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add barplots

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dr. M.S. (Matthijs) Berends
2018-03-13 14:34:10 +01:00
parent e4b371d30a
commit 04fc3573ec
8 changed files with 86 additions and 35 deletions
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4
man/ablist.Rd
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@ -12,9 +12,9 @@
\item{\code{official}}{Official name by the WHO, like \code{"amoxicillin and enzyme inhibitor"}}
\item{\code{official_nl}}{Official name in the Netherlands, like \code{"Amoxicilline met enzymremmer"}}
\item{\code{trivial_nl}}{Trivial name in Dutch, like \code{"Amoxicilline/clavulaanzuur"}}
\item{\code{oral_ddd}}{Daily Defined Dose (DDD) according to the WHO, oral treatment}
\item{\code{oral_ddd}}{Defined Daily Dose (DDD) according to the WHO, oral treatment}
\item{\code{oral_units}}{Units of \code{ddd_units}}
\item{\code{iv_ddd}}{Daily Defined Dose (DDD) according to the WHO, parenteral treatment}
\item{\code{iv_ddd}}{Defined Daily Dose (DDD) according to the WHO, parenteral treatment}
\item{\code{iv_units}}{Units of \code{iv_ddd}}
\item{\code{atc_group1}}{ATC group in Dutch, like \code{"Macroliden, lincosamiden en streptograminen"}}
\item{\code{atc_group2}}{Subgroup of \code{atc_group1} in Dutch, like \code{"Macroliden"}}

3
man/as.mic.Rd
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@ -18,12 +18,13 @@ is.mic(x)
New class \code{mic}
}
\description{
This transforms a vector to a new class\code{mic}, which is an ordered factor valid MIC values as levels. Invalid MIC values will be translated as \code{NA} with a warning.
This transforms a vector to a new class\code{mic}, which is an ordered factor with valid MIC values as levels. Invalid MIC values will be translated as \code{NA} with a warning.
}
\examples{
mic_data <- as.mic(c(">=32", "1.0", "1", "1.00", 8, "<=0.128", "8", "16", "16"))
is.mic(mic_data)
plot(mic_data)
barplot(mic_data)
\donttest{
library(dplyr)

6
man/atc_property.Rd
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@ -20,7 +20,7 @@ atc_property(atc_code, property, administration = "O",
\item{url}{url of website of the WHO. The sign \code{\%s} can be used as a placeholder for ATC codes.}
}
\description{
Gets data from the WHO to determine properties of an ATC of e.g. an antibiotic. \strong{This function requires an internet connection.}
Gets data from the WHO to determine properties of an ATC (e.g. an antibiotic) like name, defined daily dose (DDD) or standard unit. \strong{This function requires an internet connection.}
}
\details{
Abbreviations for the property \code{"Adm.R"} (parameter \code{administration}):
@ -51,7 +51,7 @@ Abbreviations for the property \code{"U"} (unit):
}
\examples{
\donttest{
atc_property("J01CA04", "DDD", "O") # oral DDD of amoxicillin
atc_property("J01CA04", "DDD", "P") # parenteral DDD of amoxicillin
atc_property("J01CA04", "DDD", "O") # oral DDD (Defined Daily Dose) of amoxicillin
atc_property("J01CA04", "DDD", "P") # parenteral DDD (Defined Daily Dose) of amoxicillin
}
}

2
man/first_isolate.Rd
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@ -53,7 +53,7 @@ Determine first (weighted) isolates of all microorganisms of every patient per e
\strong{Why this is so important} \cr
To conduct an analysis of antimicrobial resistance, you should only include the first isolate of every patient per episode \href{https://www.ncbi.nlm.nih.gov/pubmed/17304462}{[1]}. If you would not do this, you could easily get an overestimate or underestimate of the resistance of an antibiotic. Imagine that a patient was admitted with an MRSA and that it was found in 5 different blood cultures the following week. The resistance percentage of oxacillin of all \emph{S. aureus} isolates would be overestimated, because you included this MRSA more than once. It would be \href{https://en.wikipedia.org/wiki/Selection_bias}{selection bias}.
\strong{\code{points_threshold}} \cr
\strong{Using parameter \code{points_threshold}} \cr
To compare key antibiotics, the difference between antimicrobial interpretations will be measured. A difference from I to S|R (or vice versa) means 0.5 points. A difference from S to R (or vice versa) means 1 point. When the sum of points exceeds \code{points_threshold}, an isolate will be (re)selected as a first weighted isolate.
}
\examples{