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(v1.0.1.9005) as.mo() improvements
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@ -17,16 +17,16 @@
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@ -47,8 +47,7 @@
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<meta property="og:title" content="Use predefined reference data set — mo_source" />
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<meta property="og:description" content="These functions can be used to predefine your own reference to be used in as.mo() and consequently all mo_* functions like mo_genus() and mo_gramstain().
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This is the fastest way to have your organisation (or analysis) specific codes picked up and translated by this package." />
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@ -80,7 +79,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
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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="Latest development version">1.0.1</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
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</span>
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</div>
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@ -116,6 +115,13 @@ This is the fastest way to have your organisation (or analysis) specific codes p
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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/PCA.html">
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<span class="fa fa-compress"></span>
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Conduct principal component analysis for AMR
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</a>
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</li>
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<li>
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<a href="../articles/MDR.html">
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<span class="fa fa-skull-crossbones"></span>
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@ -256,9 +262,8 @@ This is the fastest way to have your organisation (or analysis) specific codes p
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4 | | |
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</pre>
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<p>We save it as <code>"home/me/ourcodes.xlsx"</code>. Now we have to set it as a source:</p><pre>set_mo_source("home/me/ourcodes.xlsx")
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# Created mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'.
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</pre>
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<p>We save it as <code>"home/me/ourcodes.xlsx"</code>. Now we have to set it as a source:</p><pre><span class='fu'>set_mo_source</span>(<span class='st'>"home/me/ourcodes.xlsx"</span>)
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<span class='co'># Created mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'.</span></pre>
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<p>It has now created a file <code>"~/.mo_source.rds"</code> with the contents of our Excel file, but only the first column with foreign values and the 'mo' column will be kept.</p>
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<p>And now we can use it in our functions:</p><pre>as.mo("lab_mo_ecoli")
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@ -289,9 +294,8 @@ mo_genus("lab_Staph_aureus")
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[1] "Staphylococcus"
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</pre>
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<p>To remove the reference data file completely, just use <code>""</code> or <code>NULL</code> as input for <code>[set_mo_source()]</code>:</p><pre>set_mo_source(NULL)
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# Removed mo_source file '~/.mo_source.rds'.
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</pre>
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<p>To remove the reference data file completely, just use <code>""</code> or <code>NULL</code> as input for <code>[set_mo_source()]</code>:</p><pre><span class='fu'>set_mo_source</span>(<span class='kw'>NULL</span>)
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<span class='co'># Removed mo_source file '~/.mo_source.rds'.</span></pre>
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<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
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@ -308,7 +312,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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<p>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 comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
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</div>
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<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
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<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
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<h2>Contents</h2>
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<ul class="nav nav-pills nav-stacked">
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<li><a href="#arguments">Arguments</a></li>
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@ -327,7 +331,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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</div>
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
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