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eucast updates

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dr. M.S. (Matthijs) Berends
2018-11-01 17:06:08 +01:00
parent d3f5236690
commit f7687557c9
5 changed files with 147 additions and 76 deletions
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14
man/EUCAST.Rd
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@ -35,11 +35,12 @@ EUCAST_rules(tbl, col_mo = "mo", info = TRUE,
line = "line", mero = "mero", mezl = "mezl", mino = "mino",
moxi = "moxi", nali = "nali", neom = "neom", neti = "neti",
nitr = "nitr", norf = "norf", novo = "novo", oflo = "oflo",
oxac = "oxac", peni = "peni", pita = "pita", poly = "poly",
pris = "pris", qida = "qida", rifa = "rifa", roxi = "roxi",
siso = "siso", teic = "teic", tetr = "tetr", tica = "tica",
tige = "tige", tobr = "tobr", trim = "trim", trsu = "trsu",
vanc = "vanc", col_bactid = "bactid", verbose = FALSE)
oxac = "oxac", peni = "peni", pipe = "pipe", pita = "pita",
poly = "poly", pris = "pris", qida = "qida", rifa = "rifa",
roxi = "roxi", siso = "siso", teic = "teic", tetr = "tetr",
tica = "tica", tige = "tige", tobr = "tobr", trim = "trim",
trsu = "trsu", vanc = "vanc", col_bactid = "bactid",
verbose = FALSE)
interpretive_reading(...)
}
@ -52,7 +53,7 @@ interpretive_reading(...)
\item{rules}{a character vector that specifies which rules should be applied - one or more of \code{c("breakpoints", "expert", "other", "all")}}
\item{amcl, amik, amox, ampi, azit, azlo, aztr, cefa, cfep, cfot, cfox, cfra, cfta, cftr, cfur, chlo, cipr, clar, clin, clox, coli, czol, dapt, doxy, erta, eryt, fosf, fusi, gent, imip, kana, levo, linc, line, mero, mezl, mino, moxi, nali, neom, neti, nitr, norf, novo, oflo, oxac, peni, pita, poly, pris, qida, rifa, roxi, siso, teic, tetr, tica, tige, tobr, trim, trsu, vanc}{column name of an antibiotic, see Details}
\item{amcl, amik, amox, ampi, azit, azlo, aztr, cefa, cfep, cfot, cfox, cfra, cfta, cftr, cfur, chlo, cipr, clar, clin, clox, coli, czol, dapt, doxy, erta, eryt, fosf, fusi, gent, imip, kana, levo, linc, line, mero, mezl, mino, moxi, nali, neom, neti, nitr, norf, novo, oflo, oxac, peni, pipe, pita, poly, pris, qida, rifa, roxi, siso, teic, tetr, tica, tige, tobr, trim, trsu, vanc}{column name of an antibiotic, see Details}
\item{col_bactid}{Deprecated. Use \code{col_mo} instead.}
@ -119,6 +120,7 @@ Abbrevations of the column containing antibiotics in the form: \strong{abbreviat
\strong{novo}: novobiocin (an ATCvet code: \emph{QJ01XX95}),
\strong{oflo}: ofloxacin (\emph{J01MA01}),
\strong{peni}: penicillin (\emph{J01RA01}),
\strong{pipe}: piperacillin (\emph{J01CA12}),
\strong{pita}: piperacillin+tazobactam (\emph{J01CR05}),
\strong{poly}: polymyxin B (\emph{J01XB02}),
\strong{pris}: pristinamycin (\emph{J01FG01}),

1
man/MDRO.Rd
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@ -220,6 +220,7 @@ Abbrevations of the column containing antibiotics in the form: \strong{abbreviat
\strong{novo}: novobiocin (an ATCvet code: \emph{QJ01XX95}),
\strong{oflo}: ofloxacin (\emph{J01MA01}),
\strong{peni}: penicillin (\emph{J01RA01}),
\strong{pipe}: piperacillin (\emph{J01CA12}),
\strong{pita}: piperacillin+tazobactam (\emph{J01CR05}),
\strong{poly}: polymyxin B (\emph{J01XB02}),
\strong{pris}: pristinamycin (\emph{J01FG01}),