mirror of https://github.com/msberends/AMR.git
(v1.3.0) v1.3.0
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Package: AMR
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Version: 1.2.0.9040
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Version: 1.3.0
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Date: 2020-07-29
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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4
NEWS.md
4
NEWS.md
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# AMR 1.2.0.9040
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## <small>Last updated: 29 July 2020</small>
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# AMR 1.3.0
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### New
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* 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
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68
R/rsi.R
68
R/rsi.R
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@ -143,6 +143,40 @@ as.rsi <- function(x, ...) {
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UseMethod("as.rsi")
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}
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#' @rdname as.rsi
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#' @export
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is.rsi <- function(x) {
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inherits(x, "rsi")
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}
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#' @rdname as.rsi
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#' @export
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is.rsi.eligible <- function(x, threshold = 0.05) {
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stop_if(NCOL(x) > 1, "`x` must be a one-dimensional vector.")
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if (any(c("logical",
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"numeric",
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"integer",
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"mo",
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"Date",
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"POSIXct",
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"rsi",
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"raw",
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"hms")
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%in% class(x))) {
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# no transformation needed
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FALSE
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} else {
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x <- x[!is.na(x) & !is.null(x) & !identical(x, "")]
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if (length(x) == 0) {
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return(FALSE)
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}
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checked <- suppressWarnings(as.rsi(x))
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outcome <- sum(is.na(checked)) / length(x)
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outcome <= threshold
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}
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}
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#' @export
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as.rsi.default <- function(x, ...) {
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if (is.rsi(x)) {
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@ -513,40 +547,6 @@ exec_as.rsi <- function(method, x, mo, ab, guideline, uti, conserve_capped_value
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class = c("rsi", "ordered", "factor"))
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}
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#' @rdname as.rsi
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#' @export
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is.rsi <- function(x) {
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inherits(x, "rsi")
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}
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#' @rdname as.rsi
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#' @export
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is.rsi.eligible <- function(x, threshold = 0.05) {
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stop_if(NCOL(x) > 1, "`x` must be a one-dimensional vector.")
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if (any(c("logical",
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"numeric",
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"integer",
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"mo",
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"Date",
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"POSIXct",
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"rsi",
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"raw",
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"hms")
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%in% class(x))) {
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# no transformation needed
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FALSE
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} else {
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x <- x[!is.na(x) & !is.null(x) & !identical(x, "")]
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if (length(x) == 0) {
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return(FALSE)
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}
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checked <- suppressWarnings(as.rsi(x))
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outcome <- sum(is.na(checked)) / length(x)
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outcome <= threshold
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}
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}
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#' @method print rsi
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#' @export
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#' @noRd
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9040</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
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</span>
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</div>
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9040</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
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</span>
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</div>
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9040</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
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</span>
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</div>
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9040</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
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</span>
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</div>
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9040</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
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</span>
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</div>
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9040</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
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</span>
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</div>
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<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
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</div>
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<div id="amr-1209040" class="section level1">
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<h1 class="page-header" data-toc-text="1.2.0.9040">
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<a href="#amr-1209040" class="anchor"></a>AMR 1.2.0.9040<small> Unreleased </small>
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<div id="amr-130" class="section level1">
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<h1 class="page-header" data-toc-text="1.3.0">
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<a href="#amr-130" class="anchor"></a>AMR 1.3.0<small> Unreleased </small>
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</h1>
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<div id="last-updated-29-july-2020" class="section level2">
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<h2 class="hasAnchor">
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<a href="#last-updated-29-july-2020" class="anchor"></a><small>Last updated: 29 July 2020</small>
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</h2>
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<div id="new" class="section level3">
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<h3 class="hasAnchor">
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<a href="#new" class="anchor"></a>New</h3>
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<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>
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</ul>
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</div>
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</div>
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</div>
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<div id="amr-120" class="section level1">
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<h1 class="page-header" data-toc-text="1.2.0">
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@ -10,7 +10,7 @@ articles:
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WHONET: WHONET.html
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benchmarks: benchmarks.html
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resistance_predict: resistance_predict.html
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last_built: 2020-07-29T10:44Z
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last_built: 2020-07-29T11:47Z
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urls:
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reference: https://msberends.github.io/AMR/reference
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article: https://msberends.github.io/AMR/articles
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@ -82,7 +82,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9040</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
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</span>
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</div>
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<pre class="usage"><span class='fu'>as.rsi</span>(<span class='no'>x</span>, <span class='no'>...</span>)
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<span class='fu'>is.rsi</span>(<span class='no'>x</span>)
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<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>)
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<span class='co'># S3 method for mic</span>
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<span class='fu'>as.rsi</span>(
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<span class='no'>x</span>,
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<span class='kw'>uti</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
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<span class='kw'>conserve_capped_values</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
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<span class='no'>...</span>
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)
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<span class='fu'>is.rsi</span>(<span class='no'>x</span>)
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<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>
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)</pre>
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<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
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<table class="ref-arguments">
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<th>...</th>
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<td><p>parameters passed on to methods</p></td>
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</tr>
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<tr>
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<th>threshold</th>
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<td><p>maximum fraction of invalid antimicrobial interpretations of <code>x</code>, please see <em>Examples</em></p></td>
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</tr>
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<tr>
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<th>mo</th>
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<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>
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<th>col_mo</th>
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<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>
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</tr>
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<tr>
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<th>threshold</th>
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<td><p>maximum fraction of invalid antimicrobial interpretations of <code>x</code>, please see <em>Examples</em></p></td>
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</tr>
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</table>
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<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9040</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
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</span>
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</div>
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9038</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
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</span>
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</div>
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9040</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
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</span>
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</div>
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\name{as.rsi}
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\alias{as.rsi}
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\alias{rsi}
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\alias{is.rsi}
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\alias{is.rsi.eligible}
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\alias{as.rsi.mic}
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\alias{as.rsi.disk}
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\alias{as.rsi.data.frame}
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\alias{is.rsi}
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\alias{is.rsi.eligible}
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\title{Class 'rsi'}
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\usage{
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as.rsi(x, ...)
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is.rsi(x)
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is.rsi.eligible(x, threshold = 0.05)
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\method{as.rsi}{mic}(
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x,
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mo,
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conserve_capped_values = FALSE,
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...
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)
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is.rsi(x)
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is.rsi.eligible(x, threshold = 0.05)
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}
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\arguments{
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\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)}
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\item{...}{parameters passed on to methods}
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\item{threshold}{maximum fraction of invalid antimicrobial interpretations of \code{x}, please see \emph{Examples}}
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\item{mo}{any (vector of) text that can be coerced to a valid microorganism code with \code{\link[=as.mo]{as.mo()}}}
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\item{ab}{any (vector of) text that can be coerced to a valid antimicrobial code with \code{\link[=as.ab]{as.ab()}}}
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\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"}
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\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()}}.}
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\item{threshold}{maximum fraction of invalid antimicrobial interpretations of \code{x}, please see \emph{Examples}}
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}
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\value{
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Ordered factor with new class \code{\link{rsi}}
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