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guess_ab

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dr. M.S. (Matthijs) Berends
2019-01-03 23:56:19 +01:00
parent 6b2d464f8c
commit 80ea555663
14 changed files with 533 additions and 270 deletions
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37
man/mdro.Rd
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@@ -8,21 +8,26 @@
\title{Determine multidrug-resistant organisms (MDRO)}
\usage{
mdro(tbl, country = NULL, col_mo = NULL, info = TRUE,
amcl = "amcl", amik = "amik", amox = "amox", ampi = "ampi",
azit = "azit", aztr = "aztr", cefa = "cefa", cfra = "cfra",
cfep = "cfep", cfot = "cfot", cfox = "cfox", cfta = "cfta",
cftr = "cftr", cfur = "cfur", chlo = "chlo", cipr = "cipr",
clar = "clar", clin = "clin", clox = "clox", coli = "coli",
czol = "czol", dapt = "dapt", doxy = "doxy", erta = "erta",
eryt = "eryt", fosf = "fosf", fusi = "fusi", gent = "gent",
imip = "imip", kana = "kana", levo = "levo", linc = "linc",
line = "line", mero = "mero", metr = "metr", mino = "mino",
moxi = "moxi", nali = "nali", neom = "neom", neti = "neti",
nitr = "nitr", novo = "novo", norf = "norf", oflo = "oflo",
peni = "peni", pipe = "pipe", pita = "pita", poly = "poly",
qida = "qida", rifa = "rifa", roxi = "roxi", siso = "siso",
teic = "teic", tetr = "tetr", tica = "tica", tige = "tige",
tobr = "tobr", trim = "trim", trsu = "trsu", vanc = "vanc")
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())
brmo(..., country = "nl")
@@ -172,7 +177,7 @@ When \code{country} will be left blank, guidelines will be taken from EUCAST Exp
}
\section{Antibiotics}{
To define antibiotics column names, 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.
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.
Abbrevations of the column containing antibiotics in the form: \strong{abbreviation}: generic name (\emph{ATC code})