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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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55
man/eucast_rules.Rd
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@@ -25,27 +25,38 @@
\usage{
eucast_rules(tbl, col_mo = NULL, info = TRUE,
rules = c("breakpoints", "expert", "other", "all"), verbose = FALSE,
amcl = guess_ab(), amik = guess_ab(), amox = guess_ab(),
ampi = guess_ab(), azit = guess_ab(), azlo = guess_ab(),
aztr = guess_ab(), cefa = guess_ab(), cfep = guess_ab(),
cfot = guess_ab(), cfox = guess_ab(), cfra = 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(), mezl = guess_ab(),
mino = guess_ab(), moxi = guess_ab(), nali = guess_ab(),
neom = guess_ab(), neti = guess_ab(), nitr = guess_ab(),
norf = guess_ab(), novo = guess_ab(), oflo = guess_ab(),
oxac = guess_ab(), peni = guess_ab(), pipe = guess_ab(),
pita = guess_ab(), poly = guess_ab(), pris = 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(), azlo = guess_ab_col(),
aztr = guess_ab_col(), cefa = guess_ab_col(),
cfep = guess_ab_col(), cfot = guess_ab_col(),
cfox = guess_ab_col(), cfra = 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(), mezl = 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(),
norf = guess_ab_col(), novo = guess_ab_col(),
oflo = guess_ab_col(), oxac = guess_ab_col(),
peni = guess_ab_col(), pipe = guess_ab_col(),
pita = guess_ab_col(), poly = guess_ab_col(),
pris = 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())
EUCAST_rules(...)
@@ -74,7 +85,7 @@ Apply susceptibility rules as defined by the European Committee on Antimicrobial
}
\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})