P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-08 18:41:58 +02:00
Code Releases Activity

(v0.8.0.9036) complete documentation rewrite

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2019-11-28 22:32:17 +01:00
parent 7c28b392b1
commit c5f00f4a9f
138 changed files with 2797 additions and 2484 deletions
Download Patch File Download Diff File Expand all files Collapse all files

10
docs/reference/catalogue_of_life.html
View File

@ -85,7 +85,7 @@
</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">0.8.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9036</span>
</span>
</div>
@ -245,7 +245,7 @@
<p><img src='figures/logo_col.png' height=40px style=margin-bottom:5px /> <br />
This package contains the complete taxonomic tree of almost all microorganisms (~70,000 species) from the authoritative and comprehensive Catalogue of Life (<a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.</p>
<p>Click here for more information about the included taxa. Check which version of the Catalogue of Life was included in this package with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version</a>()</code>.</p>
<p>Click here for more information about the included taxa. Check which version of the Catalogue of Life was included in this package with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version()</a></code>.</p>
<h2 class="hasAnchor" id="included-taxa"><a class="anchor" href="#included-taxa"></a>Included taxa</h2>
@ -268,8 +268,8 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<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 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>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p>Data set <code><a href='microorganisms.html'>microorganisms</a></code> for the actual data. <br />
Function <code><a href='as.mo.html'>as.mo</a>()</code> to use the data for intelligent determination of microorganisms.</p></div>
<div class='dont-index'><p>Data set <a href='microorganisms.html'>microorganisms</a> for the actual data. <br />
Function <code><a href='as.mo.html'>as.mo()</a></code> to use the data for intelligent determination of microorganisms.</p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># Get version info of included data set</span>
@ -295,7 +295,7 @@ Function <code><a href='as.mo.html'>as.mo</a>()</code> to use the data for intel
<span class='fu'><a href='mo_property.html'>mo_ref</a></span>(<span class='st'>"E. coli"</span>)
<span class='co'># [1] "Castellani et al., 1919"</span>
<span class='co'># Do not get mistaken - the package only includes microorganisms</span>
<span class='co'># Do not get mistaken - this package is about microorganisms</span>
<span class='fu'><a href='mo_property.html'>mo_kingdom</a></span>(<span class='st'>"C. elegans"</span>)
<span class='co'># [1] "Bacteria" # Bacteria?!</span>
<span class='fu'><a href='mo_property.html'>mo_name</a></span>(<span class='st'>"C. elegans"</span>)