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6 changes: 3 additions & 3 deletions index.html
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Expand Up @@ -198,7 +198,7 @@ <h2 class="anchored" data-anchor-id="why-a-forecasting-challenge">Why a forecast
<div class="value-box-showcase html-fill-item html-fill-container"><svg xmlns="http://www.w3.org/2000/svg" viewbox="0 0 16 16" class="bi bi-graph-up " style="height:1em;width:1em;fill:currentColor;vertical-align:-0.125em;" aria-hidden="true" role="img"><path fill-rule="evenodd" d="M0 0h1v15h15v1H0V0Zm14.817 3.113a.5.5 0 0 1 .07.704l-4.5 5.5a.5.5 0 0 1-.74.037L7.06 6.767l-3.656 5.027a.5.5 0 0 1-.808-.588l4-5.5a.5.5 0 0 1 .758-.06l2.609 2.61 4.15-5.073a.5.5 0 0 1 .704-.07Z"></path></svg></div>
<div class="value-box-area html-fill-item html-fill-container">
<p class="value-box-title">Total forecasts submitted to the EFI-USGS Challenge</p>
<p class="value-box-value">251</p>
<p class="value-box-value">253</p>
</div>
</div>
</div>
Expand All @@ -215,7 +215,7 @@ <h2 class="anchored" data-anchor-id="why-a-forecasting-challenge">Why a forecast
<path d="M9.5 8a1.5 1.5 0 1 1-3 0 1.5 1.5 0 0 1 3 0z"></path></svg></div>
<div class="value-box-area html-fill-item html-fill-container">
<p class="value-box-title">Most recent data for model training</p>
<div class="value-box-value html-fill-item html-fill-container">2024-05-06</div>
<div class="value-box-value html-fill-item html-fill-container">2024-05-07</div>
</div>
</div>
</div>
Expand Down Expand Up @@ -272,7 +272,7 @@ <h2 class="anchored" data-anchor-id="contact">Contact</h2>
</section>
<section id="acknowledgements" class="level2">
<h2 class="anchored" data-anchor-id="acknowledgements">Acknowledgements</h2>
<p>Thomas, R. Q., Boettiger, C., Carey, C. C., Dietze, M. C., Johnson, L. R., Kenney, M. A., et al.&nbsp;(2023). The NEON Ecological Forecasting Challenge. Frontiers in Ecology and the Environment, 21(3), 112<e2>&lt;80&gt;&lt;93&gt;113. <a href="https://doi.org/10.1002/fee.2616">https://doi.org/10.1002/fee.2616</a> <br> <br> We thank the EFI community for feedback on the design of the Challenge. This material is based upon work supported by the National Science Foundation under Grant DEB-1926388. <br> <br> Page last updated on 2024-05-06</e2></p>
<p>Thomas, R. Q., Boettiger, C., Carey, C. C., Dietze, M. C., Johnson, L. R., Kenney, M. A., et al.&nbsp;(2023). The NEON Ecological Forecasting Challenge. Frontiers in Ecology and the Environment, 21(3), 112<e2>&lt;80&gt;&lt;93&gt;113. <a href="https://doi.org/10.1002/fee.2616">https://doi.org/10.1002/fee.2616</a> <br> <br> We thank the EFI community for feedback on the design of the Challenge. This material is based upon work supported by the National Science Foundation under Grant DEB-1926388. <br> <br> Page last updated on 2024-05-07</e2></p>


</section>
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168 changes: 99 additions & 69 deletions instructions.html
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Expand Up @@ -318,8 +318,7 @@ <h4 data-number="5.0.2" class="anchored" data-anchor-id="ensemble-or-sample-fore
<h3 data-number="5.1" class="anchored" data-anchor-id="example-forecasts"><span class="header-section-number">5.1</span> Example forecasts</h3>
<p>Here is an example of a forecast that uses a normal distribution:</p>
<div class="cell">
<div class="sourceCode cell-code" id="cb1"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="co"># </span><span class="al">TODO</span><span class="co">: need to update to different example</span></span>
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a>df <span class="ot">&lt;-</span> readr<span class="sc">::</span><span class="fu">read_csv</span>(<span class="st">"https://sdsc.osn.xsede.org/bio230014-bucket01/challenges/forecasts/raw/T20231102190926_aquatics-2023-10-19-climatology.csv.gz"</span>, <span class="at">show_col_types =</span> <span class="cn">FALSE</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="sourceCode cell-code" id="cb1"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a>df <span class="ot">&lt;-</span> readr<span class="sc">::</span><span class="fu">read_csv</span>(<span class="st">"https://sdsc.osn.xsede.org/bio230014-bucket01/challenges/forecasts/raw/project_id=usgsrc4cast/T20240506050515_usgsrc4cast-2024-05-05-climatology.csv.gz"</span>, <span class="at">show_col_types =</span> <span class="cn">FALSE</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<div class="cell">
<div class="sourceCode cell-code" id="cb2"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a>df <span class="sc">|&gt;</span> </span>
Expand All @@ -328,20 +327,24 @@ <h3 data-number="5.1" class="anchored" data-anchor-id="example-forecasts"><span
<div class="cell-output-display">
<table class="table table-sm table-striped small">
<colgroup>
<col style="width: 13%">
<col style="width: 10%">
<col style="width: 10%">
<col style="width: 9%">
<col style="width: 16%">
<col style="width: 7%">
<col style="width: 12%">
<col style="width: 21%">
<col style="width: 6%">
<col style="width: 8%">
<col style="width: 7%">
<col style="width: 11%">
<col style="width: 13%">
<col style="width: 12%">
<col style="width: 9%">
</colgroup>
<thead>
<tr class="header">
<th style="text-align: left;">project_id</th>
<th style="text-align: left;">model_id</th>
<th style="text-align: left;">datetime</th>
<th style="text-align: left;">reference_datetime</th>
<th style="text-align: left;">duration</th>
<th style="text-align: left;">site_id</th>
<th style="text-align: left;">family</th>
<th style="text-align: left;">parameter</th>
Expand All @@ -351,73 +354,84 @@ <h3 data-number="5.1" class="anchored" data-anchor-id="example-forecasts"><span
</thead>
<tbody>
<tr class="odd">
<td style="text-align: left;">usgsrc4cast</td>
<td style="text-align: left;">climatology</td>
<td style="text-align: left;">2023-10-20</td>
<td style="text-align: left;">2023-10-19</td>
<td style="text-align: left;">ARIK</td>
<td style="text-align: left;">2024-05-06</td>
<td style="text-align: left;">2024-05-05</td>
<td style="text-align: left;">P1D</td>
<td style="text-align: left;">USGS-01427510</td>
<td style="text-align: left;">normal</td>
<td style="text-align: left;">mu</td>
<td style="text-align: left;">oxygen</td>
<td style="text-align: right;">4.542862</td>
<td style="text-align: left;">chla</td>
<td style="text-align: right;">2.316215</td>
</tr>
<tr class="even">
<td style="text-align: left;">usgsrc4cast</td>
<td style="text-align: left;">climatology</td>
<td style="text-align: left;">2023-10-20</td>
<td style="text-align: left;">2023-10-19</td>
<td style="text-align: left;">ARIK</td>
<td style="text-align: left;">2024-05-06</td>
<td style="text-align: left;">2024-05-05</td>
<td style="text-align: left;">P1D</td>
<td style="text-align: left;">USGS-01427510</td>
<td style="text-align: left;">normal</td>
<td style="text-align: left;">sigma</td>
<td style="text-align: left;">oxygen</td>
<td style="text-align: right;">1.448393</td>
<td style="text-align: left;">chla</td>
<td style="text-align: right;">1.013190</td>
</tr>
<tr class="odd">
<td style="text-align: left;">usgsrc4cast</td>
<td style="text-align: left;">climatology</td>
<td style="text-align: left;">2023-10-20</td>
<td style="text-align: left;">2023-10-19</td>
<td style="text-align: left;">ARIK</td>
<td style="text-align: left;">2024-05-07</td>
<td style="text-align: left;">2024-05-05</td>
<td style="text-align: left;">P1D</td>
<td style="text-align: left;">USGS-01427510</td>
<td style="text-align: left;">normal</td>
<td style="text-align: left;">mu</td>
<td style="text-align: left;">temperature</td>
<td style="text-align: right;">8.070854</td>
<td style="text-align: left;">chla</td>
<td style="text-align: right;">2.016441</td>
</tr>
<tr class="even">
<td style="text-align: left;">usgsrc4cast</td>
<td style="text-align: left;">climatology</td>
<td style="text-align: left;">2023-10-20</td>
<td style="text-align: left;">2023-10-19</td>
<td style="text-align: left;">ARIK</td>
<td style="text-align: left;">2024-05-07</td>
<td style="text-align: left;">2024-05-05</td>
<td style="text-align: left;">P1D</td>
<td style="text-align: left;">USGS-01427510</td>
<td style="text-align: left;">normal</td>
<td style="text-align: left;">sigma</td>
<td style="text-align: left;">temperature</td>
<td style="text-align: right;">1.330059</td>
<td style="text-align: left;">chla</td>
<td style="text-align: right;">1.013190</td>
</tr>
<tr class="odd">
<td style="text-align: left;">usgsrc4cast</td>
<td style="text-align: left;">climatology</td>
<td style="text-align: left;">2023-10-21</td>
<td style="text-align: left;">2023-10-19</td>
<td style="text-align: left;">ARIK</td>
<td style="text-align: left;">2024-05-08</td>
<td style="text-align: left;">2024-05-05</td>
<td style="text-align: left;">P1D</td>
<td style="text-align: left;">USGS-01427510</td>
<td style="text-align: left;">normal</td>
<td style="text-align: left;">mu</td>
<td style="text-align: left;">oxygen</td>
<td style="text-align: right;">4.194895</td>
<td style="text-align: left;">chla</td>
<td style="text-align: right;">2.694340</td>
</tr>
<tr class="even">
<td style="text-align: left;">usgsrc4cast</td>
<td style="text-align: left;">climatology</td>
<td style="text-align: left;">2023-10-21</td>
<td style="text-align: left;">2023-10-19</td>
<td style="text-align: left;">ARIK</td>
<td style="text-align: left;">2024-05-08</td>
<td style="text-align: left;">2024-05-05</td>
<td style="text-align: left;">P1D</td>
<td style="text-align: left;">USGS-01427510</td>
<td style="text-align: left;">normal</td>
<td style="text-align: left;">sigma</td>
<td style="text-align: left;">oxygen</td>
<td style="text-align: right;">1.448393</td>
<td style="text-align: left;">chla</td>
<td style="text-align: right;">1.013190</td>
</tr>
</tbody>
</table>
</div>
</div>
<p>For an ensemble (or sample) forecast, the <code>family</code> column uses the word <code>ensemble</code> to designate that it is a ensemble forecast and the parameter column is the ensemble member number (<code>1</code>, <code>2</code>, <code>3</code> …)</p>
<div class="cell">
<div class="sourceCode cell-code" id="cb3"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a><span class="co"># </span><span class="al">TODO</span><span class="co">: need to update to different example </span></span>
<span id="cb3-2"><a href="#cb3-2" aria-hidden="true" tabindex="-1"></a>df <span class="ot">&lt;-</span> readr<span class="sc">::</span><span class="fu">read_csv</span>(<span class="st">"https://sdsc.osn.xsede.org/bio230014-bucket01/challenges/forecasts/raw/T20231102190926_aquatics-2023-10-19-persistenceRW.csv.gz"</span>, <span class="at">show_col_types =</span> <span class="cn">FALSE</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="sourceCode cell-code" id="cb3"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a>df <span class="ot">&lt;-</span> readr<span class="sc">::</span><span class="fu">read_csv</span>(<span class="st">"https://sdsc.osn.xsede.org/bio230014-bucket01/challenges/forecasts/raw/project_id=usgsrc4cast/T20240506050515_usgsrc4cast-2024-05-05-persistenceRW.csv.gz"</span>, <span class="at">show_col_types =</span> <span class="cn">FALSE</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<div class="cell">
<div class="sourceCode cell-code" id="cb4"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb4-1"><a href="#cb4-1" aria-hidden="true" tabindex="-1"></a>df <span class="sc">|&gt;</span> </span>
Expand All @@ -427,20 +441,24 @@ <h3 data-number="5.1" class="anchored" data-anchor-id="example-forecasts"><span
<div class="cell-output-display">
<table class="table table-sm table-striped small">
<colgroup>
<col style="width: 15%">
<col style="width: 12%">
<col style="width: 20%">
<col style="width: 8%">
<col style="width: 9%">
<col style="width: 10%">
<col style="width: 11%">
<col style="width: 9%">
<col style="width: 16%">
<col style="width: 7%">
<col style="width: 11%">
<col style="width: 7%">
<col style="width: 8%">
<col style="width: 7%">
<col style="width: 9%">
<col style="width: 12%">
</colgroup>
<thead>
<tr class="header">
<th style="text-align: left;">project_id</th>
<th style="text-align: left;">model_id</th>
<th style="text-align: left;">datetime</th>
<th style="text-align: left;">reference_datetime</th>
<th style="text-align: left;">duration</th>
<th style="text-align: left;">site_id</th>
<th style="text-align: left;">family</th>
<th style="text-align: right;">parameter</th>
Expand All @@ -450,64 +468,76 @@ <h3 data-number="5.1" class="anchored" data-anchor-id="example-forecasts"><span
</thead>
<tbody>
<tr class="odd">
<td style="text-align: left;">usgsrc4cast</td>
<td style="text-align: left;">persistenceRW</td>
<td style="text-align: left;">2023-10-20</td>
<td style="text-align: left;">2023-10-19</td>
<td style="text-align: left;">BARC</td>
<td style="text-align: left;">2024-05-06</td>
<td style="text-align: left;">2024-05-05</td>
<td style="text-align: left;">P1D</td>
<td style="text-align: left;">USGS-01427510</td>
<td style="text-align: left;">ensemble</td>
<td style="text-align: right;">1</td>
<td style="text-align: left;">chla</td>
<td style="text-align: right;">3.795652</td>
<td style="text-align: right;">0.1739193</td>
</tr>
<tr class="even">
<td style="text-align: left;">usgsrc4cast</td>
<td style="text-align: left;">persistenceRW</td>
<td style="text-align: left;">2023-10-20</td>
<td style="text-align: left;">2023-10-19</td>
<td style="text-align: left;">BARC</td>
<td style="text-align: left;">2024-05-06</td>
<td style="text-align: left;">2024-05-05</td>
<td style="text-align: left;">P1D</td>
<td style="text-align: left;">USGS-01427510</td>
<td style="text-align: left;">ensemble</td>
<td style="text-align: right;">2</td>
<td style="text-align: left;">chla</td>
<td style="text-align: right;">3.963322</td>
<td style="text-align: right;">0.1651993</td>
</tr>
<tr class="odd">
<td style="text-align: left;">usgsrc4cast</td>
<td style="text-align: left;">persistenceRW</td>
<td style="text-align: left;">2023-10-20</td>
<td style="text-align: left;">2023-10-19</td>
<td style="text-align: left;">BARC</td>
<td style="text-align: left;">2024-05-06</td>
<td style="text-align: left;">2024-05-05</td>
<td style="text-align: left;">P1D</td>
<td style="text-align: left;">USGS-01427510</td>
<td style="text-align: left;">ensemble</td>
<td style="text-align: right;">3</td>
<td style="text-align: left;">chla</td>
<td style="text-align: right;">2.053637</td>
<td style="text-align: right;">0.2120872</td>
</tr>
<tr class="even">
<td style="text-align: left;">usgsrc4cast</td>
<td style="text-align: left;">persistenceRW</td>
<td style="text-align: left;">2023-10-20</td>
<td style="text-align: left;">2023-10-19</td>
<td style="text-align: left;">BARC</td>
<td style="text-align: left;">2024-05-06</td>
<td style="text-align: left;">2024-05-05</td>
<td style="text-align: left;">P1D</td>
<td style="text-align: left;">USGS-01427510</td>
<td style="text-align: left;">ensemble</td>
<td style="text-align: right;">4</td>
<td style="text-align: left;">chla</td>
<td style="text-align: right;">3.294723</td>
<td style="text-align: right;">0.1574321</td>
</tr>
<tr class="odd">
<td style="text-align: left;">usgsrc4cast</td>
<td style="text-align: left;">persistenceRW</td>
<td style="text-align: left;">2023-10-20</td>
<td style="text-align: left;">2023-10-19</td>
<td style="text-align: left;">BARC</td>
<td style="text-align: left;">2024-05-06</td>
<td style="text-align: left;">2024-05-05</td>
<td style="text-align: left;">P1D</td>
<td style="text-align: left;">USGS-01427510</td>
<td style="text-align: left;">ensemble</td>
<td style="text-align: right;">5</td>
<td style="text-align: left;">chla</td>
<td style="text-align: right;">1.847344</td>
<td style="text-align: right;">0.2035837</td>
</tr>
<tr class="even">
<td style="text-align: left;">usgsrc4cast</td>
<td style="text-align: left;">persistenceRW</td>
<td style="text-align: left;">2023-10-20</td>
<td style="text-align: left;">2023-10-19</td>
<td style="text-align: left;">BARC</td>
<td style="text-align: left;">2024-05-06</td>
<td style="text-align: left;">2024-05-05</td>
<td style="text-align: left;">P1D</td>
<td style="text-align: left;">USGS-01427510</td>
<td style="text-align: left;">ensemble</td>
<td style="text-align: right;">6</td>
<td style="text-align: left;">chla</td>
<td style="text-align: right;">7.829229</td>
<td style="text-align: right;">0.3037156</td>
</tr>
</tbody>
</table>
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