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(v0.9.0.9023) EUCAST 2020 guidelines

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dr. M.S. (Matthijs) Berends
2020-02-14 19:54:13 +01:00
parent 5a98e6b777
commit 9b8b02960e
43 changed files with 16588 additions and 14564 deletions
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13
man/as.rsi.Rd
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@ -31,7 +31,7 @@ is.rsi.eligible(x, threshold = 0.05)
\item{ab}{an antimicrobial code, generated with \code{\link[=as.ab]{as.ab()}}}
\item{guideline}{defaults to the latest included EUCAST guideline, run \code{unique(AMR::rsi_translation$guideline)} for all options}
\item{guideline}{defaults to the latest included EUCAST guideline, run \code{unique(rsi_translation$guideline)} for all options}
\item{col_mo}{column name of the IDs of the microorganisms (see \code{\link[=as.mo]{as.mo()}}), defaults to the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.}
@ -44,7 +44,7 @@ Ordered factor with new class \code{\link{rsi}}
Interpret MIC values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing R/SI values. This transforms the input to a new class \code{\link{rsi}}, which is an ordered factor with levels \verb{S < I < R}. Invalid antimicrobial interpretations will be translated as \code{NA} with a warning.
}
\details{
Run \code{unique(AMR::rsi_translation$guideline)} for a list of all supported guidelines. The repository of this package contains \href{https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt}{this machine readable version} of these guidelines.
Run \code{unique(rsi_translation$guideline)} for a list of all supported guidelines. The repository of this package contains \href{https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt}{this machine readable version} of these guidelines.
These guidelines are machine readable, since \href{https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt}{}.
@ -91,11 +91,12 @@ as.rsi("<= 0.002; S") # will return S
# interpret MIC values
as.rsi(x = as.mic(2),
mo = as.mo("S. pneumoniae"),
ab = "AMX",
ab = "AMP",
guideline = "EUCAST")
as.rsi(x = as.mic(4),
mo = as.mo("S. pneumoniae"),
ab = "AMX",
as.rsi(x = as.disk(18),
mo = "Strep pneu", # `mo` will be coerced with as.mo()
ab = "ampicillin", # and `ab` with as.ab()
guideline = "EUCAST")
plot(rsi_data) # for percentages

2
man/filter_ab_class.Rd
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@ -45,7 +45,7 @@ filter_tetracyclines(x, result = NULL, scope = "any", ...)
\arguments{
\item{x}{a data set}
\item{ab_class}{an antimicrobial class, like \code{"carbapenems"}, as can be found in \code{\link[=antibiotics]{AMR::antibiotics$group}}}
\item{ab_class}{an antimicrobial class, like \code{"carbapenems"}, as can be found in \code{\link[=antibiotics]{antibiotics$group}}}
\item{result}{an antibiotic result: S, I or R (or a combination of more of them)}

6
man/like.Rd
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@ -55,15 +55,15 @@ b \%like\% a
# also supports multiple patterns, length must be equal to x
a <- c("Test case", "Something different", "Yet another thing")
b <- c("case", "diff", "yet")
b <- c( "case", "diff", "yet")
a \%like\% b
#> TRUE TRUE TRUE
# get frequencies of bacteria whose name start with 'Ent' or 'ent'
library(dplyr)
example_isolates \%>\%
filter(mo_genus(mo) \%like\% '^ent') \%>\%
freq(mo_fullname(mo))
filter(mo_name(mo) \%like\% '^ent') \%>\%
freq(mo_genus(mo))
}
\seealso{
\code{\link[base:grep]{base::grep()}}