P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-09 19:41:49 +02:00
Code Releases Activity

add NEWS

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2018-02-22 21:37:10 +01:00
parent d8da8daf9a
commit 10380bcfae
4 changed files with 117 additions and 58 deletions
Download Patch File Download Diff File Expand all files Collapse all files

47
man/EUCAST.Rd
View File

@ -3,6 +3,7 @@
\name{EUCAST}
\alias{EUCAST}
\alias{EUCAST_rules}
\alias{EUCAST}
\alias{interpretive_reading}
\title{EUCAST expert rules}
\source{
@ -14,22 +15,22 @@ EUCAST Expert Rules Version 2.0: \cr
\url{http://www.eucast.org/expert_rules_and_intrinsic_resistance}
}
\usage{
EUCAST_rules(tbl, col_bactcode = "bacteriecode", 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", mino = "mino", moxi = "moxi",
nali = "nali", neom = "neom", neti = "neti", nitr = "nitr",
novo = "novo", norf = "norf", oflo = "oflo", peni = "peni",
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")
EUCAST_rules(tbl, col_bactcode = "bactid", 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", mino = "mino", moxi = "moxi", nali = "nali",
neom = "neom", neti = "neti", nitr = "nitr", novo = "novo",
norf = "norf", oflo = "oflo", peni = "peni", 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")
interpretive_reading(...)
}
@ -51,7 +52,15 @@ table with edited variables of antibiotics.
Apply expert rules (like intrinsic resistance), as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, \url{http://eucast.org}), see \emph{Source}.
}
\examples{
\dontrun{
tbl <- EUCAST_rules(tbl)
}
a <- data.frame(bactid = c("STAAUR", "ESCCOL", "KLEPNE", "PSEAER"),
vanc = "-",
amox = "-",
coli = "-",
cfta = "-",
cfur = "-",
stringsAsFactors = FALSE)
a
b <- EUCAST_rules(a)
b
}