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AMR
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(v1.3.0) v1.3.0

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dr. M.S. (Matthijs) Berends 2020-07-29 13:48:50 +02:00
parent de0f7b8950
commit ea4e5e5b81
15 changed files with 68 additions and 73 deletions
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2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR
Version: 1.2.0.9040
Version: 1.3.0
Date: 2020-07-29
Title: Antimicrobial Resistance Analysis
Authors@R: c(

4
NEWS.md
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@ -1,5 +1,5 @@
# AMR 1.2.0.9040
## <small>Last updated: 29 July 2020</small>
# AMR 1.3.0
### New
* Function `ab_from_text()` to retrieve antimicrobial drug names, doses and forms of administration from clinical texts in e.g. health care records, which also corrects for misspelling since it uses `as.ab()` internally

68
R/rsi.R
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@ -143,6 +143,40 @@ as.rsi <- function(x, ...) {
UseMethod("as.rsi")
}
#' @rdname as.rsi
#' @export
is.rsi <- function(x) {
inherits(x, "rsi")
}
#' @rdname as.rsi
#' @export
is.rsi.eligible <- function(x, threshold = 0.05) {
stop_if(NCOL(x) > 1, "`x` must be a one-dimensional vector.")
if (any(c("logical",
"numeric",
"integer",
"mo",
"Date",
"POSIXct",
"rsi",
"raw",
"hms")
%in% class(x))) {
# no transformation needed
FALSE
} else {
x <- x[!is.na(x) & !is.null(x) & !identical(x, "")]
if (length(x) == 0) {
return(FALSE)
}
checked <- suppressWarnings(as.rsi(x))
outcome <- sum(is.na(checked)) / length(x)
outcome <= threshold
}
}
#' @export
as.rsi.default <- function(x, ...) {
if (is.rsi(x)) {
@ -513,40 +547,6 @@ exec_as.rsi <- function(method, x, mo, ab, guideline, uti, conserve_capped_value
class = c("rsi", "ordered", "factor"))
}
#' @rdname as.rsi
#' @export
is.rsi <- function(x) {
inherits(x, "rsi")
}
#' @rdname as.rsi
#' @export
is.rsi.eligible <- function(x, threshold = 0.05) {
stop_if(NCOL(x) > 1, "`x` must be a one-dimensional vector.")
if (any(c("logical",
"numeric",
"integer",
"mo",
"Date",
"POSIXct",
"rsi",
"raw",
"hms")
%in% class(x))) {
# no transformation needed
FALSE
} else {
x <- x[!is.na(x) & !is.null(x) & !identical(x, "")]
if (length(x) == 0) {
return(FALSE)
}
checked <- suppressWarnings(as.rsi(x))
outcome <- sum(is.na(checked)) / length(x)
outcome <= threshold
}
}
#' @method print rsi
#' @export
#' @noRd

2
docs/404.html
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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9040</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
</span>
</div>

2
docs/LICENSE-text.html
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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9040</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
</span>
</div>

2
docs/articles/index.html
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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9040</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
</span>
</div>

2
docs/authors.html
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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9040</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
</span>
</div>

2
docs/index.html
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@ -43,7 +43,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9040</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
</span>
</div>

13
docs/news/index.html
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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9040</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
</span>
</div>
@ -229,14 +229,10 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
<div id="amr-1209040" class="section level1">
<h1 class="page-header" data-toc-text="1.2.0.9040">
<a href="#amr-1209040" class="anchor"></a>AMR 1.2.0.9040<small> Unreleased </small>
<div id="amr-130" class="section level1">
<h1 class="page-header" data-toc-text="1.3.0">
<a href="#amr-130" class="anchor"></a>AMR 1.3.0<small> Unreleased </small>
</h1>
<div id="last-updated-29-july-2020" class="section level2">
<h2 class="hasAnchor">
<a href="#last-updated-29-july-2020" class="anchor"></a><small>Last updated: 29 July 2020</small>
</h2>
<div id="new" class="section level3">
<h3 class="hasAnchor">
<a href="#new" class="anchor"></a>New</h3>
@ -311,7 +307,6 @@
<li>Moved primary location of this project from GitLab to <a href="https://github.com/msberends/AMR">GitHub</a>, giving us native support for automated syntax checking without being dependent on external services such as AppVeyor and Travis CI.</li>
</ul>
</div>
</div>
</div>
<div id="amr-120" class="section level1">
<h1 class="page-header" data-toc-text="1.2.0">

2
docs/pkgdown.yml
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@ -10,7 +10,7 @@ articles:
WHONET: WHONET.html
benchmarks: benchmarks.html
resistance_predict: resistance_predict.html
last_built: 2020-07-29T10:44Z
last_built: 2020-07-29T11:47Z
urls:
reference: https://msberends.github.io/AMR/reference
article: https://msberends.github.io/AMR/articles

20
docs/reference/as.rsi.html
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@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9040</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
</span>
</div>
@ -237,6 +237,10 @@
<pre class="usage"><span class='fu'>as.rsi</span>(<span class='no'>x</span>, <span class='no'>...</span>)
<span class='fu'>is.rsi</span>(<span class='no'>x</span>)
<span class='fu'>is.rsi.eligible</span>(<span class='no'>x</span>, <span class='kw'>threshold</span> <span class='kw'>=</span> <span class='fl'>0.05</span>)
<span class='co'># S3 method for mic</span>
<span class='fu'>as.rsi</span>(
<span class='no'>x</span>,
@ -266,11 +270,7 @@
<span class='kw'>uti</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>conserve_capped_values</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='no'>...</span>
)
<span class='fu'>is.rsi</span>(<span class='no'>x</span>)
<span class='fu'>is.rsi.eligible</span>(<span class='no'>x</span>, <span class='kw'>threshold</span> <span class='kw'>=</span> <span class='fl'>0.05</span>)</pre>
)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@ -283,6 +283,10 @@
<th>...</th>
<td><p>parameters passed on to methods</p></td>
</tr>
<tr>
<th>threshold</th>
<td><p>maximum fraction of invalid antimicrobial interpretations of <code>x</code>, please see <em>Examples</em></p></td>
</tr>
<tr>
<th>mo</th>
<td><p>any (vector of) text that can be coerced to a valid microorganism code with <code><a href='as.mo.html'>as.mo()</a></code></p></td>
@ -307,10 +311,6 @@
<th>col_mo</th>
<td><p>column name of the IDs of the microorganisms (see <code><a href='as.mo.html'>as.mo()</a></code>), defaults to the first column of class <code><a href='as.mo.html'>mo</a></code>. Values will be coerced using <code><a href='as.mo.html'>as.mo()</a></code>.</p></td>
</tr>
<tr>
<th>threshold</th>
<td><p>maximum fraction of invalid antimicrobial interpretations of <code>x</code>, please see <em>Examples</em></p></td>
</tr>
</table>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>

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docs/reference/index.html
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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9040</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
</span>
</div>

2
docs/reference/rsi_translation.html
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@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9038</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
</span>
</div>

2
docs/survey.html
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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9040</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
</span>
</div>

16
man/as.rsi.Rd
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@ -3,15 +3,19 @@
\name{as.rsi}
\alias{as.rsi}
\alias{rsi}
\alias{is.rsi}
\alias{is.rsi.eligible}
\alias{as.rsi.mic}
\alias{as.rsi.disk}
\alias{as.rsi.data.frame}
\alias{is.rsi}
\alias{is.rsi.eligible}
\title{Class 'rsi'}
\usage{
as.rsi(x, ...)
is.rsi(x)
is.rsi.eligible(x, threshold = 0.05)
\method{as.rsi}{mic}(
x,
mo,
@ -39,16 +43,14 @@ as.rsi(x, ...)
conserve_capped_values = FALSE,
...
)
is.rsi(x)
is.rsi.eligible(x, threshold = 0.05)
}
\arguments{
\item{x}{vector of values (for class \code{\link{mic}}: an MIC value in mg/L, for class \code{\link{disk}}: a disk diffusion radius in millimetres)}
\item{...}{parameters passed on to methods}
\item{threshold}{maximum fraction of invalid antimicrobial interpretations of \code{x}, please see \emph{Examples}}
\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()}}}
@ -60,8 +62,6 @@ is.rsi.eligible(x, threshold = 0.05)
\item{conserve_capped_values}{a logical to indicate that MIC values starting with \code{">"} (but not \code{">="}) must always return "R" , and that MIC values starting with \code{"<"} (but not \code{"<="}) must always return "S"}
\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{threshold}{maximum fraction of invalid antimicrobial interpretations of \code{x}, please see \emph{Examples}}
}
\value{
Ordered factor with new class \code{\link{rsi}}