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Replace RSI with SIR

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This commit is contained in:
Dr. Matthijs Berends
2023-01-21 23:47:20 +01:00
committed by GitHub
parent 24b12024ce
commit 98e62c9af2
127 changed files with 1746 additions and 1648 deletions
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16
man/mean_amr_distance.Rd
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@@ -2,21 +2,21 @@
% Please edit documentation in R/mean_amr_distance.R
\name{mean_amr_distance}
\alias{mean_amr_distance}
\alias{mean_amr_distance.rsi}
\alias{mean_amr_distance.sir}
\alias{mean_amr_distance.data.frame}
\alias{amr_distance_from_row}
\title{Calculate the Mean AMR Distance}
\usage{
mean_amr_distance(x, ...)
\method{mean_amr_distance}{rsi}(x, ..., combine_SI = TRUE)
\method{mean_amr_distance}{sir}(x, ..., combine_SI = TRUE)
\method{mean_amr_distance}{data.frame}(x, ..., combine_SI = TRUE)
amr_distance_from_row(amr_distance, row)
}
\arguments{
\item{x}{a vector of class \link[=as.rsi]{rsi}, \link[=as.mic]{mic} or \link[=as.disk]{disk}, or a \link{data.frame} containing columns of any of these classes}
\item{x}{a vector of class \link[=as.sir]{sir}, \link[=as.mic]{mic} or \link[=as.disk]{disk}, or a \link{data.frame} containing columns of any of these classes}
\item{...}{variables to select (supports \link[tidyselect:language]{tidyselect language} such as \code{column1:column4} and \code{where(is.mic)}, and can thus also be \link[=ab_selector]{antibiotic selectors}}
@@ -34,7 +34,7 @@ The mean AMR distance is effectively \href{https://en.wikipedia.org/wiki/Standar
MIC values (see \code{\link[=as.mic]{as.mic()}}) are transformed with \code{\link[=log2]{log2()}} first; their distance is thus calculated as \code{(log2(x) - mean(log2(x))) / sd(log2(x))}.
R/SI values (see \code{\link[=as.rsi]{as.rsi()}}) are transformed using \code{"S"} = 1, \code{"I"} = 2, and \code{"R"} = 3. If \code{combine_SI} is \code{TRUE} (default), the \code{"I"} will be considered to be 1.
SIR values (see \code{\link[=as.sir]{as.sir()}}) are transformed using \code{"S"} = 1, \code{"I"} = 2, and \code{"R"} = 3. If \code{combine_SI} is \code{TRUE} (default), the \code{"I"} will be considered to be 1.
For data sets, the mean AMR distance will be calculated per column, after which the mean per row will be returned, see \emph{Examples}.
@@ -46,9 +46,9 @@ Isolates with distances less than 0.01 difference from each other should be cons
}
\examples{
rsi <- random_rsi(10)
rsi
mean_amr_distance(rsi)
sir <- random_sir(10)
sir
mean_amr_distance(sir)
mic <- random_mic(10)
mic
@@ -62,7 +62,7 @@ mean_amr_distance(disk)
y <- data.frame(
id = LETTERS[1:10],
amox = random_rsi(10, ab = "amox", mo = "Escherichia coli"),
amox = random_sir(10, ab = "amox", mo = "Escherichia coli"),
cipr = random_disk(10, ab = "cipr", mo = "Escherichia coli"),
gent = random_mic(10, ab = "gent", mo = "Escherichia coli"),
tobr = random_mic(10, ab = "tobr", mo = "Escherichia coli")