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guess_ab_col, benchmarks

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dr. M.S. (Matthijs) Berends
2019-01-11 20:37:23 +01:00
parent 193a2d2863
commit 641d866db2
86 changed files with 2181 additions and 767 deletions
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52
man/mdro.Rd
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@@ -8,26 +8,36 @@
\title{Determine multidrug-resistant organisms (MDRO)}
\usage{
mdro(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())
brmo(..., country = "nl")
@@ -177,7 +187,7 @@ When \code{country} will be left blank, guidelines will be taken from EUCAST Exp
}
\section{Antibiotics}{
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.
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.
Abbrevations of the column containing antibiotics in the form: \strong{abbreviation}: generic name (\emph{ATC code})