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@@ -9,7 +9,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9037</small>
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@@ -104,7 +104,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
<p>It has now created a file <code>"~/mo_source.rds"</code> with the contents of our Excel file. Only the first column with foreign values and the 'mo' column will be kept when creating the RDS file.</p>
<p>And now we can use it in our functions:</p>
<p></p><div class="sourceCode"><pre><code><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a><span class="fu">as.mo</span>(<span class="st">"lab_mo_ecoli"</span>)</span>
<span id="cb1-2"><a href="#cb1-2" tabindex="-1"></a><span class="co">#&gt; Class 'mo'</span></span>
<span id="cb1-2"><a href="#cb1-2" tabindex="-1"></a><span class="co">#&gt; Class &lt;mo&gt;</span></span>
<span id="cb1-3"><a href="#cb1-3" tabindex="-1"></a><span class="co">#&gt; [1] B_ESCHR_COLI</span></span>
<span id="cb1-4"><a href="#cb1-4" tabindex="-1"></a></span>
<span id="cb1-5"><a href="#cb1-5" tabindex="-1"></a><span class="fu">mo_genus</span>(<span class="st">"lab_mo_kpneumoniae"</span>)</span>
@@ -114,7 +114,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
<span id="cb1-9"><a href="#cb1-9" tabindex="-1"></a><span class="fu">as.mo</span>(<span class="fu">c</span>(<span class="st">"Escherichia coli"</span>, <span class="st">"E. coli"</span>, <span class="st">"lab_mo_ecoli"</span>))</span>
<span id="cb1-10"><a href="#cb1-10" tabindex="-1"></a><span class="co">#&gt; </span><span class="al">NOTE</span><span class="co">: Translation to one microorganism was guessed with uncertainty.</span></span>
<span id="cb1-11"><a href="#cb1-11" tabindex="-1"></a><span class="co">#&gt; Use mo_uncertainties() to review it.</span></span>
<span id="cb1-12"><a href="#cb1-12" tabindex="-1"></a><span class="co">#&gt; Class 'mo'</span></span>
<span id="cb1-12"><a href="#cb1-12" tabindex="-1"></a><span class="co">#&gt; Class &lt;mo&gt;</span></span>
<span id="cb1-13"><a href="#cb1-13" tabindex="-1"></a><span class="co">#&gt; [1] B_ESCHR_COLI B_ESCHR_COLI B_ESCHR_COLI</span></span></code></pre><p></p></div>
<p>If we edit the Excel file by, let's say, adding row 4 like this:</p>
<p></p><div class="sourceCode"><pre><code><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a> <span class="sc">|</span> A <span class="sc">|</span> B <span class="sc">|</span></span>
@@ -129,7 +129,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
<span id="cb1-2"><a href="#cb1-2" tabindex="-1"></a><span class="co">#&gt; </span><span class="al">NOTE</span><span class="co">: Updated mo_source file '/Users/me/mo_source.rds' (0.3 kB) from</span></span>
<span id="cb1-3"><a href="#cb1-3" tabindex="-1"></a><span class="co">#&gt; '/Users/me/Documents/ourcodes.xlsx' (9 kB), columns</span></span>
<span id="cb1-4"><a href="#cb1-4" tabindex="-1"></a><span class="co">#&gt; "Organisation XYZ" and "mo"</span></span>
<span id="cb1-5"><a href="#cb1-5" tabindex="-1"></a><span class="co">#&gt; Class 'mo'</span></span>
<span id="cb1-5"><a href="#cb1-5" tabindex="-1"></a><span class="co">#&gt; Class &lt;mo&gt;</span></span>
<span id="cb1-6"><a href="#cb1-6" tabindex="-1"></a><span class="co">#&gt; [1] B_ESCHR_COLI</span></span>
<span id="cb1-7"><a href="#cb1-7" tabindex="-1"></a></span>
<span id="cb1-8"><a href="#cb1-8" tabindex="-1"></a><span class="fu">mo_genus</span>(<span class="st">"lab_Staph_aureus"</span>)</span>