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(v1.3.0.9001) website update

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dr. M.S. (Matthijs) Berends
2020-08-10 12:46:03 +02:00
parent 0d9602a6a9
commit 7d16bec21f
79 changed files with 2221 additions and 1974 deletions
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docs/reference/as.mo.html
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@ -82,7 +82,7 @@
</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="Latest development version">1.3.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
</span>
</div>
@ -236,15 +236,15 @@
</div>
<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>,
<span class='kw'>reference_df</span> <span class='kw'>=</span> <span class='fu'><a href='mo_source.html'>get_mo_source</a></span>(),
<span class='no'>...</span>
<span class='kw'>x</span>,
Becker = <span class='fl'>FALSE</span>,
Lancefield = <span class='fl'>FALSE</span>,
allow_uncertain = <span class='fl'>TRUE</span>,
reference_df = <span class='fu'><a href='mo_source.html'>get_mo_source</a></span>(),
<span class='kw'>...</span>
)
<span class='fu'>is.mo</span>(<span class='no'>x</span>)
<span class='fu'>is.mo</span>(<span class='kw'>x</span>)
<span class='fu'>mo_failures</span>()
@ -299,10 +299,10 @@
B_KLBSL_PNMN_RHNS Klebsiella pneumoniae rhinoscleromatis
| | | |
| | | |
| | | ---&amp;gt; subspecies, a 4-5 letter acronym
| | ----&amp;gt; species, a 4-5 letter acronym
| ----&amp;gt; genus, a 5-7 letter acronym
----&amp;gt; taxonomic kingdom: A (Archaea), AN (Animalia), B (Bacteria),
| | | ---&gt; subspecies, a 4-5 letter acronym
| | ----&gt; species, a 4-5 letter acronym
| ----&gt; genus, a 5-7 letter acronym
----&gt; taxonomic kingdom: A (Archaea), AN (Animalia), B (Bacteria),
C (Chromista), F (Fungi), P (Protozoa)
</pre>
@ -412,32 +412,32 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<span class='fu'>as.mo</span>(<span class='st'>"GBS"</span>) <span class='co'># Group B Streptococci</span>
<span class='fu'>as.mo</span>(<span class='st'>"S. epidermidis"</span>) <span class='co'># will remain species: B_STPHY_EPDR</span>
<span class='fu'>as.mo</span>(<span class='st'>"S. epidermidis"</span>, <span class='kw'>Becker</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='co'># will not remain species: B_STPHY_CONS</span>
<span class='fu'>as.mo</span>(<span class='st'>"S. epidermidis"</span>, Becker = <span class='fl'>TRUE</span>) <span class='co'># will not remain species: B_STPHY_CONS</span>
<span class='fu'>as.mo</span>(<span class='st'>"S. pyogenes"</span>) <span class='co'># will remain species: B_STRPT_PYGN</span>
<span class='fu'>as.mo</span>(<span class='st'>"S. pyogenes"</span>, <span class='kw'>Lancefield</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='co'># will not remain species: B_STRPT_GRPA</span>
<span class='fu'>as.mo</span>(<span class='st'>"S. pyogenes"</span>, Lancefield = <span class='fl'>TRUE</span>) <span class='co'># will not remain species: B_STRPT_GRPA</span>
<span class='co'># All mo_* functions use as.mo() internally too (see ?mo_property):</span>
<span class='fu'><a href='mo_property.html'>mo_genus</a></span>(<span class='st'>"E. coli"</span>) <span class='co'># returns "Escherichia"</span>
<span class='fu'><a href='mo_property.html'>mo_gramstain</a></span>(<span class='st'>"E. coli"</span>) <span class='co'># returns "Gram negative"</span>
<span class='co'># }</span>
<span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
<span class='no'>df</span>$<span class='no'>mo</span> <span class='kw'>&lt;-</span> <span class='fu'>as.mo</span>(<span class='no'>df</span>$<span class='no'>microorganism_name</span>)
<span class='co'>if</span> (<span class='fl'>FALSE</span>) {
<span class='kw'>df</span><span class='op'>$</span><span class='kw'>mo</span> <span class='op'>&lt;-</span> <span class='fu'>as.mo</span>(<span class='kw'>df</span><span class='op'>$</span><span class='kw'>microorganism_name</span>)
<span class='co'># the select function of the Tidyverse is also supported:</span>
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
<span class='no'>df</span>$<span class='no'>mo</span> <span class='kw'>&lt;-</span> <span class='no'>df</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>microorganism_name</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='kw'><a href='https://dplyr.tidyverse.org'>dplyr</a></span>)
<span class='kw'>df</span><span class='op'>$</span><span class='kw'>mo</span> <span class='op'>&lt;-</span> <span class='kw'>df</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='kw'>microorganism_name</span>) <span class='op'>%&gt;%</span>
<span class='fu'>as.mo</span>()
<span class='co'># and can even contain 2 columns, which is convenient for genus/species combinations:</span>
<span class='no'>df</span>$<span class='no'>mo</span> <span class='kw'>&lt;-</span> <span class='no'>df</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>genus</span>, <span class='no'>species</span>) <span class='kw'>%&gt;%</span>
<span class='kw'>df</span><span class='op'>$</span><span class='kw'>mo</span> <span class='op'>&lt;-</span> <span class='kw'>df</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='kw'>genus</span>, <span class='kw'>species</span>) <span class='op'>%&gt;%</span>
<span class='fu'>as.mo</span>()
<span class='co'># although this works easier and does the same:</span>
<span class='no'>df</span> <span class='kw'>&lt;-</span> <span class='no'>df</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>mo</span> <span class='kw'>=</span> <span class='fu'>as.mo</span>(<span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span>(<span class='no'>genus</span>, <span class='no'>species</span>)))
<span class='kw'>df</span> <span class='op'>&lt;-</span> <span class='kw'>df</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(mo = <span class='fu'>as.mo</span>(<span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span>(<span class='kw'>genus</span>, <span class='kw'>species</span>)))
}</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
@ -454,7 +454,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
</div>
</footer>