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(v1.4.0.9044) mo tibble printing, mo_shortname() fix

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dr. M.S. (Matthijs) Berends
2020-12-24 23:29:10 +01:00
parent 128ebcfd62
commit df37584189
96 changed files with 1039 additions and 2847 deletions
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39
docs/reference/AMR-deprecated.html
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@@ -6,22 +6,6 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
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and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
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// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
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document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
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);
}
</script>
<title>Deprecated functions — AMR-deprecated • AMR (for R)</title>
<!-- favicons -->
@@ -36,21 +20,10 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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<script src="../bootstrap-toc.js"></script>
@@ -86,9 +59,6 @@
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<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -112,7 +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">1.4.0.9042</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
</div>
@@ -236,7 +206,6 @@
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -303,7 +272,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>retired</
</div>
<div class="pkgdown">
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
</div>
</footer>

39
docs/reference/AMR.html
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@@ -6,22 +6,6 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
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and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
<script>
// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>The AMR Package — AMR • AMR (for R)</title>
<!-- favicons -->
@@ -36,21 +20,10 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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<link rel="stylesheet" href="../bootstrap-toc.css">
<script src="../bootstrap-toc.js"></script>
@@ -86,9 +59,6 @@
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<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -112,7 +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">1.4.0.9042</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
</div>
@@ -236,7 +206,6 @@
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -341,7 +310,7 @@ The Netherlands
</div>
<div class="pkgdown">
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
</div>
</footer>

39
docs/reference/WHOCC.html
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@@ -6,22 +6,6 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<!-- Inform modern browsers that this page supports both dark and light color schemes,
and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
<script>
// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>WHOCC: WHO Collaborating Centre for Drug Statistics Methodology — WHOCC • AMR (for R)</title>
<!-- favicons -->
@@ -36,21 +20,10 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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<link rel="stylesheet" href="../bootstrap-toc.css">
<script src="../bootstrap-toc.js"></script>
@@ -86,9 +59,6 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -112,7 +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">1.4.0.9042</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
</div>
@@ -236,7 +206,6 @@
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -311,7 +280,7 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
</div>
<div class="pkgdown">
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
</div>
</footer>

39
docs/reference/WHONET.html
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@@ -6,22 +6,6 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<!-- Inform modern browsers that this page supports both dark and light color schemes,
and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
<script>
// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>Data set with 500 isolates - WHONET example — WHONET • AMR (for R)</title>
<!-- favicons -->
@@ -36,21 +20,10 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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<!-- bootstrap-toc -->
<link rel="stylesheet" href="../bootstrap-toc.css">
<script src="../bootstrap-toc.js"></script>
@@ -86,9 +59,6 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -112,7 +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">1.4.0.9042</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
</div>
@@ -236,7 +206,6 @@
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -333,7 +302,7 @@
</div>
<div class="pkgdown">
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
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</footer>

39
docs/reference/ab_from_text.html
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@@ -6,22 +6,6 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
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and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
<script>
// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>Retrieve antimicrobial drug names and doses from clinical text — ab_from_text • AMR (for R)</title>
<!-- favicons -->
@@ -36,21 +20,10 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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<!-- bootstrap-toc -->
<link rel="stylesheet" href="../bootstrap-toc.css">
<script src="../bootstrap-toc.js"></script>
@@ -86,9 +59,6 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -112,7 +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">1.4.0.9043</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
</div>
@@ -236,7 +206,6 @@
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -394,7 +363,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
</div>
<div class="pkgdown">
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
</div>
</footer>

39
docs/reference/ab_property.html
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@@ -6,22 +6,6 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<!-- Inform modern browsers that this page supports both dark and light color schemes,
and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
<script>
// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>Get properties of an antibiotic — ab_property • AMR (for R)</title>
<!-- favicons -->
@@ -36,21 +20,10 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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@@ -86,9 +59,6 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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@@ -112,7 +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">1.4.0.9043</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
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@@ -236,7 +206,6 @@
</li>
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<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -432,7 +401,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
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39
docs/reference/age.html
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@@ -6,22 +6,6 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
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and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
<script>
// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
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document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>Age in years of individuals — age • AMR (for R)</title>
<!-- favicons -->
@@ -36,21 +20,10 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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@@ -86,9 +59,6 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -112,7 +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">1.4.0.9043</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
</div>
@@ -236,7 +206,6 @@
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -347,7 +316,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
</div>
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39
docs/reference/age_groups.html
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@@ -6,22 +6,6 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
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and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
<script>
// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>Split ages into age groups — age_groups • AMR (for R)</title>
<!-- favicons -->
@@ -36,21 +20,10 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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<script src="../bootstrap-toc.js"></script>
@@ -86,9 +59,6 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -112,7 +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">1.4.0.9043</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
</div>
@@ -236,7 +206,6 @@
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -372,7 +341,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
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39
docs/reference/antibiotic_class_selectors.html
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@@ -6,22 +6,6 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
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and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
<script>
// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>Antibiotic class selectors — antibiotic_class_selectors • AMR (for R)</title>
<!-- favicons -->
@@ -36,21 +20,10 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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<link rel="stylesheet" href="../bootstrap-toc.css">
<script src="../bootstrap-toc.js"></script>
@@ -86,9 +59,6 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -112,7 +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">1.4.0.9042</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
</div>
@@ -236,7 +206,6 @@
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -373,7 +342,7 @@
</div>
<div class="pkgdown">
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
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39
docs/reference/antibiotics.html
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@@ -6,22 +6,6 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
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and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
<script>
// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>Data sets with 557 antimicrobials — antibiotics • AMR (for R)</title>
<!-- favicons -->
@@ -36,21 +20,10 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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<link rel="stylesheet" href="../bootstrap-toc.css">
<script src="../bootstrap-toc.js"></script>
@@ -86,9 +59,6 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
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<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -112,7 +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">1.4.0.9042</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
</div>
@@ -236,7 +206,6 @@
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -377,7 +346,7 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
</div>
<div class="pkgdown">
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
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39
docs/reference/as.ab.html
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@@ -6,22 +6,6 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
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and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
<script>
// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>Transform input to an antibiotic ID — as.ab • AMR (for R)</title>
<!-- favicons -->
@@ -36,21 +20,10 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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@@ -86,9 +59,6 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -112,7 +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">1.4.0.9043</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
</div>
@@ -236,7 +206,6 @@
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -394,7 +363,7 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
</div>
<div class="pkgdown">
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
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39
docs/reference/as.disk.html
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@@ -6,22 +6,6 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
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and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
<script>
// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
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"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>Transform input to disk diffusion diameters — as.disk • AMR (for R)</title>
<!-- favicons -->
@@ -36,21 +20,10 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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@@ -86,9 +59,6 @@
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@@ -112,7 +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">1.4.0.9043</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
</div>
@@ -236,7 +206,6 @@
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -348,7 +317,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
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39
docs/reference/as.mic.html
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@@ -6,22 +6,6 @@
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<meta name="viewport" content="width=device-width, initial-scale=1.0">
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and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
<script>
// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
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"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>Transform input to minimum inhibitory concentrations (MIC) — as.mic • AMR (for R)</title>
<!-- favicons -->
@@ -36,21 +20,10 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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@@ -86,9 +59,6 @@
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<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -112,7 +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">1.4.0.9043</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
</div>
@@ -236,7 +206,6 @@
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -347,7 +316,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
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39
docs/reference/as.mo.html
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@@ -6,22 +6,6 @@
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and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
<script>
// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
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"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>Transform input to a microorganism ID — as.mo • AMR (for R)</title>
<!-- favicons -->
@@ -36,21 +20,10 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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<script src="../bootstrap-toc.js"></script>
@@ -86,9 +59,6 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -112,7 +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">1.4.0.9043</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
</div>
@@ -236,7 +206,6 @@
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -506,7 +475,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
</div>
<div class="pkgdown">
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
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39
docs/reference/as.rsi.html
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@@ -6,22 +6,6 @@
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and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
<script>
// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>Interpret MIC and disk values, or clean raw R/SI data — as.rsi • AMR (for R)</title>
<!-- favicons -->
@@ -36,21 +20,10 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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<script src="../bootstrap-toc.js"></script>
@@ -86,9 +59,6 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -112,7 +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">1.4.0.9043</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
</div>
@@ -236,7 +206,6 @@
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -547,7 +516,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
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39
docs/reference/atc_online.html
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@@ -6,22 +6,6 @@
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<meta name="viewport" content="width=device-width, initial-scale=1.0">
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and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
<script>
// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
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document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>Get ATC properties from WHOCC website — atc_online_property • AMR (for R)</title>
<!-- favicons -->
@@ -36,21 +20,10 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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@@ -86,9 +59,6 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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@@ -112,7 +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">1.4.0.9043</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
</div>
@@ -236,7 +206,6 @@
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -383,7 +352,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
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39
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<meta name="color-scheme" content="dark light">
<script>
// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
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document.documentElement.style.display = "none";
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<title>Check availability of columns — availability • AMR (for R)</title>
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</div>
<div class="pkgdown">
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@@ -6,22 +6,6 @@
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<title>Determine bug-drug combinations — bug_drug_combinations • AMR (for R)</title>
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<span class="navbar-brand">
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
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<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -403,7 +372,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
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39
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@@ -6,22 +6,6 @@
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<title>The Catalogue of Life — catalogue_of_life • AMR (for R)</title>
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@@ -112,7 +82,7 @@
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
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</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -352,7 +321,7 @@ Function <code><a href='as.mo.html'>as.mo()</a></code> to use the data for intel
</div>
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@@ -6,22 +6,6 @@
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<title>Version info of included Catalogue of Life — catalogue_of_life_version • AMR (for R)</title>
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@@ -36,21 +20,10 @@
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@@ -112,7 +82,7 @@
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
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@@ -236,7 +206,6 @@
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@@ -313,7 +282,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
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<title>Count available isolates — count • AMR (for R)</title>
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@@ -87,9 +60,6 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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@@ -113,7 +83,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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@@ -237,7 +207,6 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
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<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">1.4.0.9042</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
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<li>
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<span class="fab fa-github"></span>
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<title>Filter isolates on result in antimicrobial class — filter_ab_class • AMR (for R)</title>
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</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">1.4.0.9043</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
</div>
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<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -395,7 +364,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
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@@ -112,7 +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">1.4.0.9043</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
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<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
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<title>G-test for Count Data — g.test • AMR (for R)</title>
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</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">1.4.0.9042</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
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<ul class="nav navbar-nav navbar-right">
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<span class="fab fa-github"></span>
@@ -434,7 +403,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
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<title>PCA biplot with ggplot2 — ggplot_pca • AMR (for R)</title>
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@@ -112,7 +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">1.4.0.9043</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
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@@ -236,7 +206,6 @@
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docs/reference/intrinsic_resistant.html
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
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docs/reference/is_new_episode.html
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</button>
<span class="navbar-brand">
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
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<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
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@@ -372,7 +341,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
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<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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@@ -112,7 +82,7 @@
</button>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
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</li>
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<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -360,7 +329,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
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@@ -6,22 +6,6 @@
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<meta name="viewport" content="width=device-width, initial-scale=1.0">
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and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
<script>
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// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
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document.documentElement.style.display = "none";
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"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>Key antibiotics for first weighted isolates — key_antibiotics • AMR (for R)</title>
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@@ -36,21 +20,10 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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<script src="../bootstrap-toc.js"></script>
@@ -86,9 +59,6 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -112,7 +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">1.4.0.9043</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
</div>
@@ -236,7 +206,6 @@
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -471,7 +440,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
</div>
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@@ -6,22 +6,6 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
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and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
<script>
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// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
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"beforeend",
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);
}
</script>
<title>Kurtosis of the sample — kurtosis • AMR (for R)</title>
<!-- favicons -->
@@ -36,21 +20,10 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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@@ -86,9 +59,6 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -112,7 +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">1.4.0.9043</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
</div>
@@ -236,7 +206,6 @@
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -332,7 +301,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
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39
docs/reference/lifecycle.html
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<meta name="color-scheme" content="dark light">
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// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>Lifecycles of functions in the AMR package — lifecycle • AMR (for R)</title>
<!-- favicons -->
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<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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@@ -88,9 +61,6 @@ This page contains a section for every lifecycle (with text borrowed from the af
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -114,7 +84,7 @@ This page contains a section for every lifecycle (with text borrowed from the af
</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">1.4.0.9043</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
</div>
@@ -238,7 +208,6 @@ This page contains a section for every lifecycle (with text borrowed from the af
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -326,7 +295,7 @@ The lifecycle of this function is <strong>questioning</strong>. This function mi
</div>
<div class="pkgdown">
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
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@@ -6,22 +6,6 @@
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<meta name="viewport" content="width=device-width, initial-scale=1.0">
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and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
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// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>Pattern matching with keyboard shortcut — like • AMR (for R)</title>
<!-- favicons -->
@@ -36,21 +20,10 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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<script src="../bootstrap-toc.js"></script>
@@ -86,9 +59,6 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -112,7 +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">1.4.0.9043</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
</div>
@@ -236,7 +206,6 @@
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -366,7 +335,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
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39
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@@ -6,22 +6,6 @@
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<meta name="viewport" content="width=device-width, initial-scale=1.0">
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and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
<script>
// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>Data set with 5,583 common microorganism codes — microorganisms.codes • AMR (for R)</title>
<!-- favicons -->
@@ -36,21 +20,10 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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@@ -86,9 +59,6 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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@@ -112,7 +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">1.4.0.9042</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
</div>
@@ -236,7 +206,6 @@
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
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@@ -319,7 +288,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
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<title>Data set with 67,151 microorganisms — microorganisms • AMR (for R)</title>
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@@ -112,7 +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">1.4.0.9042</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
</div>
@@ -236,7 +206,6 @@
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@@ -362,7 +331,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
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<title>Data set with previously accepted taxonomic names — microorganisms.old • AMR (for R)</title>
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@@ -36,21 +20,10 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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@@ -112,7 +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">1.4.0.9042</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
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@@ -236,7 +206,6 @@
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@@ -325,7 +294,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
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<title>Calculate the matching score for microorganisms — mo_matching_score • AMR (for R)</title>
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<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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@@ -112,7 +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">1.4.0.9043</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
</div>
@@ -236,7 +206,6 @@
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<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -338,7 +307,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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// i.e. In this case, inject the `light` CSS before the others, with
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if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
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"beforeend",
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<title>Get properties of a microorganism — mo_property • AMR (for R)</title>
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<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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@@ -112,7 +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">1.4.0.9043</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
</div>
@@ -236,7 +206,6 @@
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -332,7 +301,7 @@
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>x</th>
<td><p>any character (vector) that can be coerced to a valid microorganism code with <code><a href='as.mo.html'>as.mo()</a></code>. Can be omitted for auto-guessing in <code>mo_is_*()</code> functions when used inside <code>dplyr</code> verbs, such as <code><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter()</a></code>, <code><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate()</a></code> and <code><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise()</a></code>, please see <em>Examples</em>.</p></td>
<td><p>any character (vector) that can be coerced to a valid microorganism code with <code><a href='as.mo.html'>as.mo()</a></code>. Can be omitted for auto-guessing the column containing microorganism codes when used inside <code>dplyr</code> verbs, such as <code><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter()</a></code>, <code><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate()</a></code> and <code><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise()</a></code>, please see <em>Examples</em>.</p></td>
</tr>
<tr>
<th>language</th>
@@ -348,7 +317,7 @@
</tr>
<tr>
<th>open</th>
<td><p>browse the URL using <code><a href='https://rdrr.io/r/utils/browseURL.html'>utils::browseURL()</a></code></p></td>
<td><p>browse the URL using <code><a href='https://rdrr.io/r/utils/browseURL.html'>browseURL()</a></code></p></td>
</tr>
<tr>
<th>property</th>
@@ -550,7 +519,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
</div>
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if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
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);
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<title>User-defined reference data set for microorganisms — mo_source • AMR (for R)</title>
<!-- favicons -->
@@ -36,21 +20,10 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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@@ -76,8 +49,8 @@
<script src="../extra.js"></script>
<meta property="og:title" content="User-defined reference data set for microorganisms — mo_source" />
<meta property="og:description" content="These functions can be used to predefine your own reference to be used in as.mo() and consequently all mo_* functions like mo_genus() and mo_gramstain().
This is the fastest way to have your organisation (or analysis) specific codes picked up and translated by this package." />
<meta property="og:description" content="These functions can be used to predefine your own reference to be used in as.mo() and consequently all mo_* functions (such as mo_genus() and mo_gramstain()).
This is the fastest way to have your organisation (or analysis) specific codes picked up and translated by this package, since you don't have to bother about it again after setting it up once." />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.png" />
@@ -87,9 +60,6 @@ This is the fastest way to have your organisation (or analysis) specific codes p
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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@@ -113,7 +83,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
</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">1.4.0.9043</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
</div>
@@ -237,7 +207,6 @@ This is the fastest way to have your organisation (or analysis) specific codes p
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -271,8 +240,8 @@ This is the fastest way to have your organisation (or analysis) specific codes p
</div>
<div class="ref-description">
<p>These functions can be used to predefine your own reference to be used in <code><a href='as.mo.html'>as.mo()</a></code> and consequently all <code>mo_*</code> functions like <code><a href='mo_property.html'>mo_genus()</a></code> and <code><a href='mo_property.html'>mo_gramstain()</a></code>.</p>
<p>This is <strong>the fastest way</strong> to have your organisation (or analysis) specific codes picked up and translated by this package.</p>
<p>These functions can be used to predefine your own reference to be used in <code><a href='as.mo.html'>as.mo()</a></code> and consequently all <code><a href='mo_property.html'>mo_*</a></code> functions (such as <code><a href='mo_property.html'>mo_genus()</a></code> and <code><a href='mo_property.html'>mo_gramstain()</a></code>).</p>
<p>This is <strong>the fastest way</strong> to have your organisation (or analysis) specific codes picked up and translated by this package, since you don't have to bother about it again after setting it up once.</p>
</div>
<pre class="usage"><span class='fu'>set_mo_source</span><span class='op'>(</span>
@@ -348,7 +317,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
<p>...any new usage of an MO function in this package will update your data file:</p><pre><span class='fu'><a href='as.mo.html'>as.mo</a></span><span class='op'>(</span><span class='st'>"lab_mo_ecoli"</span><span class='op'>)</span>
<span class='co'>#&gt; NOTE: Updated mo_source file '/Users/me/mo_source.rds' (0.3 kB) from </span>
<span class='co'>#&gt; '/Users/me/Documents/ourcodes.xlsx' (9 kB), columns</span>
<span class='co'>#&gt; '/Users/me/Documents/ourcodes.xlsx' (9 kB), columns</span>
<span class='co'>#&gt; "Organisation XYZ" and "mo"</span>
<span class='co'>#&gt; Class &lt;mo&gt;</span>
<span class='co'>#&gt; [1] B_ESCHR_COLI</span>
@@ -361,7 +330,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
<span class='co'>#&gt; Removed mo_source file '/Users/me/mo_source.rds'</span>
</pre>
<p>If the original Excel file is moved or deleted, the mo_source file will be removed upon the next use of <code><a href='as.mo.html'>as.mo()</a></code>.</p>
<p>If the original file (in the previous case an Excel file) is moved or deleted, the <code>mo_source.rds</code> file will be removed upon the next use of <code><a href='as.mo.html'>as.mo()</a></code> or any <code><a href='mo_property.html'>mo_*</a></code> function.</p>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
@@ -390,7 +359,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
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39
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@@ -6,22 +6,6 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<!-- Inform modern browsers that this page supports both dark and light color schemes,
and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
<script>
// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>Principal Component Analysis (for AMR) — pca • AMR (for R)</title>
<!-- favicons -->
@@ -36,21 +20,10 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
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<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
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<!-- bootstrap-toc -->
<link rel="stylesheet" href="../bootstrap-toc.css">
<script src="../bootstrap-toc.js"></script>
@@ -86,9 +59,6 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
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<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -112,7 +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">1.4.0.9042</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
</div>
@@ -236,7 +206,6 @@
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -388,7 +357,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
</div>
<div class="pkgdown">
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
</div>
</footer>

39
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View File

@@ -6,22 +6,6 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<!-- Inform modern browsers that this page supports both dark and light color schemes,
and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
<script>
// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>Plotting for classes rsi, mic and disk — plot • AMR (for R)</title>
<!-- favicons -->
@@ -36,21 +20,10 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
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<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
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<!-- bootstrap-toc -->
<link rel="stylesheet" href="../bootstrap-toc.css">
<script src="../bootstrap-toc.js"></script>
@@ -86,9 +59,6 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
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<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -112,7 +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">1.4.0.9043</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
</div>
@@ -236,7 +206,6 @@
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -416,7 +385,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
</div>
</footer>

39
docs/reference/proportion.html
View File

@@ -6,22 +6,6 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<!-- Inform modern browsers that this page supports both dark and light color schemes,
and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
<script>
// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>Calculate microbial resistance — proportion • AMR (for R)</title>
<!-- favicons -->
@@ -36,21 +20,10 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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@@ -87,9 +60,6 @@ resistance() should be used to calculate resistance, susceptibility() should be
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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@@ -113,7 +83,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
</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">1.4.0.9043</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
</div>
@@ -237,7 +207,6 @@ resistance() should be used to calculate resistance, susceptibility() should be
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -511,7 +480,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
</div>
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@@ -6,22 +6,6 @@
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<meta name="viewport" content="width=device-width, initial-scale=1.0">
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and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
<script>
// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>Random MIC values/disk zones/RSI generation — random • AMR (for R)</title>
<!-- favicons -->
@@ -36,21 +20,10 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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@@ -86,9 +59,6 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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@@ -112,7 +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">1.4.0.9043</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
</div>
@@ -236,7 +206,6 @@
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -354,7 +323,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
</div>
<div class="pkgdown">
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
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39
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@@ -6,22 +6,6 @@
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and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
<script>
// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>Predict antimicrobial resistance — resistance_predict • AMR (for R)</title>
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@@ -36,21 +20,10 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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@@ -86,9 +59,6 @@
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@@ -112,7 +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">1.4.0.9043</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
</div>
@@ -236,7 +206,6 @@
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</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -491,7 +460,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
</div>
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document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
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<title>Data set for R/SI interpretation — rsi_translation • AMR (for R)</title>
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@@ -36,21 +20,10 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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@@ -112,7 +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">1.4.0.9042</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
</div>
@@ -236,7 +206,6 @@
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<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -323,7 +292,7 @@
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<div class="pkgdown">
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docs/reference/skewness.html
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"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
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<title>Skewness of the sample — skewness • AMR (for R)</title>
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<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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@@ -87,9 +60,6 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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@@ -113,7 +83,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
</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">1.4.0.9043</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
</div>
@@ -237,7 +207,6 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
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@@ -330,7 +299,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
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<title>Translate strings from AMR package — translate • AMR (for R)</title>
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@@ -86,9 +59,6 @@
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@@ -112,7 +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">1.4.0.9043</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
</div>
@@ -236,7 +206,6 @@
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<li>
<a href="https://github.com/msberends/AMR">
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@@ -347,7 +316,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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