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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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39
man/eucast_rules.Rd
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@@ -25,22 +25,27 @@
\usage{
eucast_rules(tbl, col_mo = NULL, info = TRUE,
rules = c("breakpoints", "expert", "other", "all"), verbose = FALSE,
amcl = "amcl", amik = "amik", amox = "amox", ampi = "ampi",
azit = "azit", azlo = "azlo", aztr = "aztr", cefa = "cefa",
cfep = "cfep", cfot = "cfot", cfox = "cfox", cfra = "cfra",
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", mezl = "mezl",
mino = "mino", moxi = "moxi", nali = "nali", neom = "neom",
neti = "neti", nitr = "nitr", norf = "norf", novo = "novo",
oflo = "oflo", 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")
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())
EUCAST_rules(...)
@@ -69,7 +74,7 @@ Apply susceptibility rules as defined by the European Committee on Antimicrobial
}
\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})