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mo codes for WHONET
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@ -237,7 +237,13 @@
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<pre class="usage"><span class='fu'>as.mo</span>(<span class='no'>x</span>, <span class='kw'>Becker</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>Lancefield</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>allow_uncertain</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
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<span class='kw'>reference_df</span> <span class='kw'>=</span> <span class='fu'><a href='mo_source.html'>get_mo_source</a></span>())
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<span class='fu'>is.mo</span>(<span class='no'>x</span>)</pre>
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<span class='fu'>is.mo</span>(<span class='no'>x</span>)
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<span class='fu'>mo_failures</span>()
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<span class='fu'>mo_uncertainties</span>()
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<span class='fu'>mo_renamed</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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@ -287,7 +293,7 @@
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</pre>
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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>This function uses Artificial Intelligence (AI) to help getting fast and logical results. It tries to find matches in this order:</p><ul>
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<li><p>Taxonomic kingdom: it first searches in bacteria, then fungi, then protozoa</p></li>
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<li><p>Taxonomic kingdom: it first searches in Bacteria, then Fungi, then Protozoa</p></li>
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<li><p>Human pathogenic prevalence: it first searches in more prevalent microorganisms, then less prevalent ones</p></li>
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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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<li><p>Breakdown of input values: from here it starts to breakdown input values to find possible matches</p></li>
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@ -298,11 +304,23 @@
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<li><p>Something like <code>"p aer"</code> will return the ID of <em>Pseudomonas aeruginosa</em> and not <em>Pasteurella aerogenes</em></p></li>
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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 <strong>non</strong>-pathogenic microorganisms.</p>
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<p>When using <code>allow_uncertain = TRUE</code> (which is the default setting), it will use additional rules if all previous AI rules failed to get valid results. Examples:</p><ul>
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<p><strong>UNCERTAIN RESULTS</strong> <br />
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When using <code>allow_uncertain = TRUE</code> (which is the default setting), it will use additional rules if all previous AI rules failed to get valid results. These are:</p><ul>
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<li><p>It tries to look for previously accepted (but now invalid) taxonomic names</p></li>
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<li><p>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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<li><p>It strips off words from the end one by one and re-evaluates the input with all previous rules</p></li>
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<li><p>It strips off words from the start one by one and re-evaluates the input with all previous rules</p></li>
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<li><p>It tries to look for some manual changes which are not yet published to the ITIS database (like <em>Propionibacterium</em> not yet being <em>Cutibacterium</em>)</p></li>
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</ul>
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<p>Examples:</p><ul>
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<li><p><code>"Streptococcus group B (known as S. agalactiae)"</code>. The text between brackets will be removed and a warning will be thrown that the result <em>Streptococcus group B</em> (<code>B_STRPTC_GRB</code>) needs review.</p></li>
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<li><p><code>"S. aureus - please mind: MRSA"</code>. The last word will be stripped, after which the function will try to find a match. If it does not, the second last word will be stripped, etc. Again, a warning will be thrown that the result <em>Staphylococcus aureus</em> (<code>B_STPHY_AUR</code>) needs review.</p></li>
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<li><p><code>"D. spartina"</code>. This is the abbreviation of an old taxonomic name: <em>Didymosphaeria spartinae</em> (the last "e" was missing from the input). This fungus was renamed to <em>Leptosphaeria obiones</em>, so a warning will be thrown that this result (<code>F_LPTSP_OBI</code>) needs review.</p></li>
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<li><p><code>"Fluoroquinolone-resistant Neisseria gonorrhoeae"</code>. The first word will be stripped, after which the function will try to find a match. A warning will be thrown that the result <em>Neisseria gonorrhoeae</em> (<code>B_NESSR_GON</code>) needs review.</p></li>
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</ul>
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<p>Use <code>mo_failures()</code> to get a vector with all values that could not be coerced to a valid value.</p>
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<p>Use <code>mo_uncertainties()</code> to get a vector with all values that were coerced to a valid value, but with uncertainty.</p>
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<p>Use <code>mo_renamed()</code> to get a vector with all values that could be coerced based on an old, previously accepted taxonomic name.</p>
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<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
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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">0.5.0.9015</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9016</span>
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</span>
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</div>
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@ -294,7 +294,7 @@
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</tr>
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<tr>
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<th>verbose</th>
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<td><p>a logical to indicate whether extensive info should be returned as a <code>data.frame</code> with info about which rows and columns are effected</p></td>
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<td><p>a logical to indicate whether extensive info should be returned as a <code>data.frame</code> with info about which rows and columns are effected. It runs all EUCAST rules, but will not be applied to an output - only an informative <code>data.frame</code> with changes will be returned as output.</p></td>
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</tr>
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<tr>
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<th>amcl, amik, amox, ampi, azit, azlo, aztr, cefa, cfep, cfot, cfox, cfra, cfta, cftr, cfur, chlo, cipr, clar, clin, clox, coli, czol, dapt, doxy, erta, eryt, fosf, fusi, gent, imip, kana, levo, linc, line, mero, mezl, mino, moxi, nali, neom, neti, nitr, norf, novo, oflo, oxac, peni, pipe, pita, poly, pris, qida, rifa, roxi, siso, teic, tetr, tica, tige, tobr, trim, trsu, vanc</th>
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@ -320,7 +320,7 @@
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<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
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<p>The input of <code>tbl</code>, possibly with edited values of antibiotics. Or, if <code>verbose = TRUE</code>, a <code>data.frame</code> with verbose info.</p>
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<p>The input of <code>tbl</code>, possibly with edited values of antibiotics. Or, if <code>verbose = TRUE</code>, a <code>data.frame</code> with all original and new values of the affected bug-drug combinations.</p>
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<h2 class="hasAnchor" id="antibiotics"><a class="anchor" href="#antibiotics"></a>Antibiotics</h2>
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@ -423,7 +423,9 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
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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>
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<span class='co'># apply EUCAST rules: 18 results are forced as R or 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>)
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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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@ -432,6 +434,11 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
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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'># do not apply EUCAST rules, but rather get a a data.frame</span>
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<span class='co'># with 18 rows, containing all details about the transformations:</span>
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<span class='no'>c</span> <span class='kw'><-</span> <span class='fu'>eucast_rules</span>(<span class='no'>a</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</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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@ -368,7 +368,7 @@ top_freq can be used to get the top/bottom n items of a frequency table, with co
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<li><p>Median, using <code><a href='https://www.rdocumentation.org/packages/stats/topics/median'>median</a></code>, with percentage since oldest</p></li>
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</ul>
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<p>In factors, all factor levels that are not existing in the input data will be dropped.</p>
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<p>The function <code>top_freq</code> uses <code><a href='https://www.rdocumentation.org/packages/dplyr/topics/top_n'>top_n</a></code> internally and will include more than <code>n</code> rows if there are ties.</p>
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<p>The function <code>top_freq</code> uses <code><a href='https://dplyr.tidyverse.org/reference/top_n.html'>top_n</a></code> internally and will include more than <code>n</code> rows if there are ties.</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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@ -392,8 +392,8 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
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<span class='co'># you could also use `select` or `pull` to get your variables</span>
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<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
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<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/filter'>filter</a></span>(<span class='no'>hospital_id</span> <span class='kw'>==</span> <span class='st'>"A"</span>) <span class='kw'>%>%</span>
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<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/select'>select</a></span>(<span class='no'>mo</span>) <span class='kw'>%>%</span>
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>hospital_id</span> <span class='kw'>==</span> <span class='st'>"A"</span>) <span class='kw'>%>%</span>
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>mo</span>) <span class='kw'>%>%</span>
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<span class='fu'>freq</span>()
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@ -409,20 +409,20 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
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<span class='co'># group a variable and analyse another</span>
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<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
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<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/group_by'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%>%</span>
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%>%</span>
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<span class='fu'>freq</span>(<span class='no'>gender</span>)
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<span class='co'># get top 10 bugs of hospital A as a vector</span>
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<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
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<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/filter'>filter</a></span>(<span class='no'>hospital_id</span> <span class='kw'>==</span> <span class='st'>"A"</span>) <span class='kw'>%>%</span>
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>hospital_id</span> <span class='kw'>==</span> <span class='st'>"A"</span>) <span class='kw'>%>%</span>
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<span class='fu'>freq</span>(<span class='no'>mo</span>) <span class='kw'>%>%</span>
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<span class='fu'>top_freq</span>(<span class='fl'>10</span>)
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<span class='co'># save frequency table to an object</span>
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<span class='no'>years</span> <span class='kw'><-</span> <span class='no'>septic_patients</span> <span class='kw'>%>%</span>
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<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/mutate'>mutate</a></span>(<span class='kw'>year</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/format'>format</a></span>(<span class='no'>date</span>, <span class='st'>"%Y"</span>)) <span class='kw'>%>%</span>
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>year</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/format'>format</a></span>(<span class='no'>date</span>, <span class='st'>"%Y"</span>)) <span class='kw'>%>%</span>
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<span class='fu'>freq</span>(<span class='no'>year</span>)
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@ -473,11 +473,11 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
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<span class='co'># only get selected columns</span>
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<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
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<span class='fu'>freq</span>(<span class='no'>hospital_id</span>) <span class='kw'>%>%</span>
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<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/select'>select</a></span>(<span class='no'>item</span>, <span class='no'>percent</span>)
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>item</span>, <span class='no'>percent</span>)
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<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
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<span class='fu'>freq</span>(<span class='no'>hospital_id</span>) <span class='kw'>%>%</span>
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<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/select'>select</a></span>(-<span class='no'>count</span>, -<span class='no'>cum_count</span>)
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(-<span class='no'>count</span>, -<span class='no'>cum_count</span>)
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<span class='co'># check differences between frequency tables</span>
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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>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9016</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9017</span>
|
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</span>
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</div>
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@ -280,7 +280,7 @@
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</tr><tr>
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<td>
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<p><code><a href="as.mo.html">as.mo()</a></code> <code><a href="as.mo.html">is.mo()</a></code> </p>
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<p><code><a href="as.mo.html">as.mo()</a></code> <code><a href="as.mo.html">is.mo()</a></code> <code><a href="as.mo.html">mo_failures()</a></code> <code><a href="as.mo.html">mo_uncertainties()</a></code> <code><a href="as.mo.html">mo_renamed()</a></code> </p>
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</td>
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<td><p>Transform to microorganism ID</p></td>
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</tr><tr>
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@ -397,6 +397,12 @@
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</tr>
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<tr>
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<td>
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<p><code><a href="availability.html">availability()</a></code> </p>
|
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</td>
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<td><p>Check availability of columns</p></td>
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</tr><tr>
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<td>
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<p><code><a href="count.html">count_R()</a></code> <code><a href="count.html">count_IR()</a></code> <code><a href="count.html">count_I()</a></code> <code><a href="count.html">count_SI()</a></code> <code><a href="count.html">count_S()</a></code> <code><a href="count.html">count_all()</a></code> <code><a href="count.html">n_rsi()</a></code> <code><a href="count.html">count_df()</a></code> </p>
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</td>
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@ -521,18 +527,6 @@
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<td><p>Pattern Matching</p></td>
|
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</tr><tr>
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|
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<td>
|
||||
<p><code><a href="mo_failures.html">mo_failures()</a></code> </p>
|
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</td>
|
||||
<td><p>Vector of failed coercion attempts</p></td>
|
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</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="mo_renamed.html">mo_renamed()</a></code> </p>
|
||||
</td>
|
||||
<td><p>Vector of taxonomic renamed items</p></td>
|
||||
</tr><tr>
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||||
|
||||
<td>
|
||||
<p><code><a href="AMR-deprecated.html">ratio()</a></code> <code><a href="AMR-deprecated.html">guess_mo()</a></code> <code><a href="AMR-deprecated.html">guess_atc()</a></code> <code><a href="AMR-deprecated.html">ab_property()</a></code> <code><a href="AMR-deprecated.html">ab_atc()</a></code> <code><a href="AMR-deprecated.html">ab_official()</a></code> <code><a href="AMR-deprecated.html">ab_name()</a></code> <code><a href="AMR-deprecated.html">ab_trivial_nl()</a></code> <code><a href="AMR-deprecated.html">ab_certe()</a></code> <code><a href="AMR-deprecated.html">ab_umcg()</a></code> <code><a href="AMR-deprecated.html">ab_tradenames()</a></code> <code><a href="AMR-deprecated.html">atc_ddd()</a></code> <code><a href="AMR-deprecated.html">atc_groups()</a></code> </p>
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</td>
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@ -47,7 +47,7 @@
|
||||
<script src="../extra.js"></script>
|
||||
<meta property="og:title" content="Translation table for microorganism codes — microorganisms.codes" />
|
||||
|
||||
<meta property="og:description" content="A data set containing commonly used codes for microorganisms. Define your own with set_mo_source." />
|
||||
<meta property="og:description" content="A data set containing commonly used codes for microorganisms, from laboratory systems and WHONET. Define your own with set_mo_source." />
|
||||
|
||||
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
|
||||
<meta name="twitter:card" content="summary" />
|
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@ -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">0.5.0.9016</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9017</span>
|
||||
</span>
|
||||
</div>
|
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|
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@ -230,7 +230,7 @@
|
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|
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<div class="ref-description">
|
||||
|
||||
<p>A data set containing commonly used codes for microorganisms. Define your own with <code><a href='mo_source.html'>set_mo_source</a></code>.</p>
|
||||
<p>A data set containing commonly used codes for microorganisms, from laboratory systems and WHONET. Define your own with <code><a href='mo_source.html'>set_mo_source</a></code>.</p>
|
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|
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</div>
|
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@ -238,11 +238,19 @@
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|
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<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
|
||||
|
||||
<p>A <code><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></code> with 3,303 observations and 2 variables:</p><dl class='dl-horizontal'>
|
||||
<p>A <code><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></code> with 4,731 observations and 2 variables:</p><dl class='dl-horizontal'>
|
||||
<dt><code>certe</code></dt><dd><p>Commonly used code of a microorganism</p></dd>
|
||||
<dt><code>mo</code></dt><dd><p>Code of microorganism in <code><a href='microorganisms.html'>microorganisms</a></code></p></dd>
|
||||
<dt><code>mo</code></dt><dd><p>ID of the microorganism in the <code><a href='microorganisms.html'>microorganisms</a></code> data set</p></dd>
|
||||
</dl>
|
||||
|
||||
<h2 class="hasAnchor" id="itis"><a class="anchor" href="#itis"></a>ITIS</h2>
|
||||
|
||||
|
||||
<p><img src='figures/logo_itis.jpg' height=60px style=margin-bottom:5px /> <br />
|
||||
This package contains the <strong>complete microbial taxonomic data</strong> (with all nine taxonomic ranks - from kingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, <a href='https://www.itis.gov'>https://www.itis.gov</a>).</p>
|
||||
<p>All ~20,000 (sub)species from <strong>the taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package</strong>, as well as all their ~2,500 previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This allows users to use authoritative taxonomic information for their data analysis on any microorganism, not only human pathogens. It also helps to quickly determine the Gram stain of bacteria, since ITIS honours the taxonomic branching order of bacterial phyla according to Cavalier-Smith (2002), which defines that all bacteria are classified into either subkingdom Negibacteria or subkingdom Posibacteria.</p>
|
||||
<p>ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3].</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>
|
||||
|
||||
|
||||
@ -261,6 +269,8 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
|
||||
|
||||
<li><a href="#format">Format</a></li>
|
||||
|
||||
<li><a href="#itis">ITIS</a></li>
|
||||
|
||||
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
|
||||
|
||||
<li><a href="#see-also">See also</a></li>
|
||||
|
||||
@ -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">0.5.0.9016</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9017</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -238,7 +238,7 @@
|
||||
|
||||
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
|
||||
|
||||
<p>A <code><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></code> with 18,833 observations and 15 variables:</p><dl class='dl-horizontal'>
|
||||
<p>A <code><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></code> with 19,456 observations and 15 variables:</p><dl class='dl-horizontal'>
|
||||
<dt><code>mo</code></dt><dd><p>ID of microorganism</p></dd>
|
||||
<dt><code>tsn</code></dt><dd><p>Taxonomic Serial Number (TSN), as defined by ITIS</p></dd>
|
||||
<dt><code>genus</code></dt><dd><p>Taxonomic genus of the microorganism as found in ITIS, see Source</p></dd>
|
||||
@ -260,6 +260,18 @@
|
||||
|
||||
<p>Integrated Taxonomic Information System (ITIS) public online database, <a href='https://www.itis.gov'>https://www.itis.gov</a>.</p>
|
||||
|
||||
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
|
||||
|
||||
<p>Manually added were:</p><ul>
|
||||
<li><p>605 species of Aspergillus (as Aspergillus misses from ITIS, list from https://en.wikipedia.org/wiki/List_of_Aspergillus_species on 2019-02-05)</p></li>
|
||||
<li><p>23 species of Trichophyton (as Trichophyton misses from ITIS, list from https://en.wikipedia.org/wiki/Trichophyton on 2019-02-05)</p></li>
|
||||
<li><p>9 species of Streptococcus (beta haemolytic groups A, B, C, D, F, G, H, K and unspecified)</p></li>
|
||||
<li><p>2 species of Straphylococcus (coagulase-negative [CoNS] and coagulase-positive [CoPS])</p></li>
|
||||
<li><p>1 species of Candida (C. glabrata)</p></li>
|
||||
<li><p>2 other undefined (unknown Gram negatives and unknown Gram positives)</p></li>
|
||||
</ul>
|
||||
<p>These manual entries have no Taxonomic Serial Number (TSN), so can be looked up with <code>filter(microorganisms, is.na(tsn)</code>.</p>
|
||||
|
||||
<h2 class="hasAnchor" id="itis"><a class="anchor" href="#itis"></a>ITIS</h2>
|
||||
|
||||
|
||||
@ -288,6 +300,8 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
|
||||
|
||||
<li><a href="#source">Source</a></li>
|
||||
|
||||
<li><a href="#details">Details</a></li>
|
||||
|
||||
<li><a href="#itis">ITIS</a></li>
|
||||
|
||||
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
|
||||
|
||||
@ -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">0.5.0.9015</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9016</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -244,7 +244,7 @@
|
||||
|
||||
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
|
||||
|
||||
<p>An object of class <code>data.table</code> (inherits from <code>data.frame</code>) with 18833 rows and 15 columns.</p>
|
||||
<p>An object of class <code>data.table</code> (inherits from <code>data.frame</code>) with 19456 rows and 15 columns.</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>
|
||||
|
||||
|
||||
Reference in New Issue
Block a user