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(v0.8.0.9033) antivirals data set, cleanup

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dr. M.S. (Matthijs) Berends
2019-11-18 12:10:47 +01:00
parent 67f3f4387b
commit 267320f15f
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2
man/WHOCC.Rd
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@ -9,7 +9,7 @@ All antimicrobial drugs and their official names, ATC codes, ATC groups and defi
\section{WHOCC}{
\if{html}{\figure{logo_who.png}{options: height=60px style=margin-bottom:5px} \cr}
This package contains \strong{all ~450 antimicrobial drugs} and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, \url{https://www.whocc.no}) and the Pharmaceuticals Community Register of the European Commission (\url{http://ec.europa.eu/health/documents/community-register/html/atc.htm}).
This package contains \strong{all ~550 antibiotic, antimycotic and antiviral drugs} and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, \url{https://www.whocc.no}) and the Pharmaceuticals Community Register of the European Commission (\url{http://ec.europa.eu/health/documents/community-register/html/atc.htm}).
These have become the gold standard for international drug utilisation monitoring and research.

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man/antibiotics.Rd
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@ -16,7 +16,7 @@
\item{\code{abbr}}{List of abbreviations as used in many countries, also for antibiotic susceptibility testing (AST)}
\item{\code{synonyms}}{Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID}
\item{\code{oral_ddd}}{Defined Daily Dose (DDD), oral treatment}
\item{\code{oral_units}}{Units of \code{ddd_units}}
\item{\code{oral_units}}{Units of \code{oral_ddd}}
\item{\code{iv_ddd}}{Defined Daily Dose (DDD), parenteral treatment}
\item{\code{iv_units}}{Units of \code{iv_ddd}}
}}
@ -41,7 +41,7 @@ Synonyms (i.e. trade names) are derived from the Compound ID (\code{cid}) and co
\section{WHOCC}{
\if{html}{\figure{logo_who.png}{options: height=60px style=margin-bottom:5px} \cr}
This package contains \strong{all ~450 antimicrobial drugs} and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, \url{https://www.whocc.no}) and the Pharmaceuticals Community Register of the European Commission (\url{http://ec.europa.eu/health/documents/community-register/html/atc.htm}).
This package contains \strong{all ~550 antibiotic, antimycotic and antiviral drugs} and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, \url{https://www.whocc.no}) and the Pharmaceuticals Community Register of the European Commission (\url{http://ec.europa.eu/health/documents/community-register/html/atc.htm}).
These have become the gold standard for international drug utilisation monitoring and research.
@ -56,6 +56,6 @@ On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://
}
\seealso{
\code{\link{microorganisms}}
\code{\link{antivirals}} \code{\link{microorganisms}}
}
\keyword{datasets}

46
man/antivirals.Rd Normal file
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@ -0,0 +1,46 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/data.R
\docType{data}
\name{antivirals}
\alias{antivirals}
\title{Data set with ~100 antivirals}
\format{A \code{\link{data.frame}} with 102 observations and 7 variables:
\describe{
\item{\code{atc}}{ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC}
\item{\code{name}}{Official name as used by WHONET/EARS-Net or the WHO}
\item{\code{atc_group}}{Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC}
\item{\code{oral_ddd}}{Defined Daily Dose (DDD), oral treatment}
\item{\code{oral_units}}{Units of \code{oral_ddd}}
\item{\code{iv_ddd}}{Defined Daily Dose (DDD), parenteral treatment}
\item{\code{iv_units}}{Units of \code{iv_ddd}}
}}
\source{
World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology (WHOCC): \url{https://www.whocc.no/atc_ddd_index/}
}
\usage{
antivirals
}
\description{
A data set containing all antivirals, according to the ATC code group 'J05' (Antivirals for systemic use).
}
\section{WHOCC}{
\if{html}{\figure{logo_who.png}{options: height=60px style=margin-bottom:5px} \cr}
This package contains \strong{all ~550 antibiotic, antimycotic and antiviral drugs} and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, \url{https://www.whocc.no}) and the Pharmaceuticals Community Register of the European Commission (\url{http://ec.europa.eu/health/documents/community-register/html/atc.htm}).
These have become the gold standard for international drug utilisation monitoring and research.
The WHOCC is located in Oslo at the Norwegian Institute of Public Health and funded by the Norwegian government. The European Commission is the executive of the European Union and promotes its general interest.
\strong{NOTE: The WHOCC copyright does not allow use for commercial purposes, unlike any other info from this package. See \url{https://www.whocc.no/copyright_disclaimer/}.}
}
\section{Read more on our website!}{
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
}
\seealso{
\code{\link{antibiotics}} \code{\link{microorganisms}}
}
\keyword{datasets}

2
man/as.ab.Rd
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@ -37,7 +37,7 @@ European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{htt
\section{WHOCC}{
\if{html}{\figure{logo_who.png}{options: height=60px style=margin-bottom:5px} \cr}
This package contains \strong{all ~450 antimicrobial drugs} and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, \url{https://www.whocc.no}) and the Pharmaceuticals Community Register of the European Commission (\url{http://ec.europa.eu/health/documents/community-register/html/atc.htm}).
This package contains \strong{all ~550 antibiotic, antimycotic and antiviral drugs} and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, \url{https://www.whocc.no}) and the Pharmaceuticals Community Register of the European Commission (\url{http://ec.europa.eu/health/documents/community-register/html/atc.htm}).
These have become the gold standard for international drug utilisation monitoring and research.

2
man/eucast_rules.Rd
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@ -158,6 +158,7 @@ On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://
}
\examples{
\donttest{
a <- data.frame(mo = c("Staphylococcus aureus",
"Enterococcus faecalis",
"Escherichia coli",
@ -193,7 +194,6 @@ b
# 5 Pseudomonas aeruginosa R R - - R R R
\donttest{
# do not apply EUCAST rules, but rather get a data.frame
# with 18 rows, containing all details about the transformations:
c <- eucast_rules(a, verbose = TRUE)

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man/example_isolates.Rd
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@ -3,7 +3,7 @@
\docType{data}
\name{example_isolates}
\alias{example_isolates}
\title{Data set with 2,000 blood culture isolates}
\title{Data set with 2,000 example isolates}
\format{A \code{\link{data.frame}} with 2,000 observations and 49 variables:
\describe{
\item{\code{date}}{date of receipt at the laboratory}
@ -13,7 +13,7 @@
\item{\code{ward_outpatient}}{logical to determine if ward is an outpatient clinic}
\item{\code{age}}{age of the patient}
\item{\code{gender}}{gender of the patient}
\item{\code{patient_id}}{ID of the patient, first 10 characters of an SHA hash containing irretrievable information}
\item{\code{patient_id}}{ID of the patient}
\item{\code{mo}}{ID of microorganism created with \code{\link{as.mo}}, see also \code{\link{microorganisms}}}
\item{\code{PEN:RIF}}{40 different antibiotics with class \code{rsi} (see \code{\link{as.rsi}}); these column names occur in \code{\link{antibiotics}} data set and can be translated with \code{\link{ab_name}}}
}}
@ -21,7 +21,7 @@
example_isolates
}
\description{
An anonymised data set containing 2,000 microbial blood culture isolates with their full antibiograms found 4 different hospitals in the Netherlands, between 2001 and 2017. This \code{data.frame} can be used to practice AMR analysis. For examples, please read \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{the tutorial on our website}.
A data set containing 2,000 microbial isolates with their full antibiograms. The data set reflects reality and can be used to practice AMR analysis. For examples, please read \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{the tutorial on our website}.
}
\section{Read more on our website!}{

7
man/mdro.Rd
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@ -184,21 +184,16 @@ On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://
}
\examples{
\donttest{
library(dplyr)
example_isolates \%>\%
mdro() \%>\%
freq()
\donttest{
example_isolates \%>\%
mutate(EUCAST = eucast_exceptional_phenotypes(.),
BRMO = brmo(.),
MRGN = mrgn(.))
example_isolates \%>\%
rename(PIP = TZP) \%>\% # no piperacillin, so take piperacillin/tazobactam
mrgn() \%>\% # check German guideline
freq() # check frequencies
}
}

12
man/rsi_translation.Rd
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@ -4,17 +4,17 @@
\name{rsi_translation}
\alias{rsi_translation}
\title{Data set for RSI interpretation}
\format{A \code{\link{data.frame}} with 11,559 observations and 9 variables:
\format{A \code{\link{data.frame}} with 13,975 observations and 9 variables:
\describe{
\item{\code{guideline}}{Name of the guideline}
\item{\code{method}}{Either "MIC" or "DISK"}
\item{\code{site}}{Body site, e.g. "Oral" or "Respiratory"}
\item{\code{mo}}{Microbial ID, see \code{\link{as.mo}}}
\item{\code{ab}}{Antibiotic ID, see \code{\link{as.ab}}}
\item{\code{ref_tbl}}{Info about where the guideline rule can be found}
\item{\code{S_mic}}{Lowest MIC value that leads to "S"}
\item{\code{R_mic}}{Highest MIC value that leads to "R"}
\item{\code{dose_disk}}{Dose of the used disk diffusion method}
\item{\code{S_disk}}{Lowest number of millimeters that leads to "S"}
\item{\code{R_disk}}{Highest number of millimeters that leads to "R"}
\item{\code{disk_dose}}{Dose of the used disk diffusion method}
\item{\code{breakpoint_S}}{Lowest MIC value or highest number of millimeters that leads to "S"}
\item{\code{breakpoint_R}}{Highest MIC value or lowest number of millimeters that leads to "R"}
}}
\usage{
rsi_translation