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MDRO update

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2018-11-16 20:50:50 +01:00
parent fab64e6728
commit 4fcc2b409a
10 changed files with 207 additions and 186 deletions
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15
man/EUCAST.Rd → man/eucast_rules.Rd Executable file → Normal file
View File

@ -1,6 +1,7 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/eucast.R
\name{EUCAST_rules}
% Please edit documentation in R/eucast_rules.R
\name{eucast_rules}
\alias{eucast_rules}
\alias{EUCAST_rules}
\alias{interpretive_reading}
\title{EUCAST rules}
@ -22,7 +23,7 @@
}
}
\usage{
EUCAST_rules(tbl, col_mo = NULL, info = TRUE,
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",
@ -41,6 +42,8 @@ EUCAST_rules(tbl, col_mo = NULL, info = TRUE,
tetr = "tetr", tica = "tica", tige = "tige", tobr = "tobr",
trim = "trim", trsu = "trsu", vanc = "vanc", col_bactid = NULL)
EUCAST_rules(...)
interpretive_reading(...)
}
\arguments{
@ -58,7 +61,7 @@ interpretive_reading(...)
\item{col_bactid}{deprecated, use \code{col_mo} instead.}
\item{...}{parameters that are passed on to \code{EUCAST_rules}}
\item{...}{parameters that are passed on to \code{eucast_rules}}
}
\value{
The input of \code{tbl}, possibly with edited values of antibiotics. Or, if \code{verbose = TRUE}, a \code{data.frame} with verbose info.
@ -138,7 +141,7 @@ Abbrevations of the column containing antibiotics in the form: \strong{abbreviat
}
\examples{
a <- EUCAST_rules(septic_patients)
a <- eucast_rules(septic_patients)
a <- data.frame(mo = c("Staphylococcus aureus",
"Enterococcus faecalis",
@ -162,7 +165,7 @@ a
# 4 Klebsiella pneumoniae - - - - - S S
# 5 Pseudomonas aeruginosa - - - - - S S
b <- EUCAST_rules(a, "mo") # 18 results are forced as R or S
b <- eucast_rules(a, "mo") # 18 results are forced as R or S
b
# mo vanc amox coli cfta cfur peni cfox

24
man/MDRO.Rd → man/mdro.Rd Executable file → Normal file
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@ -1,13 +1,13 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/mdro.R
\name{MDRO}
\alias{MDRO}
\alias{BRMO}
\alias{MRGN}
\alias{EUCAST_exceptional_phenotypes}
\name{mdro}
\alias{mdro}
\alias{brmo}
\alias{mrgn}
\alias{eucast_exceptional_phenotypes}
\title{Determine multidrug-resistant organisms (MDRO)}
\usage{
MDRO(tbl, country = NULL, col_mo = NULL, info = TRUE,
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",
@ -25,11 +25,11 @@ MDRO(tbl, country = NULL, col_mo = NULL, info = TRUE,
tobr = "tobr", trim = "trim", trsu = "trsu", vanc = "vanc",
col_bactid = NULL)
BRMO(tbl, country = "nl", ...)
brmo(..., country = "nl")
MRGN(tbl, country = "de", ...)
mrgn(tbl, country = "de", ...)
EUCAST_exceptional_phenotypes(tbl, country = "EUCAST", ...)
eucast_exceptional_phenotypes(tbl, country = "EUCAST", ...)
}
\arguments{
\item{tbl}{table with antibiotic columns, like e.g. \code{amox} and \code{amcl}}
@ -165,7 +165,7 @@ EUCAST_exceptional_phenotypes(tbl, country = "EUCAST", ...)
\item{...}{parameters that are passed on to methods}
}
\value{
Ordered factor with levels \code{Unknown < Negative < Unconfirmed < Positive}.
Ordered factor with levels \code{Negative < Positive, unconfirmed < Positive}.
}
\description{
Determine which isolates are multidrug-resistant organisms (MDRO) according to country-specific guidelines.
@ -245,6 +245,6 @@ Abbrevations of the column containing antibiotics in the form: \strong{abbreviat
library(dplyr)
septic_patients \%>\%
mutate(EUCAST = MDRO(.),
BRMO = BRMO(.))
mutate(EUCAST = mdro(.),
BRMO = brmo(.))
}