+file (40 kB)
diff --git a/docs/authors.html b/docs/authors.html index 41d11c2f..a1141b1e 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -17,7 +17,7 @@ diff --git a/docs/index.html b/docs/index.html index b8ea4137..d9c261a8 100644 --- a/docs/index.html +++ b/docs/index.html @@ -47,7 +47,7 @@ @@ -195,7 +195,8 @@
AMR (for R) 
-Update March 2022: All functions in this package are considered to be stable. Updates to the AMR interpretation rules (such as by EUCAST and CLSI), the microbial taxonomy, and the antibiotic dosages will all be updated every 6 to 12 months.
+Update May 2022: EUCAST 2022 and CLSI 2022 guidelines have been added for
+as.rsi()!Updates to the AMR interpretation rules (such as by EUCAST and CLSI), the microbial taxonomy, and the antibiotic dosages will all be updated every 6 to 12 months.
What is AMR (for R)?
diff --git a/docs/news/index.html b/docs/news/index.html
index b25855ef..972f0622 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -17,7 +17,7 @@
-AMR 1.8.1.9005
+
+AMR 1.8.1.9006
Last updated: 10 May 2022
+Last updated: 10 May 2022
Changed
+New
+- EUCAST 2022 and CLSI 2022 guidelines have been added for
as.rsi(). EUCAST 2022 is now the new default guideline for all MIC and disks diffusion interpretations.
+
Changed
- Fix for
as.rsi()on certain EUCAST breakpoints for MIC values - Removed
as.integer()for MIC values, since MIC are not integer values and runningtable()on MIC values consequently failed for not being able to retrieve the level position (as that’s how normallyas.integer()onfactors work) - diff --git a/docs/reference/as.mic.html b/docs/reference/as.mic.html index 7a523999..05bfacb3 100644 --- a/docs/reference/as.mic.html +++ b/docs/reference/as.mic.html @@ -17,7 +17,7 @@
Details
-To interpret MIC values as RSI values, use as.rsi() on MIC values. It supports guidelines from EUCAST (2011-2021) and CLSI (2010-2021).
To interpret MIC values as RSI values, use as.rsi() on MIC values. It supports guidelines from EUCAST (2011-2022) and CLSI (2011-2022).
This class for MIC values is a quite a special data type: formally it is an ordered factor with valid MIC values as factor levels (to make sure only valid MIC values are retained), but for any mathematical operation it acts as decimal numbers:
x <- random_mic(10)
x
#> Class <mic>
diff --git a/docs/reference/as.rsi.html b/docs/reference/as.rsi.html
index 62cb372d..7c933165 100644
--- a/docs/reference/as.rsi.html
+++ b/docs/reference/as.rsi.html
@@ -17,7 +17,7 @@
any (vector of) text that can be coerced to a valid antimicrobial code with as.ab()
defaults to the latest included EUCAST guideline, supports EUCAST (2011-2021) and CLSI (2010-2021), see Details
defaults to the latest included EUCAST guideline, supports EUCAST (2011-2022) and CLSI (2011-2022), see Details
(Urinary Tract Infection) A vector with logicals (TRUE or FALSE) to specify whether a UTI specific interpretation from the guideline should be chosen. For using as.rsi() on a data.frame, this can also be a column containing logicals or when left blank, the data set will be searched for a column 'specimen', and rows within this column containing 'urin' (such as 'urine', 'urina') will be regarded isolates from a UTI. See Examples.
Supported Guidelines
-For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are EUCAST (2011-2021) and CLSI (2010-2021).
-Thus, the guideline argument must be set to e.g., "EUCAST 2021" or "CLSI 2021". By simply using "EUCAST" (the default) or "CLSI" as input, the latest included version of that guideline will automatically be selected. You can set your own data set using the reference_data argument. The guideline argument will then be ignored.
For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are EUCAST (2011-2022) and CLSI (2011-2022).
+Thus, the guideline argument must be set to e.g., "EUCAST 2022" or "CLSI 2022". By simply using "EUCAST" (the default) or "CLSI" as input, the latest included version of that guideline will automatically be selected. You can set your own data set using the reference_data argument. The guideline argument will then be ignored.
Machine-Readable Interpretation Guidelines
-The repository of this package contains a machine-readable version of all guidelines. This is a CSV file consisting of 20,318 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. 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.
+The repository of this package contains a machine-readable version of all guidelines. This is a CSV file consisting of 20,369 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. 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.
Data set containing reference data to interpret MIC and disk diffusion to R/SI values, according to international guidelines. Currently implemented guidelines are EUCAST (2011-2021) and CLSI (2010-2021). Use as.rsi() to transform MICs or disks measurements to R/SI values.
Data set containing reference data to interpret MIC and disk diffusion to R/SI values, according to international guidelines. Currently implemented guidelines are EUCAST (2011-2022) and CLSI (2011-2022). Use as.rsi() to transform MICs or disks measurements to R/SI values.
Format
-A data.frame with 20,318 observations and 11 variables:
guideline
Name of the guideline
+ guideline
Name of the guidelinemethod
Either "DISK" or "MIC"site
Body site, e.g. "Oral" or "Respiratory"mo
Microbial ID, seeas.mo()
@@ -212,7 +212,7 @@
A data.frame with 20,369 observations and 11 variables:
-> Update March 2022: All functions in this package are considered to be stable. Updates to the AMR interpretation rules (such as by EUCAST and CLSI), the microbial taxonomy, and the antibiotic dosages will all be updated every 6 to 12 months.
+> Update May 2022: EUCAST 2022 and CLSI 2022 guidelines have been added for `as.rsi()`!
+>
+> Updates to the AMR interpretation rules (such as by EUCAST and CLSI), the microbial taxonomy, and the antibiotic dosages will all be updated every 6 to 12 months.
### What is `AMR` (for R)?
diff --git a/man/as.mic.Rd b/man/as.mic.Rd
index 185aa44e..b5d127ef 100755
--- a/man/as.mic.Rd
+++ b/man/as.mic.Rd
@@ -38,7 +38,7 @@ Ordered \link{factor} with additional class \code{\link{mic}}, that in mathemati
This transforms vectors to a new class \code{\link{mic}}, which treats the input as decimal numbers, while maintaining operators (such as ">=") and only allowing valid MIC values known to the field of (medical) microbiology.
}
\details{
-To interpret MIC values as RSI values, use \code{\link[=as.rsi]{as.rsi()}} on MIC values. It supports guidelines from EUCAST (2011-2021) and CLSI (2010-2021).
+To interpret MIC values as RSI values, use \code{\link[=as.rsi]{as.rsi()}} on MIC values. It supports guidelines from EUCAST (2011-2022) and CLSI (2011-2022).
This class for MIC values is a quite a special data type: formally it is an ordered \link{factor} with valid MIC values as \link{factor} levels (to make sure only valid MIC values are retained), but for any mathematical operation it acts as decimal numbers:\preformatted{x <- random_mic(10)
x
diff --git a/man/as.rsi.Rd b/man/as.rsi.Rd
index c8dfcc04..ef2715e5 100755
--- a/man/as.rsi.Rd
+++ b/man/as.rsi.Rd
@@ -68,7 +68,7 @@ is.rsi.eligible(x, threshold = 0.05)
\item{ab}{any (vector of) text that can be coerced to a valid antimicrobial code with \code{\link[=as.ab]{as.ab()}}}
-\item{guideline}{defaults to the latest included EUCAST guideline, supports EUCAST (2011-2021) and CLSI (2010-2021), see \emph{Details}}
+\item{guideline}{defaults to the latest included EUCAST guideline, supports EUCAST (2011-2022) and CLSI (2011-2022), see \emph{Details}}
\item{uti}{(Urinary Tract Infection) A vector with \link{logical}s (\code{TRUE} or \code{FALSE}) to specify whether a UTI specific interpretation from the guideline should be chosen. For using \code{\link[=as.rsi]{as.rsi()}} on a \link{data.frame}, this can also be a column containing \link{logical}s or when left blank, the data set will be searched for a column 'specimen', and rows within this column containing 'urin' (such as 'urine', 'urina') will be regarded isolates from a UTI. See \emph{Examples}.}
@@ -111,9 +111,9 @@ your_data \%>\% mutate(across(where(is.disk), as.rsi)) # since dplyr 1.0.0
\subsection{Supported Guidelines}{
-For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are EUCAST (2011-2021) and CLSI (2010-2021).
+For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are EUCAST (2011-2022) and CLSI (2011-2022).
-Thus, the \code{guideline} argument must be set to e.g., \code{"EUCAST 2021"} or \code{"CLSI 2021"}. By simply using \code{"EUCAST"} (the default) or \code{"CLSI"} as input, the latest included version of that guideline will automatically be selected. You can set your own data set using the \code{reference_data} argument. The \code{guideline} argument will then be ignored.
+Thus, the \code{guideline} argument must be set to e.g., \code{"EUCAST 2022"} or \code{"CLSI 2022"}. By simply using \code{"EUCAST"} (the default) or \code{"CLSI"} as input, the latest included version of that guideline will automatically be selected. You can set your own data set using the \code{reference_data} argument. The \code{guideline} argument will then be ignored.
}
\subsection{After Interpretation}{
@@ -123,7 +123,7 @@ After using \code{\link[=as.rsi]{as.rsi()}}, you can use the \code{\link[=eucast
\subsection{Machine-Readable Interpretation Guidelines}{
-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 20,318 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.
+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 20,369 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.
}
\subsection{Other}{
diff --git a/man/plot.Rd b/man/plot.Rd
index 4a007fa2..d3c715ea 100644
--- a/man/plot.Rd
+++ b/man/plot.Rd
@@ -18,7 +18,7 @@
mo = NULL,
ab = NULL,
guideline = "EUCAST",
- main = paste("MIC values of", deparse(substitute(x))),
+ main = deparse(substitute(x)),
ylab = "Frequency",
xlab = "Minimum Inhibitory Concentration (mg/L)",
colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
@@ -45,7 +45,7 @@
\method{plot}{disk}(
x,
- main = paste("Disk zones of", deparse(substitute(x))),
+ main = deparse(substitute(x)),
ylab = "Frequency",
xlab = "Disk diffusion diameter (mm)",
mo = NULL,
@@ -77,7 +77,7 @@
x,
ylab = "Percentage",
xlab = "Antimicrobial Interpretation",
- main = paste("Resistance Overview of", deparse(substitute(x))),
+ main = deparse(substitute(x)),
...
)
@@ -125,7 +125,7 @@ Functions to plot classes \code{rsi}, \code{mic} and \code{disk}, with support f
\details{
The interpretation of "I" will be named "Increased exposure" for all EUCAST guidelines since 2019, and will be named "Intermediate" in all other cases.
-For interpreting MIC values as well as disk diffusion diameters, supported guidelines to be used as input for the \code{guideline} argument are: "EUCAST 2021", "EUCAST 2020", "EUCAST 2019", "EUCAST 2018", "EUCAST 2017", "EUCAST 2016", "EUCAST 2015", "EUCAST 2014", "EUCAST 2013", "EUCAST 2012", "EUCAST 2011", "CLSI 2021", "CLSI 2020", "CLSI 2019", "CLSI 2018", "CLSI 2017", "CLSI 2016", "CLSI 2015", "CLSI 2014", "CLSI 2013", "CLSI 2012", "CLSI 2011" and "CLSI 2010".
+For interpreting MIC values as well as disk diffusion diameters, supported guidelines to be used as input for the \code{guideline} argument are: "EUCAST 2022", "EUCAST 2021", "EUCAST 2020", "EUCAST 2019", "EUCAST 2018", "EUCAST 2017", "EUCAST 2016", "EUCAST 2015", "EUCAST 2014", "EUCAST 2013", "EUCAST 2012", "EUCAST 2011", "CLSI 2022", "CLSI 2021", "CLSI 2020", "CLSI 2019", "CLSI 2018", "CLSI 2017", "CLSI 2016", "CLSI 2015", "CLSI 2014", "CLSI 2013", "CLSI 2012" and "CLSI 2011".
Simply using \code{"CLSI"} or \code{"EUCAST"} as input will automatically select the latest version of that guideline.
}
diff --git a/man/rsi_translation.Rd b/man/rsi_translation.Rd
index cdb6aea6..fc157fce 100644
--- a/man/rsi_translation.Rd
+++ b/man/rsi_translation.Rd
@@ -5,7 +5,7 @@
\alias{rsi_translation}
\title{Data Set for R/SI Interpretation}
\format{
-A \link{data.frame} with 20,318 observations and 11 variables:
+A \link{data.frame} with 20,369 observations and 11 variables:
\itemize{
\item \code{guideline}\cr Name of the guideline
\item \code{method}\cr Either "DISK" or "MIC"
@@ -24,7 +24,7 @@ A \link{data.frame} with 20,318 observations and 11 variables:
rsi_translation
}
\description{
-Data set containing reference data to interpret MIC and disk diffusion to R/SI values, according to international guidelines. Currently implemented guidelines are EUCAST (2011-2021) and CLSI (2010-2021). Use \code{\link[=as.rsi]{as.rsi()}} to transform MICs or disks measurements to R/SI values.
+Data set containing reference data to interpret MIC and disk diffusion to R/SI values, according to international guidelines. Currently implemented guidelines are EUCAST (2011-2022) and CLSI (2011-2022). Use \code{\link[=as.rsi]{as.rsi()}} to transform MICs or disks measurements to R/SI values.
}
\details{
The repository of this \code{AMR} package contains a file comprising this exact data set: \url{https://github.com/msberends/AMR/blob/main/data-raw/rsi_translation.txt}. This file \strong{allows for machine reading EUCAST and CLSI guidelines}, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. The file is updated automatically and the \code{mo} and \code{ab} columns have been transformed to contain the full official names instead of codes.