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added mdr_tb()

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dr. M.S. (Matthijs) Berends
2019-05-23 16:58:59 +02:00
parent 07d26cd485
commit 60983a1640
60 changed files with 1479 additions and 626 deletions
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2
man/antibiotics.Rd
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@ -4,7 +4,7 @@
\name{antibiotics}
\alias{antibiotics}
\title{Data set with ~450 antibiotics}
\format{A \code{\link{data.frame}} with 455 observations and 13 variables:
\format{A \code{\link{data.frame}} with 454 observations and 13 variables:
\describe{
\item{\code{ab}}{Antibiotic ID as used in this package (like \code{AMC}), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available}
\item{\code{atc}}{ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC, like \code{J01CR02}}

6
man/as.rsi.Rd
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@ -55,9 +55,9 @@ The function \code{is.rsi.eligible} returns \code{TRUE} when a columns contains
In 2019, EUCAST has decided to change the definitions of susceptibility testing categories S, I and R as shown below. Results of several consultations on the new definitions are available on the EUCAST website under "Consultations".
\itemize{
\item{\strong{S}}{Susceptible, standard dosing regimen: A microorganism is categorised as "Susceptible, standard dosing regimen", when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent.}
\item{\strong{I}}{Susceptible, increased exposure: A microorganism is categorised as "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.}
\item{\strong{R}}{Resistant: A microorganism is categorised as "Resistant" when there is a high likelihood of therapeutic failure even when there is increased exposure.}
\item{\strong{S} - }{Susceptible, standard dosing regimen: A microorganism is categorised as "Susceptible, standard dosing regimen", when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent.}
\item{\strong{I} - }{Susceptible, increased exposure: A microorganism is categorised as "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.}
\item{\strong{R} - }{Resistant: A microorganism is categorised as "Resistant" when there is a high likelihood of therapeutic failure even when there is increased exposure.}
}
Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection.

8
man/count.Rd
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@ -43,7 +43,7 @@ count_df(data, translate_ab = "name", language = get_locale(),
\item{language}{language of the returned text, defaults to system language (see \code{\link{get_locale}}) and can also be set with \code{\link{getOption}("AMR_locale")}. Use \code{language = NULL} or \code{language = ""} to prevent translation.}
\item{combine_SI}{a logical to indicate whether all values of S and I must be merged into one, so the output only consists of S+I vs. R (susceptible vs. resistant). This used to be the parameter \code{combine_IR}, but this now follows the redefinition by EUCAST about the interpretion of I (increased exposure) in 2019, see below. Default is now \code{TRUE}.}
\item{combine_SI}{a logical to indicate whether all values of S and I must be merged into one, so the output only consists of S+I vs. R (susceptible vs. resistant). This used to be the parameter \code{combine_IR}, but this now follows the redefinition by EUCAST about the interpretion of I (increased exposure) in 2019, see section 'Interpretation of S, I and R' below. Default is \code{TRUE}.}
\item{combine_IR}{a logical to indicate whether all values of I and R must be merged into one, so the output only consists of S vs. I+R (susceptible vs. non-susceptible). This is outdated, see parameter \code{combine_SI}.}
}
@ -67,9 +67,9 @@ These functions are meant to count isolates. Use the \code{\link{portion}_*} fun
In 2019, EUCAST has decided to change the definitions of susceptibility testing categories S, I and R as shown below. Results of several consultations on the new definitions are available on the EUCAST website under "Consultations".
\itemize{
\item{\strong{S}}{Susceptible, standard dosing regimen: A microorganism is categorised as "Susceptible, standard dosing regimen", when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent.}
\item{\strong{I}}{Susceptible, increased exposure: A microorganism is categorised as "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.}
\item{\strong{R}}{Resistant: A microorganism is categorised as "Resistant" when there is a high likelihood of therapeutic failure even when there is increased exposure.}
\item{\strong{S} - }{Susceptible, standard dosing regimen: A microorganism is categorised as "Susceptible, standard dosing regimen", when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent.}
\item{\strong{I} - }{Susceptible, increased exposure: A microorganism is categorised as "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.}
\item{\strong{R} - }{Resistant: A microorganism is categorised as "Resistant" when there is a high likelihood of therapeutic failure even when there is increased exposure.}
}
Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection.

2
man/eucast_rules.Rd
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@ -43,7 +43,7 @@ eucast_rules_file()
\item{...}{column name of an antibiotic, see section Antibiotics}
}
\value{
The input of \code{tbl_}, possibly with edited values of antibiotics. Or, if \code{verbose = TRUE}, a \code{data.frame} with all original and new values of the affected bug-drug combinations.
The input of \code{x}, possibly with edited values of antibiotics. Or, if \code{verbose = TRUE}, a \code{data.frame} with all original and new values of the affected bug-drug combinations.
}
\description{
Apply susceptibility rules as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, \url{http://eucast.org}), see \emph{Source}. This includes (1) expert rules, (2) intrinsic resistance and (3) inferred resistance as defined in their breakpoint tables.

2
man/ggplot_rsi.Rd
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@ -50,7 +50,7 @@ labels_rsi_count(position = NULL, x = "Antibiotic",
\item{translate_ab}{a column name of the \code{\link{antibiotics}} data set to translate the antibiotic abbreviations to, using \code{\link{ab_property}}}
\item{combine_SI}{a logical to indicate whether all values of S and I must be merged into one, so the output only consists of S+I vs. R (susceptible vs. resistant). This used to be the parameter \code{combine_IR}, but this now follows the redefinition by EUCAST about the interpretion of I (increased exposure) in 2019, see below. Default is now \code{TRUE}.}
\item{combine_SI}{a logical to indicate whether all values of S and I must be merged into one, so the output only consists of S+I vs. R (susceptible vs. resistant). This used to be the parameter \code{combine_IR}, but this now follows the redefinition by EUCAST about the interpretion of I (increased exposure) in 2019, see section 'Interpretation of S, I and R' below. Default is \code{TRUE}.}
\item{combine_IR}{a logical to indicate whether all values of I and R must be merged into one, so the output only consists of S vs. I+R (susceptible vs. non-susceptible). This is outdated, see parameter \code{combine_SI}.}

33
man/key_antibiotics.Rd
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@ -5,26 +5,25 @@
\alias{key_antibiotics_equal}
\title{Key antibiotics for first \emph{weighted} isolates}
\usage{
key_antibiotics(tbl, col_mo = NULL, universal_1 = guess_ab_col(tbl,
"AMX"), universal_2 = guess_ab_col(tbl, "AMC"),
universal_3 = guess_ab_col(tbl, "CXM"),
universal_4 = guess_ab_col(tbl, "TZP"),
universal_5 = guess_ab_col(tbl, "CIP"),
universal_6 = guess_ab_col(tbl, "SXT"), GramPos_1 = guess_ab_col(tbl,
"VAN"), GramPos_2 = guess_ab_col(tbl, "TEC"),
GramPos_3 = guess_ab_col(tbl, "TCY"), GramPos_4 = guess_ab_col(tbl,
"ERY"), GramPos_5 = guess_ab_col(tbl, "OXA"),
GramPos_6 = guess_ab_col(tbl, "RIF"), GramNeg_1 = guess_ab_col(tbl,
"GEN"), GramNeg_2 = guess_ab_col(tbl, "TOB"),
GramNeg_3 = guess_ab_col(tbl, "COL"), GramNeg_4 = guess_ab_col(tbl,
"CTX"), GramNeg_5 = guess_ab_col(tbl, "CAZ"),
GramNeg_6 = guess_ab_col(tbl, "MEM"), warnings = TRUE, ...)
key_antibiotics(x, col_mo = NULL, universal_1 = guess_ab_col(x, "AMX"),
universal_2 = guess_ab_col(x, "AMC"), universal_3 = guess_ab_col(x,
"CXM"), universal_4 = guess_ab_col(x, "TZP"),
universal_5 = guess_ab_col(x, "CIP"), universal_6 = guess_ab_col(x,
"SXT"), GramPos_1 = guess_ab_col(x, "VAN"),
GramPos_2 = guess_ab_col(x, "TEC"), GramPos_3 = guess_ab_col(x,
"TCY"), GramPos_4 = guess_ab_col(x, "ERY"),
GramPos_5 = guess_ab_col(x, "OXA"), GramPos_6 = guess_ab_col(x,
"RIF"), GramNeg_1 = guess_ab_col(x, "GEN"),
GramNeg_2 = guess_ab_col(x, "TOB"), GramNeg_3 = guess_ab_col(x,
"COL"), GramNeg_4 = guess_ab_col(x, "CTX"),
GramNeg_5 = guess_ab_col(x, "CAZ"), GramNeg_6 = guess_ab_col(x,
"MEM"), warnings = TRUE, ...)
key_antibiotics_equal(x, y, type = c("keyantibiotics", "points"),
ignore_I = TRUE, points_threshold = 2, info = FALSE)
}
\arguments{
\item{tbl}{table with antibiotics coloms, like \code{amox} and \code{amcl}.}
\item{x}{table with antibiotics coloms, like \code{AMX} or \code{amox}}
\item{col_mo}{column name of the unique IDs of the microorganisms (see \code{\link{mo}}), defaults to the first column of class \code{mo}. Values will be coerced using \code{\link{as.mo}}.}
@ -38,8 +37,6 @@ key_antibiotics_equal(x, y, type = c("keyantibiotics", "points"),
\item{...}{other parameters passed on to function}
\item{x, y}{characters to compare}
\item{type}{type to determine weighed isolates; can be \code{"keyantibiotics"} or \code{"points"}, see Details}
\item{ignore_I}{logical to determine whether antibiotic interpretations with \code{"I"} will be ignored when \code{type = "keyantibiotics"}, see Details}
@ -47,6 +44,8 @@ key_antibiotics_equal(x, y, type = c("keyantibiotics", "points"),
\item{points_threshold}{points until the comparison of key antibiotics will lead to inclusion of an isolate when \code{type = "points"}, see Details}
\item{info}{print progress}
\item{x, y}{characters to compare}
}
\description{
These function can be used to determine first isolates (see \code{\link{first_isolate}}). Using key antibiotics to determine first isolates is more reliable than without key antibiotics. These selected isolates will then be called first \emph{weighted} isolates.

27
man/mdro.Rd
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@ -4,22 +4,27 @@
\alias{mdro}
\alias{brmo}
\alias{mrgn}
\alias{mdr_tb}
\alias{eucast_exceptional_phenotypes}
\title{Determine multidrug-resistant organisms (MDRO)}
\usage{
mdro(x, country = NULL, col_mo = NULL, info = TRUE,
verbose = FALSE, ...)
mdro(x, country = NULL, guideline = NULL, col_mo = NULL,
info = TRUE, verbose = FALSE, ...)
brmo(..., country = "nl")
mrgn(x, country = "de", ...)
eucast_exceptional_phenotypes(x, country = "EUCAST", ...)
mdr_tb(x, guideline = "TB", ...)
eucast_exceptional_phenotypes(x, guideline = "EUCAST", ...)
}
\arguments{
\item{x}{table with antibiotic columns, like e.g. \code{AMX} and \code{AMC}}
\item{country}{country code to determine guidelines. EUCAST rules will be used when left empty, see Details. Should be or a code from the \href{https://en.wikipedia.org/wiki/ISO_3166-1_alpha-2#Officially_assigned_code_elements}{list of ISO 3166-1 alpha-2 country codes}. Case-insensitive. Currently supported are \code{de} (Germany) and \code{nl} (the Netherlands).}
\item{country}{country code to determine guidelines. Should be or a code from the \href{https://en.wikipedia.org/wiki/ISO_3166-1_alpha-2#Officially_assigned_code_elements}{list of ISO 3166-1 alpha-2 country codes}. Case-insensitive.}
\item{guideline}{a specific guideline to mention. For some countries this will be determined automatically, see Details. EUCAST guidelines will be used when left empty, see Details.}
\item{col_mo}{column name of the unique IDs of the microorganisms (see \code{\link{mo}}), defaults to the first column of class \code{mo}. Values will be coerced using \code{\link{as.mo}}.}
@ -36,7 +41,19 @@ Ordered factor with levels \code{Negative < Positive, unconfirmed < Positive}.
Determine which isolates are multidrug-resistant organisms (MDRO) according to country-specific guidelines.
}
\details{
When \code{country} will be left blank, guidelines will be taken from EUCAST Expert Rules Version 3.1 "Intrinsic Resistance and Exceptional Phenotypes Tables" (\href{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf}{link}).
When \code{country} is set, the parameter guideline will be ignored as these guidelines will be used:
\itemize{
\item{\code{country = "nl"}: Rijksinstituut voor Volksgezondheid en Milieu "WIP-richtlijn BRMO (Bijzonder Resistente Micro-Organismen) [ZKH]" (\href{https://www.rivm.nl/Documenten_en_publicaties/Professioneel_Praktisch/Richtlijnen/Infectieziekten/WIP_Richtlijnen/WIP_Richtlijnen/Ziekenhuizen/WIP_richtlijn_BRMO_Bijzonder_Resistente_Micro_Organismen_ZKH}{link})}
}
Please suggest your own country's specific guidelines by letting us know: \url{https://gitlab.com/msberends/AMR/issues/new}.
Other currently supported guidelines are:
\itemize{
\item{\code{guideline = "eucast"}: EUCAST Expert Rules Version 3.1 "Intrinsic Resistance and Exceptional Phenotypes Tables" (\href{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf}{link})}
\item{\code{guideline = "tb"}: World Health Organization "Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis" (\href{https://www.who.int/tb/publications/pmdt_companionhandbook/en/}{link})}
}
}
\section{Antibiotics}{

8
man/portion.Rd
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@ -49,7 +49,7 @@ portion_df(data, translate_ab = "name", language = get_locale(),
\item{language}{language of the returned text, defaults to system language (see \code{\link{get_locale}}) and can also be set with \code{\link{getOption}("AMR_locale")}. Use \code{language = NULL} or \code{language = ""} to prevent translation.}
\item{combine_SI}{a logical to indicate whether all values of S and I must be merged into one, so the output only consists of S+I vs. R (susceptible vs. resistant). This used to be the parameter \code{combine_IR}, but this now follows the redefinition by EUCAST about the interpretion of I (increased exposure) in 2019, see below. Default is now \code{TRUE}.}
\item{combine_SI}{a logical to indicate whether all values of S and I must be merged into one, so the output only consists of S+I vs. R (susceptible vs. resistant). This used to be the parameter \code{combine_IR}, but this now follows the redefinition by EUCAST about the interpretion of I (increased exposure) in 2019, see section 'Interpretation of S, I and R' below. Default is \code{TRUE}.}
\item{combine_IR}{a logical to indicate whether all values of I and R must be merged into one, so the output only consists of S vs. I+R (susceptible vs. non-susceptible). This is outdated, see parameter \code{combine_SI}.}
}
@ -87,9 +87,9 @@ These functions are not meant to count isolates, but to calculate the portion of
In 2019, EUCAST has decided to change the definitions of susceptibility testing categories S, I and R as shown below. Results of several consultations on the new definitions are available on the EUCAST website under "Consultations".
\itemize{
\item{\strong{S}}{Susceptible, standard dosing regimen: A microorganism is categorised as "Susceptible, standard dosing regimen", when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent.}
\item{\strong{I}}{Susceptible, increased exposure: A microorganism is categorised as "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.}
\item{\strong{R}}{Resistant: A microorganism is categorised as "Resistant" when there is a high likelihood of therapeutic failure even when there is increased exposure.}
\item{\strong{S} - }{Susceptible, standard dosing regimen: A microorganism is categorised as "Susceptible, standard dosing regimen", when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent.}
\item{\strong{I} - }{Susceptible, increased exposure: A microorganism is categorised as "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.}
\item{\strong{R} - }{Resistant: A microorganism is categorised as "Resistant" when there is a high likelihood of therapeutic failure even when there is increased exposure.}
}
Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection.