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\encoding{UTF-8}
\name{coords_transpose}
\alias{coords_transpose}
\title{Transposing the output of \code{coords}}
\description{This help page desribes recent and upcoming changes in the
return values of the \code{\link{coords}} function.}
\section{Background information}{
Until the release of pROC 1.16, the \code{coords} function was returning
a matrix with thresholds in columns, and the coordinate variables in rows.
\preformatted{
data(aSAH)
rocobj <- roc(aSAH$outcome, aSAH$s100b)
coords(rocobj, c(0.05, 0.2, 0.5))
# 0.05 0.2 0.5
# threshold 0.05000000 0.2000000 0.5000000
# specificity 0.06944444 0.8055556 0.9722222
# sensitivity 0.97560976 0.6341463 0.2926829
}
This format didn't conform to the grammar of the
\href{https://www.tidyverse.org/}{tidyverse} which has become prevalent in modern
R language.
In addition, the dropping of dimensions by default makes it difficult to guess
what type of data \code{coords} is going to return.
\preformatted{
coords(rocobj, "best")
# threshold specificity sensitivity
# 0.2050000 0.8055556 0.6341463
# A numeric vector
}
Although it is possible to pass \code{drop = FALSE}, the fact that it is not the
default makes the behaviour unintuitive.
In pROC version 1.16, this was changed and \code{coords} now returns
a \code{\link{data.frame}} with the thresholds in rows and measurement in colums by default.
\preformatted{
coords(rocobj, c(0.05, 0.2, 0.5), transpose = FALSE)
# threshold specificity sensitivity
# 0.05 0.05 0.06944444 0.9756098
# 0.2 0.20 0.80555556 0.6341463
# 0.5 0.50 0.97222222 0.2926829
}
}
\section{Changes in 1.15}{
\enumerate{
\item{Addition of the \code{transpose} argument.}
\item{Display a warning if \code{transpose} is missing. Pass \code{transpose} explicitly to silence the warning.}
\item{Deprecation of \code{as.list}.}
}
}
\section{Changes in 1.16}{
\enumerate{
\item{Change of the default \code{transpose} to \code{TRUE}.}
}
THIS CHANGE IS BACKWARDS INCOMPATIBLE AND IS EXPECTED TO BREAK LEGACY CODE.
}
\section{Changes in 1.17}{
\enumerate{
\item{Dropped the warning if \code{transpose} is missing.}
}
}
\section{Changes in future versions}{
\enumerate{
\item{Support for the \code{as.list} argument might be dropped in the future.
This is still under consideration.}
\item{
The \code{transpose} and \code{drop} arguments might be deprecated in the future, but will remain available for a few additional major versions.
}
}
}
\section{Related changes in ci.coords}{
In version 1.16, the format of the \code{\link{ci.coords}} return value was changed from a matrix-like object with mixed \code{x} and \code{ret} in rows and 3 columns, into a list-like object which should be easier to use programatically.
}
\section{Recommendations}{
If you are writing a new script calling the \code{coords} function, set \code{transpose = FALSE} to silence the warning and benefit from the latest improvements in pROC and obtain a tidy data.
}
\section{See also}{
\href{https://github.com/xrobin/pROC/issues/54}{The GitHub issue tracking the changes described in this manual page}.
}
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