columns do not exist -- THIS MAY STRONGLY INFLUENCE THE OUTCOME.',
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immediate. = TRUE,
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call. = FALSE)
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}
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col.list <- check_available_columns(tbl = tbl, col.list = col.list, info = info)
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amcl <- col.list[amcl]
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amik <- col.list[amik]
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@ -221,6 +286,7 @@ mdro <- function(tbl,
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norf <- col.list[norf]
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oflo <- col.list[oflo]
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peni <- col.list[peni]
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pipe <- col.list[pipe]
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pita <- col.list[pita]
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poly <- col.list[poly]
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qida <- col.list[qida]
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