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introduction.html
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<body>
<h1 class="title toc-ignore">limony</h1>
<h3 class="subtitle">lake itag measurements over nineteen years</h3>
<p>Please cite: <a href="https://www.biorxiv.org/content/10.1101/2022.08.04.502869v1">Rohwer
& McMahon. Lake iTag measurements over nineteen years, introducing
the limony dataset. <em>bioRxiv.</em> 2022</a></p>
<p>If you use the season data provided, please also cite: <a href="https://www.biorxiv.org/content/10.1101/2022.08.04.502871v1">Rohwer
<em>et al.</em> Species invasions shift microbial phenology in a
two-decade freshwater time series. <em>bioRxiv</em>. 2022</a></p>
<div id="get-started" class="section level2">
<h2>get started</h2>
<p>This package includes the limony dataset and functions to subset it.
The limony dataset is a nineteen year 16S rRNA gene amplicon dataset
from Lake Mendota, WI USA. More information about the dataset itself is
available in the data announcement: <em>citation</em></p>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="co"># Load the limony package</span></span>
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(limony)</span>
<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a><span class="co"># Load the limony data</span></span>
<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a><span class="fu">data</span>(<span class="st">"limony"</span>)</span></code></pre></div>
<p>Let’s explore the nested list data structure:</p>
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="co"># The top level lists contain names, abundances, etc</span></span>
<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a><span class="fu">names</span>(limony)</span>
<span id="cb2-3"><a href="#cb2-3" aria-hidden="true" tabindex="-1"></a><span class="co">#> [1] "names" "av" "sd" "bq" "pd" "br"</span></span>
<span id="cb2-4"><a href="#cb2-4" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb2-5"><a href="#cb2-5" aria-hidden="true" tabindex="-1"></a><span class="co"># The nested lists are for each taxon level</span></span>
<span id="cb2-6"><a href="#cb2-6" aria-hidden="true" tabindex="-1"></a><span class="fu">names</span>(limony<span class="sc">$</span>av)</span>
<span id="cb2-7"><a href="#cb2-7" aria-hidden="true" tabindex="-1"></a><span class="co">#> [1] "Kingdom" "Phylum" "Class" "Order" </span></span>
<span id="cb2-8"><a href="#cb2-8" aria-hidden="true" tabindex="-1"></a><span class="co">#> [5] "Family/Lineage" "Genus/Clade" "Species/Tribe" "seqID"</span></span></code></pre></div>
<table>
<colgroup>
<col width="34%" />
<col width="65%" />
</colgroup>
<thead>
<tr class="header">
<th>list name</th>
<th>Matrix contents</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td>names</td>
<td>Taxonomy Assignments (character)</td>
</tr>
<tr class="even">
<td>av</td>
<td>Average abundances (numeric, the OTU table)</td>
</tr>
<tr class="odd">
<td>sd</td>
<td>Standard deviations (numeric)</td>
</tr>
<tr class="even">
<td>bq</td>
<td>Below quantification (logical, true if pd OR br)</td>
</tr>
<tr class="odd">
<td>pd</td>
<td>Partial detection (logical, true if not present in all
replicates)</td>
</tr>
<tr class="even">
<td>br</td>
<td>Below resolution (logical, true if abundance is lower than a single
read at the worst sequencing depth)</td>
</tr>
</tbody>
</table>
<p>The limony package lets you easily subset this list structure to
extract the dates or taxa you are interested in, while maintaining all
the other information about standard deviation and quantification
limits. This vignette will go through how to use the subsetting
functions.</p>
</div>
<div id="get-otu-table" class="section level2">
<h2>get OTU table</h2>
<p><em>“But wait! I just want an OTU table!”</em> No problem, do this
and skip the rest of the vignette :)</p>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a>otu.table <span class="ot"><-</span> limony<span class="sc">$</span>av<span class="sc">$</span>seqID</span>
<span id="cb3-2"><a href="#cb3-2" aria-hidden="true" tabindex="-1"></a>otu.taxonomy <span class="ot"><-</span> limony<span class="sc">$</span>names<span class="sc">$</span>seqID</span>
<span id="cb3-3"><a href="#cb3-3" aria-hidden="true" tabindex="-1"></a>sample.dates <span class="ot"><-</span> <span class="fu">convert.sample.names.to.dates</span>(<span class="at">sample.names =</span> <span class="fu">colnames</span>(otu.table))</span>
<span id="cb3-4"><a href="#cb3-4" aria-hidden="true" tabindex="-1"></a>otu.table[<span class="dv">1</span><span class="sc">:</span><span class="dv">3</span>,<span class="dv">1</span><span class="sc">:</span><span class="dv">3</span>] <span class="co"># numeric matrix</span></span>
<span id="cb3-5"><a href="#cb3-5" aria-hidden="true" tabindex="-1"></a><span class="co">#> 15Mar2000.pf 30Mar2000.D8pf 14Apr2000.D8pf</span></span>
<span id="cb3-6"><a href="#cb3-6" aria-hidden="true" tabindex="-1"></a><span class="co">#> otu_24787 0 0 0</span></span>
<span id="cb3-7"><a href="#cb3-7" aria-hidden="true" tabindex="-1"></a><span class="co">#> otu_20160 0 0 0</span></span>
<span id="cb3-8"><a href="#cb3-8" aria-hidden="true" tabindex="-1"></a><span class="co">#> otu_12395 0 0 0</span></span>
<span id="cb3-9"><a href="#cb3-9" aria-hidden="true" tabindex="-1"></a>otu.taxonomy[<span class="dv">1</span><span class="sc">:</span><span class="dv">3</span>,<span class="dv">1</span><span class="sc">:</span><span class="dv">3</span>] <span class="co"># character matrix</span></span>
<span id="cb3-10"><a href="#cb3-10" aria-hidden="true" tabindex="-1"></a><span class="co">#> kingdom phylum class </span></span>
<span id="cb3-11"><a href="#cb3-11" aria-hidden="true" tabindex="-1"></a><span class="co">#> [1,] "Archaea" "Aenigmarchaeota" "Aenigmarchaeia" </span></span>
<span id="cb3-12"><a href="#cb3-12" aria-hidden="true" tabindex="-1"></a><span class="co">#> [2,] "Archaea" "Aenigmarchaeota" "Deep_Sea_Euryarchaeotic_Group"</span></span>
<span id="cb3-13"><a href="#cb3-13" aria-hidden="true" tabindex="-1"></a><span class="co">#> [3,] "Archaea" "Crenarchaeota" "Bathyarchaeia"</span></span>
<span id="cb3-14"><a href="#cb3-14" aria-hidden="true" tabindex="-1"></a>sample.dates[<span class="dv">1</span><span class="sc">:</span><span class="dv">3</span>] <span class="co"># dates vector</span></span>
<span id="cb3-15"><a href="#cb3-15" aria-hidden="true" tabindex="-1"></a><span class="co">#> [1] "2000-03-15 +05" "2000-03-30 +05" "2000-04-14 +05"</span></span></code></pre></div>
</div>
<div id="subset-by-sample" class="section level2">
<h2>subset by sample</h2>
<p>First get the column indexes of the samples using
<code>get.sample.inexes</code> and then subset limony using
<code>subset.by.sample</code>.</p>
<p>Example: Remove non-standard samples that were pre-filtered:</p>
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb4-1"><a href="#cb4-1" aria-hidden="true" tabindex="-1"></a>index <span class="ot"><-</span> <span class="fu">get.sample.indexes</span>(<span class="at">my.list =</span> limony, <span class="at">remove.prefiltered =</span> <span class="cn">TRUE</span>)</span>
<span id="cb4-2"><a href="#cb4-2" aria-hidden="true" tabindex="-1"></a>no.pf <span class="ot"><-</span> <span class="fu">subset.by.sample</span>(<span class="at">my.list =</span> limony, <span class="at">keep.index =</span> index)</span></code></pre></div>
<p>Example: Keep only samples from 2015:</p>
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb5-1"><a href="#cb5-1" aria-hidden="true" tabindex="-1"></a>index <span class="ot"><-</span> <span class="fu">get.sample.indexes</span>(<span class="at">my.list =</span> limony, <span class="at">start.YY.MM.DD =</span> <span class="st">"15-1-1"</span>, <span class="at">end.YY.MM.DD =</span> <span class="st">"15-12-31"</span>)</span>
<span id="cb5-2"><a href="#cb5-2" aria-hidden="true" tabindex="-1"></a>only<span class="fl">.2015</span> <span class="ot"><-</span> <span class="fu">subset.by.sample</span>(<span class="at">my.list =</span> limony, <span class="at">keep.index =</span> index)</span></code></pre></div>
<p>Example: Keep only samples from June, but across all years:</p>
<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb6-1"><a href="#cb6-1" aria-hidden="true" tabindex="-1"></a>index <span class="ot"><-</span> <span class="fu">get.sample.indexes</span>(<span class="at">my.list =</span> limony, <span class="at">start.YY.MM.DD =</span> <span class="st">"00-6-1"</span>, <span class="at">end.YY.MM.DD =</span> <span class="st">"00-6-31"</span>, <span class="at">dates.are.season.range =</span> <span class="cn">TRUE</span>) <span class="co"># year is ignored, can be any year</span></span>
<span id="cb6-2"><a href="#cb6-2" aria-hidden="true" tabindex="-1"></a>only.June <span class="ot"><-</span> <span class="fu">subset.by.sample</span>(<span class="at">my.list =</span> limony, <span class="at">keep.index =</span> index)</span></code></pre></div>
<p>Example: Keep only summer season samples from after the invasions
(refer to <a href="https://www.biorxiv.org/content/10.1101/2022.08.04.502871v1">this
paper</a> for the season definitions):</p>
<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb7-1"><a href="#cb7-1" aria-hidden="true" tabindex="-1"></a><span class="co"># first load the season data</span></span>
<span id="cb7-2"><a href="#cb7-2" aria-hidden="true" tabindex="-1"></a><span class="fu">data</span>(<span class="st">"key"</span>) </span>
<span id="cb7-3"><a href="#cb7-3" aria-hidden="true" tabindex="-1"></a>index <span class="ot"><-</span> <span class="fu">get.sample.indexes</span>(<span class="at">my.list =</span> limony, <span class="at">my.key =</span> key, <span class="at">selected.seasons =</span> <span class="fu">c</span>(<span class="st">"early summer"</span>, <span class="st">"late summer"</span>), <span class="at">selected.invasions =</span> <span class="fu">c</span>(<span class="st">"spiny"</span>,<span class="st">"zebra"</span>)) </span>
<span id="cb7-4"><a href="#cb7-4" aria-hidden="true" tabindex="-1"></a>only.invaded.summer <span class="ot"><-</span> <span class="fu">subset.by.sample</span>(<span class="at">my.list =</span> limony, <span class="at">keep.index =</span> index)</span></code></pre></div>
</div>
<div id="subset-by-taxa" class="section level2">
<h2>subset by taxa</h2>
<p>First you flatten the list structure to a single taxon level using
<code>flatten.to.single.level</code>, then you find the indexes of the
taxa you want to keep using <code>get.taxon.indexes</code>, then you
subset to those taxa using <code>subset.by.taxa</code>, and finally you
re-group to get all the taxonomy levels again using
<code>group.by.tax</code>. By re-grouping the taxonomy lists you can
keep track of the average and standard deviation at each taxonomy
level.</p>
<p>Example: Keep only acI</p>
<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb8-1"><a href="#cb8-1" aria-hidden="true" tabindex="-1"></a>flat.list <span class="ot"><-</span> <span class="fu">flatten.to.single.level</span>(<span class="at">my.list =</span> limony)</span>
<span id="cb8-2"><a href="#cb8-2" aria-hidden="true" tabindex="-1"></a>index <span class="ot"><-</span> <span class="fu">get.taxon.indexes</span>(<span class="at">my.list =</span> flat.list, <span class="at">taxa =</span> <span class="st">"acI"</span>)</span>
<span id="cb8-3"><a href="#cb8-3" aria-hidden="true" tabindex="-1"></a>flat.acI <span class="ot"><-</span> <span class="fu">subset.by.taxa</span>(<span class="at">my.list =</span> flat.list, <span class="at">keep.index =</span> index)</span>
<span id="cb8-4"><a href="#cb8-4" aria-hidden="true" tabindex="-1"></a>acI <span class="ot"><-</span> <span class="fu">group.by.tax</span>(<span class="at">my.list =</span> flat.acI)</span></code></pre></div>
<p>Example: Remove chloroplasts and renormalize the data</p>
<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb9-1"><a href="#cb9-1" aria-hidden="true" tabindex="-1"></a>flat.list <span class="ot"><-</span> <span class="fu">flatten.to.single.level</span>(<span class="at">my.list =</span> limony)</span>
<span id="cb9-2"><a href="#cb9-2" aria-hidden="true" tabindex="-1"></a>index <span class="ot"><-</span> <span class="fu">get.taxon.indexes</span>(<span class="at">my.list =</span> flat.list, <span class="at">taxa =</span> <span class="st">"Chloroplast"</span>)</span>
<span id="cb9-3"><a href="#cb9-3" aria-hidden="true" tabindex="-1"></a>flat.no.chloro <span class="ot"><-</span> <span class="fu">subset.by.taxa</span>(<span class="at">my.list =</span> flat.list, <span class="at">keep.index =</span> <span class="sc">-</span>index) <span class="co"># note the minus sign in front of index</span></span>
<span id="cb9-4"><a href="#cb9-4" aria-hidden="true" tabindex="-1"></a>no.chloro <span class="ot"><-</span> <span class="fu">group.by.tax</span>(<span class="at">my.list =</span> flat.no.chloro)</span></code></pre></div>
</div>
<div id="spell-the-taxa-names-correctly" class="section level2">
<h2>spell the taxa names correctly</h2>
<p>Subsetting by taxa can be annoying, because the taxonomy name is case
sensitive and must be spelled correctly. To help you figure out what the
correct names are, there are is a handy function called
<code>print.names.under.taxon</code>.</p>
<p>Example: I want to subset Microcystis, but I don’t know exactly what
it’s called in Silva.</p>
<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb10-1"><a href="#cb10-1" aria-hidden="true" tabindex="-1"></a><span class="co"># I know it's a "Cyanobacteriales"</span></span>
<span id="cb10-2"><a href="#cb10-2" aria-hidden="true" tabindex="-1"></a><span class="fu">print.names.under.taxon</span>(<span class="at">my.list =</span> limony, <span class="at">taxon =</span> <span class="st">"Cyanobacteriales"</span>)</span>
<span id="cb10-3"><a href="#cb10-3" aria-hidden="true" tabindex="-1"></a><span class="co">#> Cyanobacteriales is a Order which is taxon level 4 </span></span>
<span id="cb10-4"><a href="#cb10-4" aria-hidden="true" tabindex="-1"></a><span class="co">#> Kingdom Phylum Class Order </span></span>
<span id="cb10-5"><a href="#cb10-5" aria-hidden="true" tabindex="-1"></a><span class="co">#> [1,] "Bacteria" "Cyanobacteria" "Cyanobacteriia" "Cyanobacteriales"</span></span>
<span id="cb10-6"><a href="#cb10-6" aria-hidden="true" tabindex="-1"></a><span class="co">#> [1] "Cyanobacteriaceae" "Gloeocapsaceae" </span></span>
<span id="cb10-7"><a href="#cb10-7" aria-hidden="true" tabindex="-1"></a><span class="co">#> [3] "Microcystaceae" "Nostocaceae" </span></span>
<span id="cb10-8"><a href="#cb10-8" aria-hidden="true" tabindex="-1"></a><span class="co">#> [5] "Oscillatoriaceae" "Phormidiaceae" </span></span>
<span id="cb10-9"><a href="#cb10-9" aria-hidden="true" tabindex="-1"></a><span class="co">#> [7] "unclassified.Cyanobacteriales"</span></span>
<span id="cb10-10"><a href="#cb10-10" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb10-11"><a href="#cb10-11" aria-hidden="true" tabindex="-1"></a><span class="co"># Aha! Looks like it's "Microcystaceae".</span></span></code></pre></div>
<p>Example putting everything together:</p>
<div class="sourceCode" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb11-1"><a href="#cb11-1" aria-hidden="true" tabindex="-1"></a><span class="co"># Now I can use this spelling to subset out Microcystis in July:</span></span>
<span id="cb11-2"><a href="#cb11-2" aria-hidden="true" tabindex="-1"></a>flat.lim <span class="ot"><-</span> <span class="fu">flatten.to.single.level</span>(<span class="at">my.list =</span> limony)</span>
<span id="cb11-3"><a href="#cb11-3" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb11-4"><a href="#cb11-4" aria-hidden="true" tabindex="-1"></a>index <span class="ot"><-</span> <span class="fu">get.taxon.indexes</span>(<span class="at">my.list =</span> flat.lim, <span class="at">taxa =</span> <span class="st">"Microcystaceae"</span>)</span>
<span id="cb11-5"><a href="#cb11-5" aria-hidden="true" tabindex="-1"></a><span class="co">#> Microcystaceae is a lineage which is taxon level 5 </span></span>
<span id="cb11-6"><a href="#cb11-6" aria-hidden="true" tabindex="-1"></a><span class="co">#> kingdom phylum class order </span></span>
<span id="cb11-7"><a href="#cb11-7" aria-hidden="true" tabindex="-1"></a><span class="co">#> [1,] "Bacteria" "Cyanobacteria" "Cyanobacteriia" "Cyanobacteriales"</span></span>
<span id="cb11-8"><a href="#cb11-8" aria-hidden="true" tabindex="-1"></a><span class="co">#> lineage </span></span>
<span id="cb11-9"><a href="#cb11-9" aria-hidden="true" tabindex="-1"></a><span class="co">#> [1,] "Microcystaceae"</span></span>
<span id="cb11-10"><a href="#cb11-10" aria-hidden="true" tabindex="-1"></a><span class="co">#> keeping 222 OTUs belonging to lineage Microcystaceae </span></span>
<span id="cb11-11"><a href="#cb11-11" aria-hidden="true" tabindex="-1"></a><span class="co">#> </span></span>
<span id="cb11-12"><a href="#cb11-12" aria-hidden="true" tabindex="-1"></a><span class="co">#> Returning the row indexes for 222 total OTUs that belong to taxa you want to keep.</span></span>
<span id="cb11-13"><a href="#cb11-13" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb11-14"><a href="#cb11-14" aria-hidden="true" tabindex="-1"></a>microcystis <span class="ot"><-</span> <span class="fu">subset.by.taxa</span>(<span class="at">my.list =</span> flat.lim, <span class="at">keep.index =</span> index)</span>
<span id="cb11-15"><a href="#cb11-15" aria-hidden="true" tabindex="-1"></a><span class="co">#> You are subsetting your samples to this percent of the orig. reads:</span></span>
<span id="cb11-16"><a href="#cb11-16" aria-hidden="true" tabindex="-1"></a><span class="co">#> Min. 1st Qu. Median Mean 3rd Qu. Max. </span></span>
<span id="cb11-17"><a href="#cb11-17" aria-hidden="true" tabindex="-1"></a><span class="co">#> 0.00000 0.04354 0.53811 1.15198 1.48219 15.27081</span></span>
<span id="cb11-18"><a href="#cb11-18" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb11-19"><a href="#cb11-19" aria-hidden="true" tabindex="-1"></a>index <span class="ot"><-</span> <span class="fu">get.sample.indexes</span>(<span class="at">my.list =</span> microcystis, <span class="at">start.YY.MM.DD =</span> <span class="st">"00-7-1"</span>, <span class="at">end.YY.MM.DD =</span> <span class="st">"19-7-31"</span>, <span class="at">dates.are.season.range =</span> <span class="cn">TRUE</span>, <span class="at">remove.prefiltered =</span> <span class="cn">TRUE</span>)</span>
<span id="cb11-20"><a href="#cb11-20" aria-hidden="true" tabindex="-1"></a><span class="co">#> The date range is: 2000-07-01 - 2000-07-31 </span></span>
<span id="cb11-21"><a href="#cb11-21" aria-hidden="true" tabindex="-1"></a><span class="co">#> The date range is: 2001-07-01 - 2001-07-31 </span></span>
<span id="cb11-22"><a href="#cb11-22" aria-hidden="true" tabindex="-1"></a><span class="co">#> The date range is: 2002-07-01 - 2002-07-31 </span></span>
<span id="cb11-23"><a href="#cb11-23" aria-hidden="true" tabindex="-1"></a><span class="co">#> The date range is: 2003-07-01 - 2003-07-31 </span></span>
<span id="cb11-24"><a href="#cb11-24" aria-hidden="true" tabindex="-1"></a><span class="co">#> The date range is: 2004-07-01 - 2004-07-31 </span></span>
<span id="cb11-25"><a href="#cb11-25" aria-hidden="true" tabindex="-1"></a><span class="co">#> The date range is: 2005-07-01 - 2005-07-31 </span></span>
<span id="cb11-26"><a href="#cb11-26" aria-hidden="true" tabindex="-1"></a><span class="co">#> The date range is: 2006-07-01 - 2006-07-31 </span></span>
<span id="cb11-27"><a href="#cb11-27" aria-hidden="true" tabindex="-1"></a><span class="co">#> The date range is: 2007-07-01 - 2007-07-31 </span></span>
<span id="cb11-28"><a href="#cb11-28" aria-hidden="true" tabindex="-1"></a><span class="co">#> The date range is: 2008-07-01 - 2008-07-31 </span></span>
<span id="cb11-29"><a href="#cb11-29" aria-hidden="true" tabindex="-1"></a><span class="co">#> The date range is: 2009-07-01 - 2009-07-31 </span></span>
<span id="cb11-30"><a href="#cb11-30" aria-hidden="true" tabindex="-1"></a><span class="co">#> The date range is: 2010-07-01 - 2010-07-31 </span></span>
<span id="cb11-31"><a href="#cb11-31" aria-hidden="true" tabindex="-1"></a><span class="co">#> The date range is: 2011-07-01 - 2011-07-31 </span></span>
<span id="cb11-32"><a href="#cb11-32" aria-hidden="true" tabindex="-1"></a><span class="co">#> The date range is: 2012-07-01 - 2012-07-31 </span></span>
<span id="cb11-33"><a href="#cb11-33" aria-hidden="true" tabindex="-1"></a><span class="co">#> The date range is: 2013-07-01 - 2013-07-31 </span></span>
<span id="cb11-34"><a href="#cb11-34" aria-hidden="true" tabindex="-1"></a><span class="co">#> The date range is: 2014-07-01 - 2014-07-31 </span></span>
<span id="cb11-35"><a href="#cb11-35" aria-hidden="true" tabindex="-1"></a><span class="co">#> The date range is: 2015-07-01 - 2015-07-31 </span></span>
<span id="cb11-36"><a href="#cb11-36" aria-hidden="true" tabindex="-1"></a><span class="co">#> The date range is: 2016-07-01 - 2016-07-31 </span></span>
<span id="cb11-37"><a href="#cb11-37" aria-hidden="true" tabindex="-1"></a><span class="co">#> The date range is: 2017-07-01 - 2017-07-31 </span></span>
<span id="cb11-38"><a href="#cb11-38" aria-hidden="true" tabindex="-1"></a><span class="co">#> The date range is: 2018-07-01 - 2018-07-31 </span></span>
<span id="cb11-39"><a href="#cb11-39" aria-hidden="true" tabindex="-1"></a><span class="co">#> The date range is: 2019-07-01 - 2019-07-31 </span></span>
<span id="cb11-40"><a href="#cb11-40" aria-hidden="true" tabindex="-1"></a><span class="co">#> Returning the column indexes for 69 total samples that you want to keep.</span></span>
<span id="cb11-41"><a href="#cb11-41" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb11-42"><a href="#cb11-42" aria-hidden="true" tabindex="-1"></a>microcystis <span class="ot"><-</span> <span class="fu">subset.by.sample</span>(<span class="at">my.list =</span> microcystis, <span class="at">keep.index =</span> index)</span>
<span id="cb11-43"><a href="#cb11-43" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb11-44"><a href="#cb11-44" aria-hidden="true" tabindex="-1"></a>microcystis <span class="ot"><-</span> <span class="fu">group.by.tax</span>(<span class="at">my.list =</span> microcystis)</span>
<span id="cb11-45"><a href="#cb11-45" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb11-46"><a href="#cb11-46" aria-hidden="true" tabindex="-1"></a><span class="co"># And I can look at Microcystis OTUs:</span></span>
<span id="cb11-47"><a href="#cb11-47" aria-hidden="true" tabindex="-1"></a>microcystis<span class="sc">$</span>av<span class="sc">$</span>seqID[<span class="dv">1</span><span class="sc">:</span><span class="dv">3</span>,<span class="dv">1</span><span class="sc">:</span><span class="dv">3</span>]</span>
<span id="cb11-48"><a href="#cb11-48" aria-hidden="true" tabindex="-1"></a><span class="co">#> 01Jul2002 17Jul2002 11Jul2003</span></span>
<span id="cb11-49"><a href="#cb11-49" aria-hidden="true" tabindex="-1"></a><span class="co">#> otu_10079 0 0 0</span></span>
<span id="cb11-50"><a href="#cb11-50" aria-hidden="true" tabindex="-1"></a><span class="co">#> otu_10125 0 0 0</span></span>
<span id="cb11-51"><a href="#cb11-51" aria-hidden="true" tabindex="-1"></a><span class="co">#> otu_10354 0 0 0</span></span>
<span id="cb11-52"><a href="#cb11-52" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb11-53"><a href="#cb11-53" aria-hidden="true" tabindex="-1"></a><span class="co"># Or at the Microcystis Genus</span></span>
<span id="cb11-54"><a href="#cb11-54" aria-hidden="true" tabindex="-1"></a>microcystis<span class="sc">$</span>av<span class="sc">$</span><span class="st">`</span><span class="at">Genus/Clade</span><span class="st">`</span>[ ,<span class="dv">1</span><span class="sc">:</span><span class="dv">3</span>, drop<span class="ot">=</span><span class="cn">FALSE</span>]</span>
<span id="cb11-55"><a href="#cb11-55" aria-hidden="true" tabindex="-1"></a><span class="co">#> 01Jul2002 17Jul2002 11Jul2003</span></span>
<span id="cb11-56"><a href="#cb11-56" aria-hidden="true" tabindex="-1"></a><span class="co">#> Microcystis.Microcystaceae 1.5151515 0.52292207 1.151832212</span></span>
<span id="cb11-57"><a href="#cb11-57" aria-hidden="true" tabindex="-1"></a><span class="co">#> Snowella 0.1176817 0.08256664 1.485489032</span></span>
<span id="cb11-58"><a href="#cb11-58" aria-hidden="true" tabindex="-1"></a><span class="co">#> Synechocystis.Microcystaceae 0.0000000 0.00000000 0.000000000</span></span>
<span id="cb11-59"><a href="#cb11-59" aria-hidden="true" tabindex="-1"></a><span class="co">#> unclassified.Microcystaceae 0.0000000 0.00000000 0.002446064</span></span></code></pre></div>
</div>
<div id="contact-me" class="section level2">
<h2>contact me</h2>
<p>If you have more questions about the limony dataset or the limony
package, or if you want to discuss a planned use of this data, please
contact me: <a href="mailto:[email protected]" class="email">[email protected]</a></p>
</div>
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