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    <h1>Extract phenological metrics</h1>
    <small class="dont-index">Source: <a href="https://github.com/ranghetti/sen2rts/blob/HEAD/R/extract_pheno.R" class="external-link"><code>R/extract_pheno.R</code></a></small>
    <div class="hidden name"><code>extract_pheno.Rd</code></div>
    </div>

    <div class="ref-description">
    <p>Extract phenological metrics from a fitted time series.</p>
    </div>

    <div id="ref-usage">
    <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">extract_pheno</span><span class="op">(</span><span class="va">data</span>, method <span class="op">=</span> <span class="st">"trs"</span>, trs <span class="op">=</span> <span class="fl">0.5</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>.</p></dd>
<dt>method</dt>
<dd><p>Thresholding method among <code>"trs"</code>, <code>"derivatives"</code>,
<code>"klosterman"</code> and <code>"gu"</code> (see <code><a href="https://rdrr.io/pkg/phenopix/man/PhenoExtract.html" class="external-link">phenopix::PhenoExtract()</a></code>).</p></dd>
<dt>trs</dt>
<dd><p>Argument passed to <code><a href="https://rdrr.io/pkg/phenopix/man/PhenoExtract.html" class="external-link">phenopix::PhenoExtract()</a></code> if <code>method = "trs"</code>.
It is valid also for <code>method = "derivatives"</code> thanks to a <code>{sen2rts}</code>
implementation (it will be documented soon).
Other methods do not make use of this argument.</p></dd>
<dt>...</dt>
<dd><p>Additional arguments passed to <code><a href="https://rdrr.io/pkg/phenopix/man/PhenoExtract.html" class="external-link">phenopix::PhenoExtract()</a></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>begin</code>, <code>end</code>, <code>maxval</code>: the dates of begin, end and maximum value in
the cycle as computed by <code><a href="cut_cycles.html">cut_cycles()</a></code>;</p></li>
<li><p>other phenology metrics, depending on <code>method</code>:</p><ul><li><p>if <code>method = "trs"</code> or <code>"derivatives"</code>: <code>sos</code>, <code>eos</code>, <code>los</code>, <code>pop</code>,
<code>mgs</code>, <code>rsp</code>, <code>rau</code>, <code>peak</code>, <code>msp</code>, <code>mau</code> (see
<code><a href="https://rdrr.io/pkg/phenopix/man/PhenoTrs.html" class="external-link">phenopix::PhenoTrs()</a></code> or <code><a href="https://rdrr.io/pkg/phenopix/man/PhenoDeriv.html" class="external-link">phenopix::PhenoDeriv()</a></code>);</p></li>
<li><p>if <code>method = "gu"</code>: <code>UD</code>, <code>SD</code>, <code>DD</code>, <code>RD</code>, <code>maxline</code>, <code>baseline</code>,
<code>prr</code>, <code>psr</code>, <code>plateau.slope</code> (see <code><a href="https://rdrr.io/pkg/phenopix/man/PhenoGu.html" class="external-link">phenopix::PhenoGu()</a></code>);</p></li>
<li><p>if <code>method = "klosterman"</code>: <code>Greenup</code>, <code>Maturity</code>, <code>Senescence</code>,
<code>Dormancy</code> (see <code><a href="https://rdrr.io/pkg/phenopix/man/PhenoKl.html" class="external-link">phenopix::PhenoKl()</a></code>).</p></li>
</ul></li>
</ul></div>
    <div id="author">
    <h2>Author</h2>
    <p>Luigi Ranghetti, PhD (2020) <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">"cf"</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">"ts_filled"</span><span class="op">)</span> <span class="co"># used for plots</span></span>
<span class="r-in"></span>
<span class="r-in"><span class="co"># Default extraction ("trs" method with 50% threshold)</span></span>
<span class="r-in"><span class="va">dt_pheno</span> <span class="op">&lt;-</span> <span class="fu">extract_pheno</span><span class="op">(</span><span class="va">cf</span><span class="op">)</span></span>
<span class="r-in"><span class="fu"><a href="plot.html">plot</a></span><span class="op">(</span><span class="va">ts_filled</span>, fitted <span class="op">=</span> <span class="va">cf</span>, pheno <span class="op">=</span> <span class="va">dt_pheno</span>, plot_dates <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
<span class="r-plt img"><img src="extract_pheno-1.png" alt="" width="864" height="432"></span>
<span class="r-in"></span>
<span class="r-in"><span class="co"># \donttest{</span></span>
<span class="r-in"><span class="co"># Customize parameters (e.g. "derivatives" method with 30% threshold)</span></span>
<span class="r-in"><span class="va">dt_pheno_2</span> <span class="op">&lt;-</span> <span class="fu">extract_pheno</span><span class="op">(</span><span class="va">cf</span>, method <span class="op">=</span> <span class="st">"derivatives"</span>, trs <span class="op">=</span> <span class="fl">0.3</span><span class="op">)</span></span>
<span class="r-in"><span class="fu"><a href="plot.html">plot</a></span><span class="op">(</span><span class="va">ts_filled</span>, fitted <span class="op">=</span> <span class="va">cf</span>, pheno <span class="op">=</span> <span class="va">dt_pheno_2</span>, plot_dates <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
<span class="r-plt img"><img src="extract_pheno-2.png" alt="" width="864" height="432"></span>
<span class="r-in"></span>
<span class="r-in"><span class="co"># Other methods: Klosterman</span></span>
<span class="r-in"><span class="va">dt_pheno_kl</span> <span class="op">&lt;-</span> <span class="fu">extract_pheno</span><span class="op">(</span><span class="va">cf</span>, method <span class="op">=</span> <span class="st">"klosterman"</span><span class="op">)</span></span>
<span class="r-in"><span class="fu"><a href="plot.html">plot</a></span><span class="op">(</span><span class="va">ts_filled</span>, fitted <span class="op">=</span> <span class="va">cf</span>, pheno <span class="op">=</span> <span class="va">dt_pheno_kl</span>, plot_dates <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
<span class="r-plt img"><img src="extract_pheno-3.png" alt="" width="864" height="432"></span>
<span class="r-in"></span>
<span class="r-in"><span class="co"># Other methods: Gu</span></span>
<span class="r-in"><span class="va">dt_pheno_gu</span> <span class="op">&lt;-</span> <span class="fu">extract_pheno</span><span class="op">(</span><span class="va">cf</span>, method <span class="op">=</span> <span class="st">"gu"</span><span class="op">)</span></span>
<span class="r-in"><span class="fu"><a href="plot.html">plot</a></span><span class="op">(</span><span class="va">ts_filled</span>, fitted <span class="op">=</span> <span class="va">cf</span>, pheno <span class="op">=</span> <span class="va">dt_pheno_gu</span>, plot_dates <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
<span class="r-plt img"><img src="extract_pheno-4.png" alt="" width="864" height="432"></span>
<span class="r-in"><span class="co"># }</span></span>
</code></pre></div>
    </div>
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