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@ -80,7 +80,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9024</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9025</span>
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</span>
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</div>
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@ -252,7 +252,7 @@
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<span class='fu'>mo_renamed</span>()
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<span class='fu'>clean_mo_history</span>()</pre>
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<span class='fu'>clean_mo_history</span>(<span class='no'>...</span>)</pre>
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<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
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<table class="ref-arguments">
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@ -263,12 +263,12 @@
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</tr>
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<tr>
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<th>Becker</th>
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<td><p>a logical to indicate whether <em>Staphylococci</em> should be categorised into Coagulase Negative <em>Staphylococci</em> ("CoNS") and Coagulase Positive <em>Staphylococci</em> ("CoPS") instead of their own species, according to Karsten Becker <em>et al.</em> [1]. Note that this does not include species that were newly named after this publication.</p>
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<td><p>a logical to indicate whether <em>Staphylococci</em> should be categorised into coagulase-negative <em>Staphylococci</em> ("CoNS") and coagulase-positive <em>Staphylococci</em> ("CoPS") instead of their own species, according to Karsten Becker <em>et al.</em> [1,2]. Note that this does not include species that were newly named after these publications, like <em>S. caeli</em>.</p>
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<p>This excludes <em>Staphylococcus aureus</em> at default, use <code>Becker = "all"</code> to also categorise <em>S. aureus</em> as "CoPS".</p></td>
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</tr>
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<tr>
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<th>Lancefield</th>
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<td><p>a logical to indicate whether beta-haemolytic <em>Streptococci</em> should be categorised into Lancefield groups instead of their own species, according to Rebecca C. Lancefield [2]. These <em>Streptococci</em> will be categorised in their first group, e.g. <em>Streptococcus dysgalactiae</em> will be group C, although officially it was also categorised into groups G and L.</p>
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<td><p>a logical to indicate whether beta-haemolytic <em>Streptococci</em> should be categorised into Lancefield groups instead of their own species, according to Rebecca C. Lancefield [3]. These <em>Streptococci</em> will be categorised in their first group, e.g. <em>Streptococcus dysgalactiae</em> will be group C, although officially it was also categorised into groups G and L.</p>
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<p>This excludes <em>Enterococci</em> at default (who are in group D), use <code>Lancefield = "all"</code> to also categorise all <em>Enterococci</em> as group D.</p></td>
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</tr>
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<tr>
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@ -287,7 +287,7 @@
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<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
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<p>Character (vector) with class <code>"mo"</code>. Unknown values will return <code>NA</code>.</p>
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<p>Character (vector) with class <code>"mo"</code></p>
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<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
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@ -303,14 +303,15 @@ A microbial ID from this package (class: <code>mo</code>) typically looks like t
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| | | ----> subspecies, a 3-4 letter acronym
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| | ----> species, a 3-4 letter acronym
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| ----> genus, a 5-7 letter acronym, mostly without vowels
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----> taxonomic kingdom: A (Archaea), AN (Animalia), B (Bacteria), C (Chromista),
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F (Fungi), P (Protozoa) or PL (Plantae)
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----> taxonomic kingdom: A (Archaea), AN (Animalia), B (Bacteria),
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C (Chromista), F (Fungi), P (Protozoa) or
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PL (Plantae)
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</pre>
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<p>Values that cannot be coered will be considered 'unknown' and have an MO code <code>UNKNOWN</code>.</p>
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<p>Values that cannot be coered will be considered 'unknown' and will get the MO code <code>UNKNOWN</code>.</p>
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<p>Use the <code><a href='mo_property.html'>mo_property</a>_*</code> functions to get properties based on the returned code, see Examples.</p>
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<p>The algorithm uses data from the Catalogue of Life (see below) and from one other source (see <code><a href='microorganisms.html'>?microorganisms</a></code>).</p>
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<p><strong>Self-learning algoritm</strong> <br />
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The <code>as.mo()</code> function gains experience from previously determined microbial IDs and learns from it. This drastically improves both speed and reliability. Use <code>clean_mo_history()</code> to reset the algorithms. Only experience from your current <code>AMR</code> package version is used. This is done because in the future the taxonomic tree (which is included in this package) may change for any organism and it consequently has to rebuild its knowledge. Usually, any guess after the first try runs 90-95% faster than the first try. The algorithm saves its previous findings to <code>~/.Rhistory_mo</code>.</p>
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The <code>as.mo()</code> function gains experience from previously determined microbial IDs and learns from it. This drastically improves both speed and reliability. Use <code>clean_mo_history()</code> to reset the algorithms. Only experience from your current <code>AMR</code> package version is used. This is done because in the future the taxonomic tree (which is included in this package) may change for any organism and it consequently has to rebuild its knowledge. Usually, any guess after the first try runs 80-95% faster than the first try. The algorithm saves its previous findings to <code>~/.Rhistory_mo</code>.</p>
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<p><strong>Intelligent rules</strong> <br />
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This function uses intelligent rules to help getting fast and logical results. It tries to find matches in this order:</p><ul>
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<li><p>Valid MO codes and full names: it first searches in already valid MO code and known genus/species combinations</p></li>
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@ -324,7 +325,7 @@ This function uses intelligent rules to help getting fast and logical results. I
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<li><p>Something like <code>"stau"</code> or <code>"S aur"</code> will return the ID of <em>Staphylococcus aureus</em> and not <em>Staphylococcus auricularis</em></p></li>
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</ul><p>This means that looking up human pathogenic microorganisms takes less time than looking up human non-pathogenic microorganisms.</p>
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<p><strong>Uncertain results</strong> <br />
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The algorithm can additionally use three different levels of uncertainty to guess valid results. The default is <code>allow_uncertain = TRUE</code>, which is uqual to uncertainty level 2. Using <code>allow_uncertain = FALSE</code> will skip all of these additional rules:</p><ul>
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The algorithm can additionally use three different levels of uncertainty to guess valid results. The default is <code>allow_uncertain = TRUE</code>, which is equal to uncertainty level 2. Using <code>allow_uncertain = FALSE</code> will skip all of these additional rules:</p><ul>
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<li><p>(uncertainty level 1): It tries to look for only matching genera</p></li>
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<li><p>(uncertainty level 1): It tries to look for previously accepted (but now invalid) taxonomic names</p></li>
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<li><p>(uncertainty level 2): It strips off values between brackets and the brackets itself, and re-evaluates the input with all previous rules</p></li>
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@ -354,8 +355,9 @@ The intelligent rules takes into account microbial prevalence of pathogens in hu
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<p>[1] Becker K <em>et al.</em> <strong>Coagulase-Negative Staphylococci</strong>. 2014. Clin Microbiol Rev. 27(4): 870–926. <a href='https://dx.doi.org/10.1128/CMR.00109-13'>https://dx.doi.org/10.1128/CMR.00109-13</a></p>
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<p>[2] Lancefield RC <strong>A serological differentiation of human and other groups of hemolytic streptococci</strong>. 1933. J Exp Med. 57(4): 571–95. <a href='https://dx.doi.org/10.1084/jem.57.4.571'>https://dx.doi.org/10.1084/jem.57.4.571</a></p>
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<p>[3] Catalogue of Life: Annual Checklist (public online taxonomic database), <a href='www.catalogueoflife.org'>www.catalogueoflife.org</a> (check included annual version with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version</a>()</code>).</p>
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<p>[2] Becker K <em>et al.</em> <strong>Implications of identifying the recently defined members of the S. aureus complex, S. argenteus and S. schweitzeri: A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS).</strong>. 2019. Clin Microbiol Infect. 2019 Mar 11. <a href='https://doi.org/10.1016/j.cmi.2019.02.028'>https://doi.org/10.1016/j.cmi.2019.02.028</a></p>
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<p>[3] Lancefield RC <strong>A serological differentiation of human and other groups of hemolytic streptococci</strong>. 1933. J Exp Med. 57(4): 571–95. <a href='https://dx.doi.org/10.1084/jem.57.4.571'>https://dx.doi.org/10.1084/jem.57.4.571</a></p>
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<p>[4] Catalogue of Life: Annual Checklist (public online taxonomic database), <a href='www.catalogueoflife.org'>www.catalogueoflife.org</a> (check included annual version with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version</a>()</code>).</p>
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<h2 class="hasAnchor" id="catalogue-of-life"><a class="anchor" href="#catalogue-of-life"></a>Catalogue of Life</h2>
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9024</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9025</span>
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</span>
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</div>
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9024</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9025</span>
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</span>
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</div>
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@ -245,11 +245,11 @@
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<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
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<p>a <code>list</code>, invisibly</p>
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<p>a <code>list</code>, which prints in pretty format</p>
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<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
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<p>The list item <code>is_latest_annual_release</code> is based on the system date.</p>
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<p>The list item <code>...$catalogue_of_life$is_latest_annual_release</code> is based on the system date.</p>
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<p>For DSMZ, see <code><a href='microorganisms.html'>?microorganisms</a></code>.</p>
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<h2 class="hasAnchor" id="catalogue-of-life"><a class="anchor" href="#catalogue-of-life"></a>Catalogue of Life</h2>
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@ -81,7 +81,7 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9023</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9025</span>
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</span>
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</div>
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@ -340,7 +340,7 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
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<span class='kw'>S</span> <span class='kw'>=</span> <span class='fu'>count_S</span>(<span class='no'>cipr</span>),
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<span class='kw'>n1</span> <span class='kw'>=</span> <span class='fu'>count_all</span>(<span class='no'>cipr</span>), <span class='co'># the actual total; sum of all three</span>
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<span class='kw'>n2</span> <span class='kw'>=</span> <span class='fu'>n_rsi</span>(<span class='no'>cipr</span>), <span class='co'># same - analogous to n_distinct</span>
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<span class='kw'>total</span> <span class='kw'>=</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/n.html'>n</a></span>()) <span class='co'># NOT the amount of tested isolates!</span>
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<span class='kw'>total</span> <span class='kw'>=</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/n.html'>n</a></span>()) <span class='co'># NOT the number of tested isolates!</span>
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<span class='co'># Count co-resistance between amoxicillin/clav acid and gentamicin,</span>
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<span class='co'># so we can see that combination therapy does a lot more than mono therapy.</span>
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@ -6,7 +6,7 @@
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<meta http-equiv="X-UA-Compatible" content="IE=edge">
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<meta name="viewport" content="width=device-width, initial-scale=1.0">
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<title>Filter on antibiotic class — filter_ab_class • AMR (for R)</title>
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<title>Filter isolates on result in antibiotic class — filter_ab_class • AMR (for R)</title>
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<!-- favicons -->
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<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
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@ -45,9 +45,9 @@
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<link href="../extra.css" rel="stylesheet">
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<script src="../extra.js"></script>
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<meta property="og:title" content="Filter on antibiotic class — filter_ab_class" />
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<meta property="og:title" content="Filter isolates on result in antibiotic class — filter_ab_class" />
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<meta property="og:description" content="Filter on specific antibiotic variables based on their class (ATC groups)." />
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<meta property="og:description" content="Filter isolates on results in specific antibiotic variables based on their class (ATC groups). This makes it easy to get a list of isolates that were tested for e.g. any aminoglycoside." />
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<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
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<meta name="twitter:card" content="summary" />
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@ -80,7 +80,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9023</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9025</span>
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</span>
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</div>
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@ -230,14 +230,14 @@
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<div class="row">
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<div class="col-md-9 contents">
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<div class="page-header">
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<h1>Filter on antibiotic class</h1>
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<h1>Filter isolates on result in antibiotic class</h1>
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<div class="hidden name"><code>filter_ab_class.Rd</code></div>
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</div>
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<div class="ref-description">
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<p>Filter on specific antibiotic variables based on their class (ATC groups).</p>
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<p>Filter isolates on results in specific antibiotic variables based on their class (ATC groups). This makes it easy to get a list of isolates that were tested for e.g. any aminoglycoside.</p>
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</div>
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</tr>
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<tr>
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<th>ab_class</th>
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<td><p>an antimicrobial class, like <code>"carbapenems"</code></p></td>
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<td><p>an antimicrobial class, like <code>"carbapenems"</code>. More specifically, this should be a text that can be found in a 4th level ATC group (chemical subgroup) or a 5th level ATC group (chemical substance), please see <a href='https://www.whocc.no/atc/structure_and_principles/'>this explanation on the WHOCC website</a>.</p></td>
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</tr>
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<tr>
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<th>result</th>
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@ -317,8 +317,14 @@
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<span class='co'># filter on isolates that show resistance to</span>
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<span class='co'># any aminoglycoside and any fluoroquinolone</span>
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<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
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<span class='fu'>filter_aminoglycosides</span>(<span class='st'>"R"</span>, <span class='st'>"any"</span>) <span class='kw'>%>%</span>
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<span class='fu'>filter_fluoroquinolones</span>(<span class='st'>"R"</span>, <span class='st'>"any"</span>)
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<span class='fu'>filter_aminoglycosides</span>(<span class='st'>"R"</span>) <span class='kw'>%>%</span>
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<span class='fu'>filter_fluoroquinolones</span>(<span class='st'>"R"</span>)
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<span class='co'># filter on isolates that show resistance to</span>
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<span class='co'># all aminoglycosides and all fluoroquinolones</span>
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<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
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<span class='fu'>filter_aminoglycosides</span>(<span class='st'>"R"</span>, <span class='st'>"all"</span>) <span class='kw'>%>%</span>
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<span class='fu'>filter_fluoroquinolones</span>(<span class='st'>"R"</span>, <span class='st'>"all"</span>)
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<span class='co'># }</span></pre>
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</div>
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<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
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@ -78,7 +78,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9024</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9025</span>
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</span>
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</div>
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@ -431,7 +431,7 @@
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<td>
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<p><code><a href="filter_ab_class.html">filter_ab_class()</a></code> <code><a href="filter_ab_class.html">filter_aminoglycosides()</a></code> <code><a href="filter_ab_class.html">filter_carbapenems()</a></code> <code><a href="filter_ab_class.html">filter_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_1st_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_2nd_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_3rd_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_4th_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_fluoroquinolones()</a></code> <code><a href="filter_ab_class.html">filter_glycopeptides()</a></code> <code><a href="filter_ab_class.html">filter_macrolides()</a></code> <code><a href="filter_ab_class.html">filter_tetracyclines()</a></code> </p>
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</td>
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<td><p>Filter on antibiotic class</p></td>
|
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<td><p>Filter isolates on result in antibiotic class</p></td>
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</tr><tr>
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<td>
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@ -80,7 +80,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9024</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9025</span>
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</span>
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</div>
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@ -80,7 +80,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9024</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9025</span>
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</span>
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</div>
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@ -80,7 +80,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9024</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9025</span>
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</span>
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</div>
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@ -341,8 +341,9 @@ This package contains the complete taxonomic tree of almost all microorganisms (
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<p>[1] Becker K <em>et al.</em> <strong>Coagulase-Negative Staphylococci</strong>. 2014. Clin Microbiol Rev. 27(4): 870–926. <a href='https://dx.doi.org/10.1128/CMR.00109-13'>https://dx.doi.org/10.1128/CMR.00109-13</a></p>
|
||||
<p>[2] Lancefield RC <strong>A serological differentiation of human and other groups of hemolytic streptococci</strong>. 1933. J Exp Med. 57(4): 571–95. <a href='https://dx.doi.org/10.1084/jem.57.4.571'>https://dx.doi.org/10.1084/jem.57.4.571</a></p>
|
||||
<p>[3] Catalogue of Life: Annual Checklist (public online taxonomic database), <a href='www.catalogueoflife.org'>www.catalogueoflife.org</a> (check included annual version with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version</a>()</code>).</p>
|
||||
<p>[2] Becker K <em>et al.</em> <strong>Implications of identifying the recently defined members of the S. aureus complex, S. argenteus and S. schweitzeri: A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS).</strong>. 2019. Clin Microbiol Infect. 2019 Mar 11. <a href='https://doi.org/10.1016/j.cmi.2019.02.028'>https://doi.org/10.1016/j.cmi.2019.02.028</a></p>
|
||||
<p>[3] Lancefield RC <strong>A serological differentiation of human and other groups of hemolytic streptococci</strong>. 1933. J Exp Med. 57(4): 571–95. <a href='https://dx.doi.org/10.1084/jem.57.4.571'>https://dx.doi.org/10.1084/jem.57.4.571</a></p>
|
||||
<p>[4] Catalogue of Life: Annual Checklist (public online taxonomic database), <a href='www.catalogueoflife.org'>www.catalogueoflife.org</a> (check included annual version with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version</a>()</code>).</p>
|
||||
|
||||
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
|
||||
|
||||
|
@ -47,7 +47,7 @@
|
||||
<script src="../extra.js"></script>
|
||||
<meta property="og:title" content="Calculate resistance of isolates — portion" />
|
||||
|
||||
<meta property="og:description" content="These functions can be used to calculate the (co-)resistance of microbial isolates (i.e. percentage S, SI, I, IR or R). All functions support quasiquotation with pipes, can be used in dplyrs summarise and support grouped variables, see Examples.
|
||||
<meta property="og:description" content="These functions can be used to calculate the (co-)resistance of microbial isolates (i.e. percentage of S, SI, I, IR or R). All functions support quasiquotation with pipes, can be used in dplyrs summarise and support grouped variables, see Examples.
|
||||
portion_R and portion_IR can be used to calculate resistance, portion_S and portion_SI can be used to calculate susceptibility." />
|
||||
|
||||
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
|
||||
@ -81,7 +81,7 @@ portion_R and portion_IR can be used to calculate resistance, portion_S and port
|
||||
</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="Released version">0.5.0.9023</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9025</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -238,7 +238,7 @@ portion_R and portion_IR can be used to calculate resistance, portion_S and port
|
||||
|
||||
<div class="ref-description">
|
||||
|
||||
<p>These functions can be used to calculate the (co-)resistance of microbial isolates (i.e. percentage S, SI, I, IR or R). All functions support quasiquotation with pipes, can be used in <code>dplyr</code>s <code><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></code> and support grouped variables, see <em>Examples</em>.</p>
|
||||
<p>These functions can be used to calculate the (co-)resistance of microbial isolates (i.e. percentage of S, SI, I, IR or R). All functions support quasiquotation with pipes, can be used in <code>dplyr</code>s <code><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></code> and support grouped variables, see <em>Examples</em>.</p>
|
||||
<p><code>portion_R</code> and <code>portion_IR</code> can be used to calculate resistance, <code>portion_S</code> and <code>portion_SI</code> can be used to calculate susceptibility.<br /></p>
|
||||
|
||||
</div>
|
||||
@ -270,7 +270,7 @@ portion_R and portion_IR can be used to calculate resistance, portion_S and port
|
||||
</tr>
|
||||
<tr>
|
||||
<th>minimum</th>
|
||||
<td><p>the minimal amount of available isolates. Any number lower than <code>minimum</code> will return <code>NA</code> with a warning. The default number of <code>30</code> isolates is advised by the Clinical and Laboratory Standards Institute (CLSI) as best practice, see Source.</p></td>
|
||||
<td><p>the minimum allowed number of available (tested) isolates. Any isolate count lower than <code>minimum</code> will return <code>NA</code> with a warning. The default number of <code>30</code> isolates is advised by the Clinical and Laboratory Standards Institute (CLSI) as best practice, see Source.</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>as_percent</th>
|
||||
@ -311,14 +311,14 @@ portion_R and portion_IR can be used to calculate resistance, portion_S and port
|
||||
<p>The old <code><a href='rsi.html'>rsi</a></code> function is still available for backwards compatibility but is deprecated.
|
||||
<br /><br />
|
||||
To calculate the probability (<em>p</em>) of susceptibility of one antibiotic, we use this formula:
|
||||
<div style="text-align: center"><img src='figures/mono_therapy.png' alt='' /></div>
|
||||
<div style="text-align: center;"><img src='figures/combi_therapy_2.png' alt='' /></div>
|
||||
To calculate the probability (<em>p</em>) of susceptibility of more antibiotics (i.e. combination therapy), we need to check whether one of them has a susceptible result (as numerator) and count all cases where all antibiotics were tested (as denominator). <br />
|
||||
<br />
|
||||
For two antibiotics:
|
||||
<div style="text-align: center"><img src='figures/combi_therapy_2.png' alt='' /></div>
|
||||
<div style="text-align: center;"><img src='figures/combi_therapy_2.png' alt='' /></div>
|
||||
<br />
|
||||
For three antibiotics:
|
||||
<div style="text-align: center"><img src='figures/combi_therapy_3.png' alt='' /></div>
|
||||
<div style="text-align: center;"><img src='figures/combi_therapy_2.png' alt='' /></div>
|
||||
<br />
|
||||
And so on.</p>
|
||||
|
||||
@ -362,8 +362,9 @@ portion_R and portion_IR can be used to calculate resistance, portion_S and port
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>R</span> <span class='kw'>=</span> <span class='fu'>portion_R</span>(<span class='no'>cipr</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
|
||||
<span class='kw'>I</span> <span class='kw'>=</span> <span class='fu'>portion_I</span>(<span class='no'>cipr</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
|
||||
<span class='kw'>S</span> <span class='kw'>=</span> <span class='fu'>portion_S</span>(<span class='no'>cipr</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
|
||||
<span class='kw'>n</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='no'>cipr</span>), <span class='co'># works like n_distinct in dplyr</span>
|
||||
<span class='kw'>total</span> <span class='kw'>=</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/n.html'>n</a></span>()) <span class='co'># NOT the amount of tested isolates!</span>
|
||||
<span class='kw'>n1</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>cipr</span>), <span class='co'># the actual total; sum of all three</span>
|
||||
<span class='kw'>n2</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='no'>cipr</span>), <span class='co'># same - analogous to n_distinct</span>
|
||||
<span class='kw'>total</span> <span class='kw'>=</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/n.html'>n</a></span>()) <span class='co'># NOT the number of tested isolates!</span>
|
||||
|
||||
<span class='co'># Calculate co-resistance between amoxicillin/clav acid and gentamicin,</span>
|
||||
<span class='co'># so we can see that combination therapy does a lot more than mono therapy:</span>
|
||||
|
@ -80,7 +80,7 @@
|
||||
</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="Released version">0.5.0.9023</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9025</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -257,7 +257,7 @@
|
||||
</tr>
|
||||
<tr>
|
||||
<th>minimum</th>
|
||||
<td><p>the minimal amount of available isolates. Any number lower than <code>minimum</code> will return <code>NA</code> with a warning. The default number of <code>30</code> isolates is advised by the Clinical and Laboratory Standards Institute (CLSI) as best practice, see Source.</p></td>
|
||||
<td><p>the minimum allowed number of available (tested) isolates. Any isolate count lower than <code>minimum</code> will return <code>NA</code> with a warning. The default number of <code>30</code> isolates is advised by the Clinical and Laboratory Standards Institute (CLSI) as best practice, see Source.</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>as_percent</th>
|
||||
|
Reference in New Issue
Block a user