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@ -36,7 +36,7 @@ A \link{list}, or a \link{character} if \code{collapse} is not \code{NULL}
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Use this function on e.g. clinical texts from health care records. It returns a \link{list} with all antimicrobial drugs, doses and forms of administration found in the texts.
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}
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\details{
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This function is also internally used by \code{\link[=as.ab]{as.ab()}}, although it then only searches for the first drug name and will throw a note if more drug names could have been returned. Note: the \code{\link[=as.ab]{as.ab()}} function may use very long regular expression to match brand names of antimicrobial agents. This may fail on some systems.
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This function is also internally used by \code{\link[=as.ab]{as.ab()}}, although it then only searches for the first drug name and will throw a note if more drug names could have been returned. Note: the \code{\link[=as.ab]{as.ab()}} function may use very long regular expression to match brand names of antimicrobial drugs. This may fail on some systems.
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\subsection{Argument \code{type}}{
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At default, the function will search for antimicrobial drug names. All text elements will be searched for official names, ATC codes and brand names. As it uses \code{\link[=as.ab]{as.ab()}} internally, it will correct for misspelling.
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@ -56,7 +56,7 @@ set_ab_names(
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)
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}
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\arguments{
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\item{x}{any (vector of) text that can be coerced to a valid antibiotic code with \code{\link[=as.ab]{as.ab()}}}
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\item{x}{any (vector of) text that can be coerced to a valid antibiotic drug code with \code{\link[=as.ab]{as.ab()}}}
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\item{language}{language of the returned text, defaults to system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}}) and can also be set with \code{getOption("AMR_locale")}. Use \code{language = NULL} or \code{language = ""} to prevent translation.}
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@ -13,7 +13,7 @@ clear_custom_antimicrobials()
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\item{x}{a \link{data.frame} resembling the \link{antibiotics} data set, at least containing columns "ab" and "name"}
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}
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\description{
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With \code{\link[=add_custom_antimicrobials]{add_custom_antimicrobials()}} you can add your own custom antimicrobial codes to the \code{AMR} package.
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With \code{\link[=add_custom_antimicrobials]{add_custom_antimicrobials()}} you can add your own custom antimicrobial drug codes to the \code{AMR} package.
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}
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\details{
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Due to how \R works, the \code{\link[=add_custom_antimicrobials]{add_custom_antimicrobials()}} function has to be run in every \R session - added antimicrobials are not stored between sessions and are thus lost when \R is exited. It is possible to save the antimicrobial additions to your \code{.Rprofile} file to circumvent this, although this requires to load the \code{AMR} package at every start-up:
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@ -21,7 +21,7 @@ Due to how \R works, the \code{\link[=add_custom_antimicrobials]{add_custom_anti
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\if{html}{\out{<div class="sourceCode r">}}\preformatted{# Open .Rprofile file
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utils::file.edit("~/.Rprofile")
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# Add custom antibiotic codes:
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# Add custom antibiotic drug codes:
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library(AMR)
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add_custom_antimicrobials(
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data.frame(ab = "TESTAB",
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@ -104,7 +104,7 @@ not_intrinsic_resistant(
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\item{only_rsi_columns}{a \link{logical} to indicate whether only columns of class \code{rsi} must be selected (defaults to \code{FALSE}), see \code{\link[=as.rsi]{as.rsi()}}}
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\item{only_treatable}{a \link{logical} to indicate whether agents that are only for laboratory tests should be excluded (defaults to \code{TRUE}), such as gentamicin-high (\code{GEH}) and imipenem/EDTA (\code{IPE})}
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\item{only_treatable}{a \link{logical} to indicate whether antimicrobial drugs should be excluded that are only for laboratory tests (defaults to \code{TRUE}), such as gentamicin-high (\code{GEH}) and imipenem/EDTA (\code{IPE})}
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\item{...}{ignored, only in place to allow future extensions}
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@ -118,7 +118,7 @@ not_intrinsic_resistant(
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(internally) a \link{character} vector of column names, with additional class \code{"ab_selector"}
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}
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\description{
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These functions allow for filtering rows and selecting columns based on antibiotic test results that are of a specific antibiotic class or group, without the need to define the columns or antibiotic abbreviations. In short, if you have a column name that resembles an antimicrobial agent, it will be picked up by any of these functions that matches its pharmaceutical class: "cefazolin", "CZO" and "J01DB04" will all be picked up by \code{\link[=cephalosporins]{cephalosporins()}}.
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These functions allow for filtering rows and selecting columns based on antibiotic test results that are of a specific antibiotic class or group, without the need to define the columns or antibiotic abbreviations. In short, if you have a column name that resembles an antimicrobial drug, it will be picked up by any of these functions that matches its pharmaceutical class: "cefazolin", "CZO" and "J01DB04" will all be picked up by \code{\link[=cephalosporins]{cephalosporins()}}.
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}
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\details{
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These functions can be used in data set calls for selecting columns and filtering rows. They are heavily inspired by the \link[tidyselect:language]{Tidyverse selection helpers} such as \code{\link[tidyselect:everything]{everything()}}, but also work in base \R and not only in \code{dplyr} verbs. Nonetheless, they are very convenient to use with \code{dplyr} functions such as \code{\link[dplyr:select]{select()}}, \code{\link[dplyr:filter]{filter()}} and \code{\link[dplyr:summarise]{summarise()}}, see \emph{Examples}.
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@ -21,7 +21,7 @@
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\item \code{oral_units}\cr Units of \code{oral_ddd}
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\item \code{iv_ddd}\cr Defined Daily Dose (DDD), parenteral (intravenous) treatment, currently available for 146 drugs
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\item \code{iv_units}\cr Units of \code{iv_ddd}
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\item \code{loinc}\cr All LOINC codes (Logical Observation Identifiers Names and Codes) associated with the name of the antimicrobial agent. Use \code{\link[=ab_loinc]{ab_loinc()}} to retrieve them quickly, see \code{\link[=ab_property]{ab_property()}}.
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\item \code{loinc}\cr All LOINC codes (Logical Observation Identifiers Names and Codes) associated with the name of the antimicrobial drug. Use \code{\link[=ab_loinc]{ab_loinc()}} to retrieve them quickly, see \code{\link[=ab_property]{ab_property()}}.
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}
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}
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@ -37,7 +37,7 @@
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\item \code{oral_units}\cr Units of \code{oral_ddd}
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\item \code{iv_ddd}\cr Defined Daily Dose (DDD), parenteral treatment
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\item \code{iv_units}\cr Units of \code{iv_ddd}
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\item \code{loinc}\cr All LOINC codes (Logical Observation Identifiers Names and Codes) associated with the name of the antimicrobial agent.
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\item \code{loinc}\cr All LOINC codes (Logical Observation Identifiers Names and Codes) associated with the name of the antimicrobial drug.
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}
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}
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@ -13,7 +13,7 @@ is.ab(x)
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\arguments{
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\item{x}{a \link{character} vector to determine to antibiotic ID}
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\item{flag_multiple_results}{a \link{logical} to indicate whether a note should be printed to the console that probably more than one antibiotic code or name can be retrieved from a single input value.}
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\item{flag_multiple_results}{a \link{logical} to indicate whether a note should be printed to the console that probably more than one antibiotic drug code or name can be retrieved from a single input value.}
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\item{info}{a \link{logical} to indicate whether a progress bar should be printed, defaults to \code{TRUE} only in interactive mode}
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@ -23,7 +23,7 @@ is.ab(x)
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A \link{character} \link{vector} with additional class \code{\link{ab}}
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}
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\description{
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Use this function to determine the antibiotic code of one or more antibiotics. The data set \link{antibiotics} will be searched for abbreviations, official names and synonyms (brand names).
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Use this function to determine the antibiotic drug code of one or more antibiotics. The data set \link{antibiotics} will be searched for abbreviations, official names and synonyms (brand names).
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}
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\details{
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All entries in the \link{antibiotics} data set have three different identifiers: a human readable EARS-Net code (column \code{ab}, used by ECDC and WHONET), an ATC code (column \code{atc}, used by WHO), and a CID code (column \code{cid}, Compound ID, used by PubChem). The data set contains more than 5,000 official brand names from many different countries, as found in PubChem. Not that some drugs contain multiple ATC codes.
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@ -38,7 +38,7 @@ All these properties will be searched for the user input. The \code{\link[=as.ab
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Use the \code{\link[=ab_property]{ab_*}} functions to get properties based on the returned antibiotic ID, see \emph{Examples}.
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Note: the \code{\link[=as.ab]{as.ab()}} and \code{\link[=ab_property]{ab_*}} functions may use very long regular expression to match brand names of antimicrobial agents. This may fail on some systems.
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Note: the \code{\link[=as.ab]{as.ab()}} and \code{\link[=ab_property]{ab_*}} functions may use very long regular expression to match brand names of antimicrobial drugs. This may fail on some systems.
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You can add your own manual codes to be considered by \code{\link[=as.ab]{as.ab()}} and all \code{\link[=ab_property]{ab_*}} functions, see \code{\link[=add_custom_antimicrobials]{add_custom_antimicrobials()}}.
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}
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12
man/as.av.Rd
12
man/as.av.Rd
@ -4,16 +4,16 @@
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\alias{as.av}
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\alias{av}
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\alias{is.av}
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\title{Transform Input to an Antiviral Agent ID}
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\title{Transform Input to an Antiviral Drug ID}
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\usage{
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as.av(x, flag_multiple_results = TRUE, info = interactive(), ...)
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is.av(x)
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}
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\arguments{
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\item{x}{a \link{character} vector to determine to antiviral agent ID}
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\item{x}{a \link{character} vector to determine to antiviral drug ID}
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\item{flag_multiple_results}{a \link{logical} to indicate whether a note should be printed to the console that probably more than one antiviral agent code or name can be retrieved from a single input value.}
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\item{flag_multiple_results}{a \link{logical} to indicate whether a note should be printed to the console that probably more than one antiviral drug code or name can be retrieved from a single input value.}
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\item{info}{a \link{logical} to indicate whether a progress bar should be printed, defaults to \code{TRUE} only in interactive mode}
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@ -23,7 +23,7 @@ is.av(x)
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A \link{character} \link{vector} with additional class \code{\link{ab}}
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}
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\description{
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Use this function to determine the antiviral agent code of one or more antiviral agents. The data set \link{antivirals} will be searched for abbreviations, official names and synonyms (brand names).
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Use this function to determine the antiviral drug code of one or more antiviral drugs. The data set \link{antivirals} will be searched for abbreviations, official names and synonyms (brand names).
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}
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\details{
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All entries in the \link{antivirals} data set have three different identifiers: a human readable EARS-Net code (column \code{ab}, used by ECDC and WHONET), an ATC code (column \code{atc}, used by WHO), and a CID code (column \code{cid}, Compound ID, used by PubChem). The data set contains more than 5,000 official brand names from many different countries, as found in PubChem. Not that some drugs contain multiple ATC codes.
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@ -36,9 +36,9 @@ All these properties will be searched for the user input. The \code{\link[=as.av
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\item Digitalised paper records, leaving artefacts like 0/o/O (zero and O's), B/8, n/r, etc.
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}
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Use the \code{\link[=av_property]{av_*}} functions to get properties based on the returned antiviral agent ID, see \emph{Examples}.
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Use the \code{\link[=av_property]{av_*}} functions to get properties based on the returned antiviral drug ID, see \emph{Examples}.
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Note: the \code{\link[=as.av]{as.av()}} and \code{\link[=av_property]{av_*}} functions may use very long regular expression to match brand names of antimicrobial agents. This may fail on some systems.
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Note: the \code{\link[=as.av]{as.av()}} and \code{\link[=av_property]{av_*}} functions may use very long regular expression to match brand names of antimicrobial drugs. This may fail on some systems.
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}
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\section{Source}{
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@ -77,7 +77,7 @@ rsi_interpretation_history(clean = FALSE)
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\item{mo}{any (vector of) text that can be coerced to valid microorganism codes with \code{\link[=as.mo]{as.mo()}}, can be left empty to determine it automatically}
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\item{ab}{any (vector of) text that can be coerced to a valid antimicrobial code with \code{\link[=as.ab]{as.ab()}}}
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\item{ab}{any (vector of) text that can be coerced to a valid antimicrobial drug code with \code{\link[=as.ab]{as.ab()}}}
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\item{guideline}{defaults to EUCAST 2022 (the latest implemented EUCAST guideline in the \link{rsi_translation} data set), supports EUCAST (2013-2022) and CLSI (2013-2022), see \emph{Details}}
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@ -142,7 +142,7 @@ After using \code{\link[=as.rsi]{as.rsi()}}, you can use the \code{\link[=eucast
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\subsection{Machine-Readable Interpretation Guidelines}{
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The repository of this package \href{https://github.com/msberends/AMR/blob/main/data-raw/rsi_translation.txt}{contains a machine-readable version} of all guidelines. This is a CSV file consisting of 18,308 rows and 11 columns. This file is machine-readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial agent and the microorganism. \strong{This allows for easy implementation of these rules in laboratory information systems (LIS)}. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.
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The repository of this package \href{https://github.com/msberends/AMR/blob/main/data-raw/rsi_translation.txt}{contains a machine-readable version} of all guidelines. This is a CSV file consisting of 18,308 rows and 11 columns. This file is machine-readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial drug and the microorganism. \strong{This allows for easy implementation of these rules in laboratory information systems (LIS)}. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.
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}
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\subsection{Other}{
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@ -166,7 +166,7 @@ A microorganism is categorised as \emph{Susceptible, standard dosing regimen}, w
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A microorganism is categorised as \emph{Susceptible, Increased exposure} when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection.
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}
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This AMR package honours this (new) insight. Use \code{\link[=susceptibility]{susceptibility()}} (equal to \code{\link[=proportion_SI]{proportion_SI()}}) to determine antimicrobial susceptibility and \code{\link[=count_susceptible]{count_susceptible()}} (equal to \code{\link[=count_SI]{count_SI()}}) to count susceptible isolates.
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This AMR package honours this insight. Use \code{\link[=susceptibility]{susceptibility()}} (equal to \code{\link[=proportion_SI]{proportion_SI()}}) to determine antimicrobial susceptibility and \code{\link[=count_susceptible]{count_susceptible()}} (equal to \code{\link[=count_SI]{count_SI()}}) to count susceptible isolates.
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}
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\section{Reference Data Publicly Available}{
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@ -36,7 +36,7 @@ A \link{list}, or a \link{character} if \code{collapse} is not \code{NULL}
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Use this function on e.g. clinical texts from health care records. It returns a \link{list} with all antiviral drugs, doses and forms of administration found in the texts.
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}
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\details{
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This function is also internally used by \code{\link[=as.av]{as.av()}}, although it then only searches for the first drug name and will throw a note if more drug names could have been returned. Note: the \code{\link[=as.av]{as.av()}} function may use very long regular expression to match brand names of antiviral agents. This may fail on some systems.
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This function is also internally used by \code{\link[=as.av]{as.av()}}, although it then only searches for the first drug name and will throw a note if more drug names could have been returned. Note: the \code{\link[=as.av]{as.av()}} function may use very long regular expression to match brand names of antiviral drugs. This may fail on some systems.
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\subsection{Argument \code{type}}{
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At default, the function will search for antiviral drug names. All text elements will be searched for official names, ATC codes and brand names. As it uses \code{\link[=as.av]{as.av()}} internally, it will correct for misspelling.
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@ -13,7 +13,7 @@
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\alias{av_ddd_units}
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\alias{av_info}
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\alias{av_url}
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\title{Get Properties of an Antiviral Agent}
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\title{Get Properties of an Antiviral Drug}
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\usage{
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av_name(x, language = get_AMR_locale(), tolower = FALSE, ...)
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@ -40,7 +40,7 @@ av_url(x, open = FALSE, ...)
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av_property(x, property = "name", language = get_AMR_locale(), ...)
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}
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\arguments{
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\item{x}{any (vector of) text that can be coerced to a valid antiviral agent code with \code{\link[=as.av]{as.av()}}}
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\item{x}{any (vector of) text that can be coerced to a valid antiviral drug code with \code{\link[=as.av]{as.av()}}}
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\item{language}{language of the returned text, defaults to system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}}) and can also be set with \code{getOption("AMR_locale")}. Use \code{language = NULL} or \code{language = ""} to prevent translation.}
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@ -63,7 +63,7 @@ av_property(x, property = "name", language = get_AMR_locale(), ...)
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}
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}
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\description{
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Use these functions to return a specific property of an antiviral agent from the \link{antivirals} data set. All input values will be evaluated internally with \code{\link[=as.av]{as.av()}}.
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Use these functions to return a specific property of an antiviral drug from the \link{antivirals} data set. All input values will be evaluated internally with \code{\link[=as.av]{as.av()}}.
|
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}
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\details{
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All output \link[=translate]{will be translated} where possible.
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@ -81,7 +81,7 @@ A microorganism is categorised as \emph{Susceptible, standard dosing regimen}, w
|
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A microorganism is categorised as \emph{Susceptible, Increased exposure} when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection.
|
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}
|
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|
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This AMR package honours this (new) insight. Use \code{\link[=susceptibility]{susceptibility()}} (equal to \code{\link[=proportion_SI]{proportion_SI()}}) to determine antimicrobial susceptibility and \code{\link[=count_susceptible]{count_susceptible()}} (equal to \code{\link[=count_SI]{count_SI()}}) to count susceptible isolates.
|
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This AMR package honours this insight. Use \code{\link[=susceptibility]{susceptibility()}} (equal to \code{\link[=proportion_SI]{proportion_SI()}}) to determine antimicrobial susceptibility and \code{\link[=count_susceptible]{count_susceptible()}} (equal to \code{\link[=count_SI]{count_SI()}}) to count susceptible isolates.
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}
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\section{Combination Therapy}{
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||||
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@ -74,7 +74,7 @@ eucast_rules(df, rules = "custom", custom_rules = y, info = FALSE)
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\subsection{Usage of antibiotic group names}{
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It is possible to define antibiotic groups instead of single antibiotics for the rule consequence, the part \emph{after} the tilde. In above examples, the antibiotic group \code{aminopenicillins} is used to include ampicillin and amoxicillin. The following groups are allowed (case-insensitive). Within parentheses are the agents that will be matched when running the rule.
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It is possible to define antibiotic groups instead of single antibiotics for the rule consequence, the part \emph{after} the tilde. In above examples, the antibiotic group \code{aminopenicillins} is used to include ampicillin and amoxicillin. The following groups are allowed (case-insensitive). Within parentheses are the drugs that will be matched when running the rule.
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\itemize{
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\item "aminoglycosides"\cr(amikacin, amikacin/fosfomycin, amphotericin B-high, apramycin, arbekacin, astromicin, bekanamycin, dibekacin, framycetin, gentamicin, gentamicin-high, habekacin, hygromycin, isepamicin, kanamycin, kanamycin-high, kanamycin/cephalexin, micronomicin, neomycin, netilmicin, pentisomicin, plazomicin, propikacin, ribostamycin, sisomicin, streptoduocin, streptomycin, streptomycin-high, tobramycin and tobramycin-high)
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\item "aminopenicillins"\cr(amoxicillin and ampicillin)
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@ -8,7 +8,7 @@
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A \link[tibble:tibble]{tibble} with 169 observations and 9 variables:
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\itemize{
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||||
\item \code{ab}\cr Antibiotic ID as used in this package (such as \code{AMC}), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available
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\item \code{name}\cr Official name of the antimicrobial agent as used by WHONET/EARS-Net or the WHO
|
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\item \code{name}\cr Official name of the antimicrobial drug as used by WHONET/EARS-Net or the WHO
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\item \code{type}\cr Type of the dosage, either "high_dosage", "standard_dosage" or "uncomplicated_uti"
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\item \code{dose}\cr Dose, such as "2 g" or "25 mg/kg"
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\item \code{dose_times}\cr Number of times a dose must be administered
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@ -50,7 +50,7 @@ eucast_dosage(ab, administration = "iv", version_breakpoints = 11)
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\item{version_expertrules}{the version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be either "3.3", "3.2" or "3.1".}
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|
||||
\item{ampc_cephalosporin_resistance}{a \link{character} value that should be applied to cefotaxime, ceftriaxone and ceftazidime for AmpC de-repressed cephalosporin-resistant mutants, defaults to \code{NA}. Currently only works when \code{version_expertrules} is \code{3.2} and higher; these version of '\emph{EUCAST Expert Rules on Enterobacterales}' state that results of cefotaxime, ceftriaxone and ceftazidime should be reported with a note, or results should be suppressed (emptied) for these three agents. A value of \code{NA} (the default) for this argument will remove results for these three agents, while e.g. a value of \code{"R"} will make the results for these agents resistant. Use \code{NULL} or \code{FALSE} to not alter results for these three agents of AmpC de-repressed cephalosporin-resistant mutants. Using \code{TRUE} is equal to using \code{"R"}. \cr For \emph{EUCAST Expert Rules} v3.2, this rule applies to: \emph{Citrobacter braakii}, \emph{Citrobacter freundii}, \emph{Citrobacter gillenii}, \emph{Citrobacter murliniae}, \emph{Citrobacter rodenticum}, \emph{Citrobacter sedlakii}, \emph{Citrobacter werkmanii}, \emph{Citrobacter youngae}, \emph{Enterobacter}, \emph{Hafnia alvei}, \emph{Klebsiella aerogenes}, \emph{Morganella morganii}, \emph{Providencia} and \emph{Serratia}.}
|
||||
\item{ampc_cephalosporin_resistance}{a \link{character} value that should be applied to cefotaxime, ceftriaxone and ceftazidime for AmpC de-repressed cephalosporin-resistant mutants, defaults to \code{NA}. Currently only works when \code{version_expertrules} is \code{3.2} and higher; these version of '\emph{EUCAST Expert Rules on Enterobacterales}' state that results of cefotaxime, ceftriaxone and ceftazidime should be reported with a note, or results should be suppressed (emptied) for these three drugs. A value of \code{NA} (the default) for this argument will remove results for these three drugs, while e.g. a value of \code{"R"} will make the results for these drugs resistant. Use \code{NULL} or \code{FALSE} to not alter results for these three drugs of AmpC de-repressed cephalosporin-resistant mutants. Using \code{TRUE} is equal to using \code{"R"}. \cr For \emph{EUCAST Expert Rules} v3.2, this rule applies to: \emph{Citrobacter braakii}, \emph{Citrobacter freundii}, \emph{Citrobacter gillenii}, \emph{Citrobacter murliniae}, \emph{Citrobacter rodenticum}, \emph{Citrobacter sedlakii}, \emph{Citrobacter werkmanii}, \emph{Citrobacter youngae}, \emph{Enterobacter}, \emph{Hafnia alvei}, \emph{Klebsiella aerogenes}, \emph{Morganella morganii}, \emph{Providencia} and \emph{Serratia}.}
|
||||
|
||||
\item{only_rsi_columns}{a \link{logical} to indicate whether only antibiotic columns must be detected that were transformed to class \code{rsi} (see \code{\link[=as.rsi]{as.rsi()}}) on beforehand (defaults to \code{FALSE})}
|
||||
|
||||
@ -58,7 +58,7 @@ eucast_dosage(ab, administration = "iv", version_breakpoints = 11)
|
||||
|
||||
\item{...}{column name of an antibiotic, see section \emph{Antibiotics} below}
|
||||
|
||||
\item{ab}{any (vector of) text that can be coerced to a valid antibiotic code with \code{\link[=as.ab]{as.ab()}}}
|
||||
\item{ab}{any (vector of) text that can be coerced to a valid antibiotic drug code with \code{\link[=as.ab]{as.ab()}}}
|
||||
|
||||
\item{administration}{route of administration, either "im", "iv" or "oral"}
|
||||
}
|
||||
|
||||
@ -151,12 +151,12 @@ This is a more reliable method, since it also \emph{weighs} the antibiogram (ant
|
||||
\enumerate{
|
||||
\item Using \code{type = "points"} and argument \code{points_threshold} (default)
|
||||
|
||||
This method weighs \emph{all} antimicrobial agents available in the data set. Any difference from I to S or R (or vice versa) counts as \code{0.5} points, a difference from S to R (or vice versa) counts as \code{1} point. When the sum of points exceeds \code{points_threshold}, which defaults to \code{2}, an isolate will be selected as a first weighted isolate.
|
||||
This method weighs \emph{all} antimicrobial drugs available in the data set. Any difference from I to S or R (or vice versa) counts as \code{0.5} points, a difference from S to R (or vice versa) counts as \code{1} point. When the sum of points exceeds \code{points_threshold}, which defaults to \code{2}, an isolate will be selected as a first weighted isolate.
|
||||
|
||||
All antimicrobials are internally selected using the \code{\link[=all_antimicrobials]{all_antimicrobials()}} function. The output of this function does not need to be passed to the \code{\link[=first_isolate]{first_isolate()}} function.
|
||||
\item Using \code{type = "keyantimicrobials"} and argument \code{ignore_I}
|
||||
|
||||
This method only weighs specific antimicrobial agents, called \emph{key antimicrobials}. Any difference from S to R (or vice versa) in these key antimicrobials will select an isolate as a first weighted isolate. With \code{ignore_I = FALSE}, also differences from I to S or R (or vice versa) will lead to this.
|
||||
This method only weighs specific antimicrobial drugs, called \emph{key antimicrobials}. Any difference from S to R (or vice versa) in these key antimicrobials will select an isolate as a first weighted isolate. With \code{ignore_I = FALSE}, also differences from I to S or R (or vice versa) will lead to this.
|
||||
|
||||
Key antimicrobials are internally selected using the \code{\link[=key_antimicrobials]{key_antimicrobials()}} function, but can also be added manually as a variable to the data and set in the \code{col_keyantimicrobials} argument. Another option is to pass the output of the \code{\link[=key_antimicrobials]{key_antimicrobials()}} function directly to the \code{col_keyantimicrobials} argument.
|
||||
}
|
||||
|
||||
@ -123,7 +123,7 @@ if (require("dplyr")) {
|
||||
filter(n() >= 30) \%>\% # filter on only 30 results per group
|
||||
summarise_if(is.rsi, resistance) # then get resistance of all drugs
|
||||
|
||||
# now conduct PCA for certain antimicrobial agents
|
||||
# now conduct PCA for certain antimicrobial drugs
|
||||
pca_result <- resistance_data \%>\%
|
||||
pca(AMC, CXM, CTX, CAZ, GEN, TOB, TMP, SXT)
|
||||
|
||||
|
||||
@ -37,13 +37,13 @@ antimicrobials_equal(
|
||||
|
||||
\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()}}.}
|
||||
|
||||
\item{universal}{names of \strong{broad-spectrum} antimicrobial agents, case-insensitive. Set to \code{NULL} to ignore. See \emph{Details} for the default agents.}
|
||||
\item{universal}{names of \strong{broad-spectrum} antimicrobial drugs, case-insensitive. Set to \code{NULL} to ignore. See \emph{Details} for the default antimicrobial drugs}
|
||||
|
||||
\item{gram_negative}{names of antibiotic agents for \strong{Gram-positives}, case-insensitive. Set to \code{NULL} to ignore. See \emph{Details} for the default agents.}
|
||||
\item{gram_negative}{names of antibiotic drugs for \strong{Gram-positives}, case-insensitive. Set to \code{NULL} to ignore. See \emph{Details} for the default antibiotic drugs}
|
||||
|
||||
\item{gram_positive}{names of antibiotic agents for \strong{Gram-negatives}, case-insensitive. Set to \code{NULL} to ignore. See \emph{Details} for the default agents.}
|
||||
\item{gram_positive}{names of antibiotic drugs for \strong{Gram-negatives}, case-insensitive. Set to \code{NULL} to ignore. See \emph{Details} for the default antibiotic drugs}
|
||||
|
||||
\item{antifungal}{names of antifungal agents for \strong{fungi}, case-insensitive. Set to \code{NULL} to ignore. See \emph{Details} for the default agents.}
|
||||
\item{antifungal}{names of antifungal drugs for \strong{fungi}, case-insensitive. Set to \code{NULL} to ignore. See \emph{Details} for the default antifungal drugs}
|
||||
|
||||
\item{only_rsi_columns}{a \link{logical} to indicate whether only columns must be included that were transformed to class \code{rsi} (see \code{\link[=as.rsi]{as.rsi()}}) on beforehand (defaults to \code{FALSE})}
|
||||
|
||||
@ -63,11 +63,11 @@ These functions can be used to determine first weighted isolates by considering
|
||||
\details{
|
||||
The \code{\link[=key_antimicrobials]{key_antimicrobials()}} and \code{\link[=all_antimicrobials]{all_antimicrobials()}} functions are context-aware. This means that the \code{x} argument can be left blank if used inside a \link{data.frame} call, see \emph{Examples}.
|
||||
|
||||
The function \code{\link[=key_antimicrobials]{key_antimicrobials()}} returns a \link{character} vector with 12 antimicrobial results for every isolate. The function \code{\link[=all_antimicrobials]{all_antimicrobials()}} returns a \link{character} vector with all antimicrobial results for every isolate. These vectors can then be compared using \code{\link[=antimicrobials_equal]{antimicrobials_equal()}}, to check if two isolates have generally the same antibiogram. Missing and invalid values are replaced with a dot (\code{"."}) by \code{\link[=key_antimicrobials]{key_antimicrobials()}} and ignored by \code{\link[=antimicrobials_equal]{antimicrobials_equal()}}.
|
||||
The function \code{\link[=key_antimicrobials]{key_antimicrobials()}} returns a \link{character} vector with 12 antimicrobial results for every isolate. The function \code{\link[=all_antimicrobials]{all_antimicrobials()}} returns a \link{character} vector with all antimicrobial drug results for every isolate. These vectors can then be compared using \code{\link[=antimicrobials_equal]{antimicrobials_equal()}}, to check if two isolates have generally the same antibiogram. Missing and invalid values are replaced with a dot (\code{"."}) by \code{\link[=key_antimicrobials]{key_antimicrobials()}} and ignored by \code{\link[=antimicrobials_equal]{antimicrobials_equal()}}.
|
||||
|
||||
Please see the \code{\link[=first_isolate]{first_isolate()}} function how these important functions enable the 'phenotype-based' method for determination of first isolates.
|
||||
|
||||
The default antimicrobial agents used for \strong{all rows} (set in \code{universal}) are:
|
||||
The default antimicrobial drugs used for \strong{all rows} (set in \code{universal}) are:
|
||||
\itemize{
|
||||
\item Ampicillin
|
||||
\item Amoxicillin/clavulanic acid
|
||||
@ -77,7 +77,7 @@ The default antimicrobial agents used for \strong{all rows} (set in \code{univer
|
||||
\item Trimethoprim/sulfamethoxazole
|
||||
}
|
||||
|
||||
The default antimicrobial agents used for \strong{Gram-negative bacteria} (set in \code{gram_negative}) are:
|
||||
The default antimicrobial drugs used for \strong{Gram-negative bacteria} (set in \code{gram_negative}) are:
|
||||
\itemize{
|
||||
\item Cefotaxime
|
||||
\item Ceftazidime
|
||||
@ -87,7 +87,7 @@ The default antimicrobial agents used for \strong{Gram-negative bacteria} (set i
|
||||
\item Tobramycin
|
||||
}
|
||||
|
||||
The default antimicrobial agents used for \strong{Gram-positive bacteria} (set in \code{gram_positive}) are:
|
||||
The default antimicrobial drugs used for \strong{Gram-positive bacteria} (set in \code{gram_positive}) are:
|
||||
\itemize{
|
||||
\item Erythromycin
|
||||
\item Oxacillin
|
||||
@ -97,7 +97,7 @@ The default antimicrobial agents used for \strong{Gram-positive bacteria} (set i
|
||||
\item Vancomycin
|
||||
}
|
||||
|
||||
The default antimicrobial agents used for \strong{fungi} (set in \code{antifungal}) are:
|
||||
The default antimicrobial drugs used for \strong{fungi} (set in \code{antifungal}) are:
|
||||
\itemize{
|
||||
\item Anidulafungin
|
||||
\item Caspofungin
|
||||
|
||||
@ -184,7 +184,7 @@ A microorganism is categorised as \emph{Susceptible, standard dosing regimen}, w
|
||||
A microorganism is categorised as \emph{Susceptible, Increased exposure} when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection.
|
||||
}
|
||||
|
||||
This AMR package honours this (new) insight. Use \code{\link[=susceptibility]{susceptibility()}} (equal to \code{\link[=proportion_SI]{proportion_SI()}}) to determine antimicrobial susceptibility and \code{\link[=count_susceptible]{count_susceptible()}} (equal to \code{\link[=count_SI]{count_SI()}}) to count susceptible isolates.
|
||||
This AMR package honours this insight. Use \code{\link[=susceptibility]{susceptibility()}} (equal to \code{\link[=proportion_SI]{proportion_SI()}}) to determine antimicrobial susceptibility and \code{\link[=count_susceptible]{count_susceptible()}} (equal to \code{\link[=count_SI]{count_SI()}}) to count susceptible isolates.
|
||||
}
|
||||
|
||||
\examples{
|
||||
|
||||
@ -266,7 +266,7 @@ mo_property(
|
||||
|
||||
\item{...}{other arguments passed on to \code{\link[=as.mo]{as.mo()}}, such as 'minimum_matching_score', 'ignore_pattern', and 'remove_from_input'}
|
||||
|
||||
\item{ab}{any (vector of) text that can be coerced to a valid antibiotic code with \code{\link[=as.ab]{as.ab()}}}
|
||||
\item{ab}{any (vector of) text that can be coerced to a valid antibiotic drug code with \code{\link[=as.ab]{as.ab()}}}
|
||||
|
||||
\item{open}{browse the URL using \code{\link[utils:browseURL]{browseURL()}}}
|
||||
|
||||
|
||||
@ -74,7 +74,7 @@ if (require("dplyr")) {
|
||||
filter(n() >= 30) \%>\% # filter on only 30 results per group
|
||||
summarise_if(is.rsi, resistance) # then get resistance of all drugs
|
||||
|
||||
# now conduct PCA for certain antimicrobial agents
|
||||
# now conduct PCA for certain antimicrobial drugs
|
||||
pca_result <- resistance_data \%>\%
|
||||
pca(AMC, CXM, CTX, CAZ, GEN, TOB, TMP, SXT)
|
||||
|
||||
|
||||
@ -99,7 +99,7 @@
|
||||
|
||||
\item{mo}{any (vector of) text that can be coerced to a valid microorganism code with \code{\link[=as.mo]{as.mo()}}}
|
||||
|
||||
\item{ab}{any (vector of) text that can be coerced to a valid antimicrobial code with \code{\link[=as.ab]{as.ab()}}}
|
||||
\item{ab}{any (vector of) text that can be coerced to a valid antimicrobial drug code with \code{\link[=as.ab]{as.ab()}}}
|
||||
|
||||
\item{guideline}{interpretation guideline to use, defaults to the latest included EUCAST guideline, see \emph{Details}}
|
||||
|
||||
|
||||
@ -153,7 +153,7 @@ A microorganism is categorised as \emph{Susceptible, standard dosing regimen}, w
|
||||
A microorganism is categorised as \emph{Susceptible, Increased exposure} when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection.
|
||||
}
|
||||
|
||||
This AMR package honours this (new) insight. Use \code{\link[=susceptibility]{susceptibility()}} (equal to \code{\link[=proportion_SI]{proportion_SI()}}) to determine antimicrobial susceptibility and \code{\link[=count_susceptible]{count_susceptible()}} (equal to \code{\link[=count_SI]{count_SI()}}) to count susceptible isolates.
|
||||
This AMR package honours this insight. Use \code{\link[=susceptibility]{susceptibility()}} (equal to \code{\link[=proportion_SI]{proportion_SI()}}) to determine antimicrobial susceptibility and \code{\link[=count_susceptible]{count_susceptible()}} (equal to \code{\link[=count_SI]{count_SI()}}) to count susceptible isolates.
|
||||
}
|
||||
|
||||
\examples{
|
||||
|
||||
@ -18,7 +18,7 @@ random_rsi(size = NULL, prob_RSI = c(0.33, 0.33, 0.33), ...)
|
||||
|
||||
\item{mo}{any \link{character} that can be coerced to a valid microorganism code with \code{\link[=as.mo]{as.mo()}}}
|
||||
|
||||
\item{ab}{any \link{character} that can be coerced to a valid antimicrobial agent code with \code{\link[=as.ab]{as.ab()}}}
|
||||
\item{ab}{any \link{character} that can be coerced to a valid antimicrobial drug code with \code{\link[=as.ab]{as.ab()}}}
|
||||
|
||||
\item{...}{ignored, only in place to allow future extensions}
|
||||
|
||||
@ -28,7 +28,7 @@ random_rsi(size = NULL, prob_RSI = c(0.33, 0.33, 0.33), ...)
|
||||
class \code{mic} for \code{\link[=random_mic]{random_mic()}} (see \code{\link[=as.mic]{as.mic()}}) and class \code{disk} for \code{\link[=random_disk]{random_disk()}} (see \code{\link[=as.disk]{as.disk()}})
|
||||
}
|
||||
\description{
|
||||
These functions can be used for generating random MIC values and disk diffusion diameters, for AMR data analysis practice. By providing a microorganism and antimicrobial agent, the generated results will reflect reality as much as possible.
|
||||
These functions can be used for generating random MIC values and disk diffusion diameters, for AMR data analysis practice. By providing a microorganism and antimicrobial drug, the generated results will reflect reality as much as possible.
|
||||
}
|
||||
\details{
|
||||
The base \R function \code{\link[=sample]{sample()}} is used for generating values.
|
||||
|
||||
@ -122,7 +122,7 @@ A microorganism is categorised as \emph{Susceptible, standard dosing regimen}, w
|
||||
A microorganism is categorised as \emph{Susceptible, Increased exposure} when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection.
|
||||
}
|
||||
|
||||
This AMR package honours this (new) insight. Use \code{\link[=susceptibility]{susceptibility()}} (equal to \code{\link[=proportion_SI]{proportion_SI()}}) to determine antimicrobial susceptibility and \code{\link[=count_susceptible]{count_susceptible()}} (equal to \code{\link[=count_SI]{count_SI()}}) to count susceptible isolates.
|
||||
This AMR package honours this insight. Use \code{\link[=susceptibility]{susceptibility()}} (equal to \code{\link[=proportion_SI]{proportion_SI()}}) to determine antimicrobial susceptibility and \code{\link[=count_susceptible]{count_susceptible()}} (equal to \code{\link[=count_SI]{count_SI()}}) to count susceptible isolates.
|
||||
}
|
||||
|
||||
\examples{
|
||||
|
||||
@ -25,7 +25,7 @@ translate_AMR(x, language = get_AMR_locale())
|
||||
For language-dependent output of AMR functions, like \code{\link[=mo_name]{mo_name()}}, \code{\link[=mo_gramstain]{mo_gramstain()}}, \code{\link[=mo_type]{mo_type()}} and \code{\link[=ab_name]{ab_name()}}.
|
||||
}
|
||||
\details{
|
||||
The currently 16 supported languages are English (en), Chinese (zh), Danish (da), Dutch (nl), French (fr), German (de), Greek (el), Italian (it), Japanese (ja), Polish (pl), Portuguese (pt), Russian (ru), Spanish (es), Swedish (sv), Turkish (tr) or Ukrainian (uk). All these languages have translations available for all antimicrobial agents and colloquial microorganism names.
|
||||
The currently 16 supported languages are English (en), Chinese (zh), Danish (da), Dutch (nl), French (fr), German (de), Greek (el), Italian (it), Japanese (ja), Polish (pl), Portuguese (pt), Russian (ru), Spanish (es), Swedish (sv), Turkish (tr) or Ukrainian (uk). All these languages have translations available for all antimicrobial drugs and colloquial microorganism names.
|
||||
|
||||
\strong{To silence language notes when this package loads} on a non-English operating system, you can set the option \code{AMR_locale} in your \code{.Rprofile} file like this:
|
||||
|
||||
|
||||
Reference in New Issue
Block a user