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big website update, licence txt update
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@ -49,7 +49,7 @@
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<meta property="og:description" content="Apply susceptibility rules as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, http://eucast.org), see Source. This includes (1) expert rules, (2) intrinsic resistance and (3) inferred resistance as defined in their breakpoint tables." />
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<meta property="og:image" content="https://msberends.gitlab.io/logo.png" />
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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">0.5.0.9008</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9009</span>
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</span>
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</div>
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@ -93,12 +93,65 @@
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Home
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</a>
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</li>
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<li>
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<a href="../articles/AMR.html">
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<span class="fa fa-directions"></span>
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<li class="dropdown">
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<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
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<span class="fa fa-question-circle"></span>
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Get Started
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How to
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<span class="caret"></span>
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</a>
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<ul class="dropdown-menu" role="menu">
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<li>
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<a href="../articles/AMR.html">
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<span class="fa fa-directions"></span>
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Conduct AMR analysis
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</a>
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</li>
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<li>
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<a href="../articles/Predict.html">
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<span class="fa fa-dice"></span>
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Predict antimicrobial resistance
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</a>
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</li>
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<li>
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<a href="../articles/EUCAST.html">
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<span class="fa fa-exchange-alt"></span>
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Apply EUCAST rules
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</a>
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<a href="../articles/mo_property.html">
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<span class="fa fa-bug"></span>
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Get properties of a microorganism
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<a href="../articles/ab_property.html">
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<span class="fa fa-capsules"></span>
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Get properties of an antibiotic
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<a href="../articles/freq.html">
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<span class="fa fa-sort-amount-down"></span>
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Create frequency tables
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</a>
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<a href="../articles/G_test.html">
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Use the G-test
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</ul>
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</li>
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<li>
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<a href="../reference/">
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@ -121,17 +174,17 @@
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Changelog
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</a>
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Source Code
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@ -307,51 +360,17 @@
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<strong>trsu</strong>: sulfamethoxazole and trimethoprim (<em>J01EE01</em>),
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<strong>vanc</strong>: vancomycin (<em>J01XA01</em>).</p>
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<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>
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<p><img src='figures/logo.png' height=40px style=margin-bottom:5px /> <br />
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On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a omprehensive tutorial</a> about how to conduct AMR analysis and find <a href='https://msberends.gitlab.io/AMR/reference'>the complete documentation of all functions</a>, which reads a lot easier than in R.</p>
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<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
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<pre class="examples"><div class='input'><span class='no'>a</span> <span class='kw'><-</span> <span class='fu'>eucast_rules</span>(<span class='no'>septic_patients</span>)</div><div class='output co'>#> <span class='message'><span style='color: #0000BB;'>NOTE: Using column `</span><span style='color: #0000BB;font-weight: bold;'>mo</span><span style='color: #0000BB;'>` as input for `col_mo`.</span><span></span></div><div class='output co'>#> <span class='warning'>Warning: These columns do not exist and will be ignored: azlo, aztr, cefa, cfra, clar, dapt, erta, fusi, levo, linc, mezl, mino, nali, neom, neti, novo, norf, oflo, pipe, poly, pris, qida, roxi, siso, tica.</span>
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#> <span class='warning'>THIS MAY STRONGLY INFLUENCE THE OUTCOME.</span></div><div class='output co'>#>
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#> Rules by the European Committee on Antimicrobial Susceptibility Testing (EUCAST)
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#> </span><span style='font-weight: bold;'>
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#> EUCAST Clinical Breakpoints (v8.1, 2018)
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#> </span><span>Enterobacteriales (Order)</span><span style='color: #00BB00;'> (no changes)
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#> </span><span style='font-style: italic;'>Staphylococcus</span><span style='color: #00BB00;'> (no changes)
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#> </span><span style='font-style: italic;'>Enterococcus</span><span style='color: #00BB00;'> (no changes)
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#> </span><span style='font-style: italic;'>Streptococcus</span><span> groups A, B, C, G</span><span style='color: #00BB00;'> (no changes)
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#> </span><span style='font-style: italic;'>Streptococcus pneumoniae</span><span style='color: #00BB00;'> (no changes)
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#> </span><span>Viridans group streptococci</span><span style='color: #00BB00;'> (no changes)
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#> </span><span style='font-style: italic;'>Haemophilus influenzae</span><span style='color: #00BB00;'> (no changes)
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#> </span><span style='font-style: italic;'>Moraxella catarrhalis</span><span style='color: #00BB00;'> (no changes)
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#> </span><span>Anaerobic Gram positives</span><span style='color: #00BB00;'> (no changes)
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#> </span><span>Anaerobic Gram negatives</span><span style='color: #00BB00;'> (no changes)
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#> </span><span style='font-style: italic;'>Pasteurella multocida</span><span style='color: #00BB00;'> (no changes)
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#> </span><span style='font-style: italic;'>Campylobacter jejuni</span><span> and </span><span style='font-style: italic;'>C. coli</span><span style='color: #00BB00;'> (no changes)
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#> </span><span style='font-style: italic;'>Aerococcus sanguinicola</span><span> and </span><span style='font-style: italic;'>A. urinae</span><span style='color: #00BB00;'> (no changes)
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#> </span><span style='font-style: italic;'>Kingella kingae</span><span style='color: #00BB00;'> (no changes)
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#> </span><span style='font-weight: bold;'>
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#> EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes (v3.1, 2016)
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#> </span><span>Table 1: Intrinsic resistance in </span><span style='font-style: italic;'>Enterobacteriaceae</span><span style='color: #00BB00;'> (no changes)
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#> </span><span>Table 2: Intrinsic resistance in non-fermentative Gram-negative bacteria</span><span style='color: #00BB00;'> (no changes)
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#> </span><span>Table 3: Intrinsic resistance in other Gram-negative bacteria</span><span style='color: #00BB00;'> (no changes)
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#> </span><span>Table 4: Intrinsic resistance in Gram-positive bacteria</span><span style='color: #00BB00;'> (no changes)
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#> </span><span>Table 8: Interpretive rules for B-lactam agents and Gram-positive cocci</span><span style='color: #00BB00;'> (no changes)
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#> </span><span>Table 9: Interpretive rules for B-lactam agents and Gram-negative rods</span><span style='color: #00BB00;'> (no changes)
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#> </span><span>Table 10: Interpretive rules for B-lactam agents and other Gram-negative bacteria</span><span style='color: #00BB00;'> (no changes)
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#> </span><span>Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins</span><span style='color: #00BB00;'> (no changes)
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#> </span><span>Table 12: Interpretive rules for aminoglycosides</span><span style='color: #00BB00;'> (no changes)
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#> </span><span>Table 13: Interpretive rules for quinolones</span><span style='color: #00BB00;'> (no changes)
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#> </span><span style='font-weight: bold;'>
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#> Other rules
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#> </span><span>Non-EUCAST: ampicillin = R where amoxicillin/clav acid = R</span><span style='color: #00BB00;'> (no changes)
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#> </span><span>Non-EUCAST: piperacillin = R where piperacillin/tazobactam = R</span><span style='color: #00BB00;'> (no changes)
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#> </span><span>Non-EUCAST: trimethoprim = R where trimethoprim/sulfa = R</span><span style='color: #00BB00;'> (no changes)
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#> </span><span>Non-EUCAST: amoxicillin/clav acid = S where ampicillin = S</span><span style='color: #00BB00;'> (no changes)
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#> </span><span>Non-EUCAST: piperacillin/tazobactam = S where piperacillin = S</span><span style='color: #00BB00;'> (no changes)
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#> </span><span>Non-EUCAST: trimethoprim/sulfa = S where trimethoprim = S</span><span style='color: #00BB00;'> (no changes)
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#> </span><span style='font-weight: bold;'>
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#> => EUCAST rules affected 1,980 out of 2,000 rows -> </span><span style='color: #00BB00;font-weight: bold;'>changed 0 test results.
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#>
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#> </span><span></div><div class='input'>
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<pre class="examples"><span class='co'># NOT RUN {</span>
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<span class='no'>a</span> <span class='kw'><-</span> <span class='fu'>eucast_rules</span>(<span class='no'>septic_patients</span>)
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<span class='no'>a</span> <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></span>(<span class='kw'>mo</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"Staphylococcus aureus"</span>,
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<span class='st'>"Enterococcus faecalis"</span>,
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<span class='st'>"Escherichia coli"</span>,
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@ -366,72 +385,24 @@
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<span class='kw'>cfox</span> <span class='kw'>=</span> <span class='st'>"S"</span>, <span class='co'># Cefoxitin</span>
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<span class='kw'>stringsAsFactors</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
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<span class='no'>a</span></div><div class='output co'>#> mo vanc amox coli cfta cfur peni cfox
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#> 1 Staphylococcus aureus - - - - - S S
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#> 2 Enterococcus faecalis - - - - - S S
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#> 3 Escherichia coli - - - - - S S
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#> 4 Klebsiella pneumoniae - - - - - S S
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#> 5 Pseudomonas aeruginosa - - - - - S S</div><div class='input'><span class='co'># mo vanc amox coli cfta cfur peni cfox</span>
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<span class='no'>a</span>
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<span class='co'># mo vanc amox coli cfta cfur peni cfox</span>
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<span class='co'># 1 Staphylococcus aureus - - - - - S S</span>
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<span class='co'># 2 Enterococcus faecalis - - - - - S S</span>
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<span class='co'># 3 Escherichia coli - - - - - S S</span>
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<span class='co'># 4 Klebsiella pneumoniae - - - - - S S</span>
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<span class='co'># 5 Pseudomonas aeruginosa - - - - - S S</span>
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<span class='no'>b</span> <span class='kw'><-</span> <span class='fu'>eucast_rules</span>(<span class='no'>a</span>, <span class='st'>"mo"</span>) <span class='co'># 18 results are forced as R or S</span></div><div class='output co'>#> <span class='warning'>Warning: These columns do not exist and will be ignored: amcl, amik, ampi, azit, azlo, aztr, cefa, cfra, cfep, cfot, cftr, chlo, cipr, clar, clin, clox, czol, dapt, doxy, erta, eryt, fosf, fusi, gent, imip, kana, levo, linc, line, mero, mezl, mino, moxi, nali, neom, neti, nitr, novo, norf, oflo, oxac, pipe, pita, poly, pris, qida, rifa, roxi, siso, teic, tetr, tica, tige, tobr, trim, trsu.</span>
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#> <span class='warning'>THIS MAY STRONGLY INFLUENCE THE OUTCOME.</span></div><div class='output co'>#>
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#> Rules by the European Committee on Antimicrobial Susceptibility Testing (EUCAST)</div><div class='output co'>#> <span class='message'></span><span style='color: #0000BB;'>NOTE: Using column `</span><span style='color: #0000BB;font-weight: bold;'>amox</span><span style='color: #0000BB;'>` as input for ampicillin (J01CA01) since many EUCAST rules depend on it.</span><span></span></div><div class='output co'>#> </span><span style='font-weight: bold;'>
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#> EUCAST Clinical Breakpoints (v8.1, 2018)
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#> </span><span>Enterobacteriales (Order)</span><span style='color: #00BB00;'> (no changes)
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#> </span><span style='font-style: italic;'>Staphylococcus</span><span style='color: #0000BB;'> (2 changes)
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#> </span><span style='font-style: italic;'>Enterococcus</span><span style='color: #00BB00;'> (no changes)
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#> </span><span style='font-style: italic;'>Streptococcus</span><span> groups A, B, C, G</span><span style='color: #00BB00;'> (no changes)
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#> </span><span style='font-style: italic;'>Streptococcus pneumoniae</span><span style='color: #00BB00;'> (no changes)
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#> </span><span>Viridans group streptococci</span><span style='color: #00BB00;'> (no changes)
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#> </span><span style='font-style: italic;'>Haemophilus influenzae</span><span style='color: #00BB00;'> (no changes)
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#> </span><span style='font-style: italic;'>Moraxella catarrhalis</span><span style='color: #00BB00;'> (no changes)
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#> </span><span>Anaerobic Gram positives</span><span style='color: #00BB00;'> (no changes)
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#> </span><span>Anaerobic Gram negatives</span><span style='color: #00BB00;'> (no changes)
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#> </span><span style='font-style: italic;'>Pasteurella multocida</span><span style='color: #00BB00;'> (no changes)
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#> </span><span style='font-style: italic;'>Campylobacter jejuni</span><span> and </span><span style='font-style: italic;'>C. coli</span><span style='color: #00BB00;'> (no changes)
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#> </span><span style='font-style: italic;'>Aerococcus sanguinicola</span><span> and </span><span style='font-style: italic;'>A. urinae</span><span style='color: #00BB00;'> (no changes)
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#> </span><span style='font-style: italic;'>Kingella kingae</span><span style='color: #00BB00;'> (no changes)
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#> </span><span style='font-weight: bold;'>
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#> EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes (v3.1, 2016)
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#> </span><span>Table 1: Intrinsic resistance in </span><span style='font-style: italic;'>Enterobacteriaceae</span><span style='color: #0000BB;'> (5 changes)
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#> </span><span>Table 2: Intrinsic resistance in non-fermentative Gram-negative bacteria</span><span style='color: #0000BB;'> (5 changes)
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#> </span><span>Table 3: Intrinsic resistance in other Gram-negative bacteria</span><span style='color: #00BB00;'> (no changes)
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#> </span><span>Table 4: Intrinsic resistance in Gram-positive bacteria</span><span style='color: #0000BB;'> (6 changes)
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#> </span><span>Table 8: Interpretive rules for B-lactam agents and Gram-positive cocci</span><span style='color: #00BB00;'> (no changes)
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#> </span><span>Table 9: Interpretive rules for B-lactam agents and Gram-negative rods</span><span style='color: #00BB00;'> (no changes)
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#> </span><span>Table 10: Interpretive rules for B-lactam agents and other Gram-negative bacteria</span><span style='color: #00BB00;'> (no changes)
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#> </span><span>Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins</span><span style='color: #00BB00;'> (no changes)
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#> </span><span>Table 12: Interpretive rules for aminoglycosides</span><span style='color: #00BB00;'> (no changes)
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#> </span><span>Table 13: Interpretive rules for quinolones</span><span style='color: #00BB00;'> (no changes)
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#> </span><span style='font-weight: bold;'>
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#> Other rules
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#> </span><span>Non-EUCAST: ampicillin = R where amoxicillin/clav acid = R</span><span style='color: #00BB00;'> (no changes)
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#> </span><span>Non-EUCAST: piperacillin = R where piperacillin/tazobactam = R</span><span style='color: #00BB00;'> (no changes)
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#> </span><span>Non-EUCAST: trimethoprim = R where trimethoprim/sulfa = R</span><span style='color: #00BB00;'> (no changes)
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#> </span><span>Non-EUCAST: amoxicillin/clav acid = S where ampicillin = S</span><span style='color: #00BB00;'> (no changes)
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#> </span><span>Non-EUCAST: piperacillin/tazobactam = S where piperacillin = S</span><span style='color: #00BB00;'> (no changes)
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#> </span><span>Non-EUCAST: trimethoprim/sulfa = S where trimethoprim = S</span><span style='color: #00BB00;'> (no changes)
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#> </span><span style='font-weight: bold;'>
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#> => EUCAST rules affected 5 out of 5 rows -> </span><span style='color: #0000BB;font-weight: bold;'>changed 18 test results.
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#>
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#> </span><span></div><div class='input'>
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<span class='no'>b</span></div><div class='output co'>#> mo vanc amox coli cfta cfur peni cfox
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#> 1 Staphylococcus aureus - S R R S S S
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#> 2 Enterococcus faecalis - - R R R S R
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#> 3 Escherichia coli R - - - - R S
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#> 4 Klebsiella pneumoniae R R - - - R S
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#> 5 Pseudomonas aeruginosa R R - - R R R</div><div class='input'># mo vanc amox coli cfta cfur peni cfox
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# 1 Staphylococcus aureus - S R R S S S
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# 2 Enterococcus faecalis - - R R R S R
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# 3 Escherichia coli R - - - - R S
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# 4 Klebsiella pneumoniae R R - - - R S
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# 5 Pseudomonas aeruginosa R R - - R R R
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</div></span></pre>
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<span class='no'>b</span> <span class='kw'><-</span> <span class='fu'>eucast_rules</span>(<span class='no'>a</span>, <span class='st'>"mo"</span>) <span class='co'># 18 results are forced as R or S</span>
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<span class='no'>b</span>
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<span class='co'># mo vanc amox coli cfta cfur peni cfox</span>
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<span class='co'># 1 Staphylococcus aureus - S R R S S S</span>
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||||
<span class='co'># 2 Enterococcus faecalis - - R R R S R</span>
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<span class='co'># 3 Escherichia coli R - - - - R S</span>
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<span class='co'># 4 Klebsiella pneumoniae R R - - - R S</span>
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||||
<span class='co'># 5 Pseudomonas aeruginosa R R - - R R R</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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<h2>Contents</h2>
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@ -443,6 +414,8 @@
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<li><a href="#value">Value</a></li>
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||||
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||||
<li><a href="#antibiotics">Antibiotics</a></li>
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||||
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||||
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
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||||
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||||
<li><a href="#examples">Examples</a></li>
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||||
</ul>
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||||
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||||
Reference in New Issue
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