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  <div class="col-md-9 contents">
    <div class="page-header">
    <h1>Temporally aggregate time series values</h1>
    <small class="dont-index">Source: <a href="https://github.com/ranghetti/sen2rts/blob/HEAD/R/aggregate_pheno.R" class="external-link"><code>R/aggregate_pheno.R</code></a></small>
    <div class="hidden name"><code>aggregate_pheno.Rd</code></div>
    </div>

    <div class="ref-description">
    <p>Aggregate values of time series over phenological
time windows.</p>
    </div>

    <div id="ref-usage">
    <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">aggregate_pheno</span><span class="op">(</span>
  <span class="va">data</span>,
  <span class="va">pheno</span>,
  metrics <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"begin"</span>, <span class="st">"end"</span><span class="op">)</span>,
  fun <span class="op">=</span> <span class="st">"median"</span>,
  reshape <span class="op">=</span> <span class="cn">TRUE</span>,
  skip_fun <span class="op">=</span> <span class="cn">TRUE</span>,
  include_pheno <span class="op">=</span> <span class="cn">FALSE</span>,
  <span class="va">...</span>
<span class="op">)</span></code></pre></div>
    </div>

    <div id="arguments">
    <h2>Arguments</h2>
    <dl><dt>data</dt>
<dd><p>List of fitted time series as generated by function <code><a href="fit_curve.html">fit_curve()</a></code>
or time series in <code>s2ts</code> format (generated using <code><a href="fill_s2ts.html">fill_s2ts()</a></code>).</p></dd>
<dt>pheno</dt>
<dd><p>(optional) Output of <code><a href="extract_pheno.html">extract_pheno()</a></code> or <code><a href="cut_cycles.html">cut_cycles()</a></code>.
If missing, the whole windows are used (in this case, <code>data</code> can only be
a list of fitted time series as generated by function <code><a href="fit_curve.html">fit_curve()</a></code>).</p></dd>
<dt>metrics</dt>
<dd><p>(optional) Two-length character: name of metrics to be used
as beginning and ending dates of the windows. Object <code>pheno</code> must contain
two fields with the corresponding names.
Default is <code>c("begin", "end")</code> (but they could be e.g. <code>c("sos", "eos")</code>).
This parameter is skipped if <code>pheno</code> is missing.</p></dd>
<dt>fun</dt>
<dd><p>(optional) A vector of aggregation function names
(default is <code>"median"</code>).</p></dd>
<dt>reshape</dt>
<dd><p>(optional) Logical: should outputs be wide-to-log reshaped?
If TRUE (default), the output is returned in the "long" format (as described)
here below); if FALSE, n columns named as <code>fun</code> argument are returned
instead than columns <code>fun</code> and <code>value</code>.</p></dd>
<dt>skip_fun</dt>
<dd><p>(optional) Logical: return also the aggregation function name
among outputs (default is FALSE)?
This parameter is used only if <code>fun</code> is 1-length (otherwise it is coerced
to TRUE) and if <code>reshape = TRUE</code>.</p></dd>
<dt>include_pheno</dt>
<dd><p>(optional) Logical: return also the input information
provided in  argument <code>pheno</code> (default is FALSE)?</p></dd>
<dt>...</dt>
<dd><p>Additional arguments passed to <code>fun</code>.</p></dd>
</dl></div>
    <div id="value">
    <h2>Value</h2>
    <p>A data table with the following fields:</p><ul><li><p><code>id</code>: the time series ID (see <code>s2ts</code>);</p></li>
<li><p><code>year</code>: the year (integer);</p></li>
<li><p><code>cycle</code>: the cycle ID (integer);</p></li>
<li><p><code>fun</code>: the aggregation function (if <code>skip_fun = TRUE</code> and <code>fun</code> is a
1-length argument value, this is skipped);</p></li>
<li><p><code>value</code>: output aggregated value.</p></li>
</ul></div>
    <div id="author">
    <h2>Author</h2>
    <p>Luigi Ranghetti, PhD (2021) <a href="mailto:luigi@ranghetti.info">luigi@ranghetti.info</a></p>
    </div>

    <div id="ref-examples">
    <h2>Examples</h2>
    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span class="co"># Load input data</span></span>
<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="st">"ts_filled"</span><span class="op">)</span></span>
<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="st">"dt_cycles"</span><span class="op">)</span></span>
<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="st">"dt_pheno"</span><span class="op">)</span></span>
<span class="r-in"></span>
<span class="r-in"><span class="co"># Aggregate time series over detected cycles (computing the median, as default)</span></span>
<span class="r-in"><span class="va">dt_aggr_0</span> <span class="op">&lt;-</span> <span class="fu">aggregate_pheno</span><span class="op">(</span><span class="va">ts_filled</span>, <span class="va">dt_cycles</span><span class="op">)</span></span>
<span class="r-in"><span class="va">dt_aggr_0</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span>    id year cycle     value</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1:  1 2020     1 0.4956109</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2:  2 2020     1 0.3652678</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3:  2 2020     2 0.1298273</span>
<span class="r-in"></span>
<span class="r-in"><span class="co"># Aggregate time series over phenological metrics using 95% percentile</span></span>
<span class="r-in"><span class="va">dt_aggr</span> <span class="op">&lt;-</span> <span class="fu">aggregate_pheno</span><span class="op">(</span></span>
<span class="r-in">  <span class="va">ts_filled</span>, <span class="va">dt_pheno</span>, </span>
<span class="r-in">  metrics <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"sos"</span>, <span class="st">"eos"</span><span class="op">)</span>, </span>
<span class="r-in">  fun <span class="op">=</span> <span class="st">"quantile"</span>, probs <span class="op">=</span> <span class="fl">0.95</span>, na.rm <span class="op">=</span> <span class="cn">TRUE</span></span>
<span class="r-in"><span class="op">)</span></span>
<span class="r-in"><span class="va">dt_aggr</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span>    id year cycle     value</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1:  1 2020     1 0.9102608</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2:  2 2020     1 0.8379835</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3:  2 2020     2 0.4919376</span>
</code></pre></div>
    </div>
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