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2
docs/advanced-functionality/drag-drop-csv-tsv.html

@ -80,4 +80,4 @@ The tree will now look like:</p>
<li>The type of the data is currently always categorical -- i.e. numeric data will work, but won't be very usable if there are many values.</li>
<li>Any of following columns specified in the CSV/TSV will be ignored: &quot;name&quot;, &quot;div&quot;, &quot;num_date&quot;, &quot;vaccine&quot;, &quot;labels&quot;, &quot;hidden&quot;, &quot;mutations&quot;, &quot;url&quot;, &quot;authors&quot;, &quot;accession&quot;, &quot;traits&quot;, &quot;children&quot;.</li>
</ul>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 3/15/2020</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/advanced-functionality/view-settings"><span class="arrow-prev"></span><span>View Settings</span></a><a class="docs-next button" href="/auspice/advanced-functionality/misc"><span>Miscellaneous</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 15/03/2020</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/advanced-functionality/view-settings"><span class="arrow-prev"></span><span>View Settings</span></a><a class="docs-next button" href="/auspice/advanced-functionality/misc"><span>Miscellaneous</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>

2
docs/advanced-functionality/drag-drop-csv-tsv/index.html

@ -80,4 +80,4 @@ The tree will now look like:</p>
<li>The type of the data is currently always categorical -- i.e. numeric data will work, but won't be very usable if there are many values.</li>
<li>Any of following columns specified in the CSV/TSV will be ignored: &quot;name&quot;, &quot;div&quot;, &quot;num_date&quot;, &quot;vaccine&quot;, &quot;labels&quot;, &quot;hidden&quot;, &quot;mutations&quot;, &quot;url&quot;, &quot;authors&quot;, &quot;accession&quot;, &quot;traits&quot;, &quot;children&quot;.</li>
</ul>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 3/15/2020</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/advanced-functionality/view-settings"><span class="arrow-prev"></span><span>View Settings</span></a><a class="docs-next button" href="/auspice/advanced-functionality/misc"><span>Miscellaneous</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 15/03/2020</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/advanced-functionality/view-settings"><span class="arrow-prev"></span><span>View Settings</span></a><a class="docs-next button" href="/auspice/advanced-functionality/misc"><span>Miscellaneous</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>

2
docs/advanced-functionality/misc.html

@ -62,4 +62,4 @@ Note that, if a discrete trait is selected, then a proportion of the pie-chart o
<p>If a trait is not set on a node it is considered missing, as well as if (after coersion to lower-case) it has one of the following values:</p>
<pre><code class="hljs css language-js">[<span class="hljs-string">"unknown"</span>, <span class="hljs-string">"?"</span>, <span class="hljs-string">"nan"</span>, <span class="hljs-string">"na"</span>, <span class="hljs-string">"n/a"</span>, <span class="hljs-string">""</span>, <span class="hljs-string">"unassigned"</span>]
</code></pre>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 10/25/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/advanced-functionality/drag-drop-csv-tsv"><span class="arrow-prev"></span><span>Adding extra metadata via CSV/TSV</span></a><a class="docs-next button" href="/auspice/customise-client/introduction"><span>Customising Auspice</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#how-auspice-handles-unknown-or-missing-data">How auspice handles unknown or missing data</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 25/10/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/advanced-functionality/drag-drop-csv-tsv"><span class="arrow-prev"></span><span>Adding extra metadata via CSV/TSV</span></a><a class="docs-next button" href="/auspice/customise-client/introduction"><span>Customising Auspice</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#how-auspice-handles-unknown-or-missing-data">How auspice handles unknown or missing data</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>

2
docs/advanced-functionality/misc/index.html

@ -62,4 +62,4 @@ Note that, if a discrete trait is selected, then a proportion of the pie-chart o
<p>If a trait is not set on a node it is considered missing, as well as if (after coersion to lower-case) it has one of the following values:</p>
<pre><code class="hljs css language-js">[<span class="hljs-string">"unknown"</span>, <span class="hljs-string">"?"</span>, <span class="hljs-string">"nan"</span>, <span class="hljs-string">"na"</span>, <span class="hljs-string">"n/a"</span>, <span class="hljs-string">""</span>, <span class="hljs-string">"unassigned"</span>]
</code></pre>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 10/25/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/advanced-functionality/drag-drop-csv-tsv"><span class="arrow-prev"></span><span>Adding extra metadata via CSV/TSV</span></a><a class="docs-next button" href="/auspice/customise-client/introduction"><span>Customising Auspice</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#how-auspice-handles-unknown-or-missing-data">How auspice handles unknown or missing data</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 25/10/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/advanced-functionality/drag-drop-csv-tsv"><span class="arrow-prev"></span><span>Adding extra metadata via CSV/TSV</span></a><a class="docs-next button" href="/auspice/customise-client/introduction"><span>Customising Auspice</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#how-auspice-handles-unknown-or-missing-data">How auspice handles unknown or missing data</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>

2
docs/advanced-functionality/second-trees.html

@ -73,4 +73,4 @@ Currently, the logic in <code>auspice view</code> is to match all datasets which
<li>have the same number of &quot;parts&quot; in the URL (parts are delimited by a <code>_</code> in the filename or a <code>/</code> in the URL).</li>
<li>differ from the currently selected dataset by only 1 part.</li>
</ul>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 2/5/2020</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/introduction/how-to-run"><span class="arrow-prev"></span><span>How to Run Auspice</span></a><a class="docs-next button" href="/auspice/advanced-functionality/view-settings"><span>View Settings</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#how-to-load-multiple-trees">How to load multiple trees</a></li><li><a href="#showing-potential-datasets-in-the-sidebar">Showing potential datasets in the sidebar</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 05/02/2020</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/introduction/how-to-run"><span class="arrow-prev"></span><span>How to Run Auspice</span></a><a class="docs-next button" href="/auspice/advanced-functionality/view-settings"><span>View Settings</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#how-to-load-multiple-trees">How to load multiple trees</a></li><li><a href="#showing-potential-datasets-in-the-sidebar">Showing potential datasets in the sidebar</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>

2
docs/advanced-functionality/second-trees/index.html

@ -73,4 +73,4 @@ Currently, the logic in <code>auspice view</code> is to match all datasets which
<li>have the same number of &quot;parts&quot; in the URL (parts are delimited by a <code>_</code> in the filename or a <code>/</code> in the URL).</li>
<li>differ from the currently selected dataset by only 1 part.</li>
</ul>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 2/5/2020</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/introduction/how-to-run"><span class="arrow-prev"></span><span>How to Run Auspice</span></a><a class="docs-next button" href="/auspice/advanced-functionality/view-settings"><span>View Settings</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#how-to-load-multiple-trees">How to load multiple trees</a></li><li><a href="#showing-potential-datasets-in-the-sidebar">Showing potential datasets in the sidebar</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 05/02/2020</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/introduction/how-to-run"><span class="arrow-prev"></span><span>How to Run Auspice</span></a><a class="docs-next button" href="/auspice/advanced-functionality/view-settings"><span>View Settings</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#how-to-load-multiple-trees">How to load multiple trees</a></li><li><a href="#showing-potential-datasets-in-the-sidebar">Showing potential datasets in the sidebar</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>

3
docs/advanced-functionality/view-settings.html

@ -126,8 +126,9 @@ All URL queries modify the view away from the default settings -- if you change
<tr><td><code>sidebar</code></td><td>Force the sidebar into a certain state</td><td><code>sidebar=closed</code> or <code>sidebar=open</code></td></tr>
<tr><td><code>legend</code></td><td>Force the legend into a certain state</td><td><code>legend=closed</code> or <code>legend=open</code></td></tr>
<tr><td><code>onlyPanels</code></td><td>Do not display the footer / header. Useful for iframes.</td><td><code>onlyPanels</code></td></tr>
<tr><td><code>ci</code></td><td>Display confidence intervals on the tree.</td><td><code>ci</code></td></tr>
</tbody>
</table>
<p><strong>See this in action:</strong></p>
<p>For instance, go to <a href="https://nextstrain.org/flu/seasonal/h3n2/ha/2y?c=num_date&amp;d=tree,map&amp;m=div&amp;p=grid&amp;r=region">nextstrain.org/flu/seasonal/h3n2/ha/2y?c=num_date&amp;d=tree,map&amp;m=div&amp;r=region</a> and you'll see how we've changed the coloring to a temporal scale (<code>c=num_date</code>), we're only showing the tree &amp; map panels (<code>d=tree,map</code>), the tree x-axis is divergence (<code>m=div</code>) and the map resolution is region (<code>r=region</code>).</p>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 4/8/2020</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/advanced-functionality/second-trees"><span class="arrow-prev"></span><span>Displaying multiple trees</span></a><a class="docs-next button" href="/auspice/advanced-functionality/drag-drop-csv-tsv"><span>Adding extra metadata via CSV/TSV</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#auspice-hardcoded-defaults">Auspice (hardcoded) defaults</a></li><li><a href="#dataset-json-configurable-defaults">Dataset (JSON) configurable defaults</a></li><li><a href="#url-query-options">URL query options</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 15/04/2020</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/advanced-functionality/second-trees"><span class="arrow-prev"></span><span>Displaying multiple trees</span></a><a class="docs-next button" href="/auspice/advanced-functionality/drag-drop-csv-tsv"><span>Adding extra metadata via CSV/TSV</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#auspice-hardcoded-defaults">Auspice (hardcoded) defaults</a></li><li><a href="#dataset-json-configurable-defaults">Dataset (JSON) configurable defaults</a></li><li><a href="#url-query-options">URL query options</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>

3
docs/advanced-functionality/view-settings/index.html

@ -126,8 +126,9 @@ All URL queries modify the view away from the default settings -- if you change
<tr><td><code>sidebar</code></td><td>Force the sidebar into a certain state</td><td><code>sidebar=closed</code> or <code>sidebar=open</code></td></tr>
<tr><td><code>legend</code></td><td>Force the legend into a certain state</td><td><code>legend=closed</code> or <code>legend=open</code></td></tr>
<tr><td><code>onlyPanels</code></td><td>Do not display the footer / header. Useful for iframes.</td><td><code>onlyPanels</code></td></tr>
<tr><td><code>ci</code></td><td>Display confidence intervals on the tree.</td><td><code>ci</code></td></tr>
</tbody>
</table>
<p><strong>See this in action:</strong></p>
<p>For instance, go to <a href="https://nextstrain.org/flu/seasonal/h3n2/ha/2y?c=num_date&amp;d=tree,map&amp;m=div&amp;p=grid&amp;r=region">nextstrain.org/flu/seasonal/h3n2/ha/2y?c=num_date&amp;d=tree,map&amp;m=div&amp;r=region</a> and you'll see how we've changed the coloring to a temporal scale (<code>c=num_date</code>), we're only showing the tree &amp; map panels (<code>d=tree,map</code>), the tree x-axis is divergence (<code>m=div</code>) and the map resolution is region (<code>r=region</code>).</p>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 4/8/2020</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/advanced-functionality/second-trees"><span class="arrow-prev"></span><span>Displaying multiple trees</span></a><a class="docs-next button" href="/auspice/advanced-functionality/drag-drop-csv-tsv"><span>Adding extra metadata via CSV/TSV</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#auspice-hardcoded-defaults">Auspice (hardcoded) defaults</a></li><li><a href="#dataset-json-configurable-defaults">Dataset (JSON) configurable defaults</a></li><li><a href="#url-query-options">URL query options</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 15/04/2020</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/advanced-functionality/second-trees"><span class="arrow-prev"></span><span>Displaying multiple trees</span></a><a class="docs-next button" href="/auspice/advanced-functionality/drag-drop-csv-tsv"><span>Adding extra metadata via CSV/TSV</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#auspice-hardcoded-defaults">Auspice (hardcoded) defaults</a></li><li><a href="#dataset-json-configurable-defaults">Dataset (JSON) configurable defaults</a></li><li><a href="#url-query-options">URL query options</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>

22
docs/contributing/overview.html

@ -64,9 +64,25 @@
<p>Code contributions are welcomed! <a href="https://nextstrain.github.io/auspice/introduction/install">Please see the main auspice docs</a> for details on how to install and run auspice from source.</p>
<p>Please comment on an open issue if you are working on it.
For changes unrelated to an open issue, please make an issue outlining what you would like to change/add.</p>
<p>Please ensure there are no <strong>linting</strong> errors by running <code>npm run lint</code> (which uses <a href="https://eslint.org/">eslint</a>).
In the future we will make this a requirement for PRs or commits.</p>
<p>Where possible, <strong>please rebase</strong> your work onto master rather than merging changes from master into your PR.</p>
<h3><a class="anchor" aria-hidden="true" id="make-sure-tests-are-passing"></a><a href="#make-sure-tests-are-passing" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>Make sure tests are passing</h3>
<p>When you submit a pull request to the auspice repository, a variety of integration and unit tests will need to pass before it can be merged.</p>
<p>You will likely want to run these tests locally before submitting:</p>
<p>First, install the dependencies with <code>npm i</code>, then:</p>
<h4><a class="anchor" aria-hidden="true" id="for-unit-tests"></a><a href="#for-unit-tests" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>For unit tests:</h4>
<p>Run <code>npm test</code>.</p>
<h4><a class="anchor" aria-hidden="true" id="for-linting"></a><a href="#for-linting" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>For linting:</h4>
<p>Run <code>npm run lint</code>. If there are issues run <code>npm run lint:fix</code>.</p>
<h4><a class="anchor" aria-hidden="true" id="for-integration-tests"></a><a href="#for-integration-tests" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>For integration tests:</h4>
<ol>
<li>Fetch the datasets with <code>npm run get-data</code> and <code>npm run get-narratives</code>.</li>
<li>Ensure you are <strong>not</strong> currently running the site locally, then run <code>npm run integration-test:ci</code>.</li>
</ol>
<h4><a class="anchor" aria-hidden="true" id="for-smoke-tests"></a><a href="#for-smoke-tests" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>For smoke tests:</h4>
<ol>
<li>Fetch the datasets with <code>npm run get-data</code> and <code>npm run get-narratives</code>.</li>
<li>Ensure you are <strong>not</strong> currently running the site locally, then run <code>npm run smoke-test:ci</code>.</li>
</ol>
<h2><a class="anchor" aria-hidden="true" id="contributing-to-documentation"></a><a href="#contributing-to-documentation" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>Contributing to Documentation</h2>
<p>Nextstrain documentation is available at <a href="https://nextstrain.github.io/auspice/">nextstrain.github.io/auspice/</a>.</p>
<p>This documentation is built from files contained within the Auspice GitHub repo -- see the <a href="https://github.com/nextstrain/auspice/tree/master/docs-src">docs-src/README</a> within the <code>docs-src</code> directory for more details and instructions on how to contribute.</p>
@ -107,4 +123,4 @@ This will display the strings which:</p>
</ol>
<h2><a class="anchor" aria-hidden="true" id="releases-versioning"></a><a href="#releases-versioning" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>Releases &amp; versioning</h2>
<p>New versions are released via the <code>./releaseNewVersion.sh</code> script from an up-to-date <code>master</code> branch. It will prompt you for the version number increase, push changes to the <code>release</code> branch and, as long as Travis-CI is successful then a new version will be automatically published to <a href="https://www.npmjs.com/package/auspice">npm</a>.</p>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 3/24/2020</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/releases/v2"><span class="arrow-prev"></span><span>Auspice Version 2.0</span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#contributing-code">Contributing code</a></li><li><a href="#contributing-to-documentation">Contributing to Documentation</a></li><li><a href="#contributing-to-internationalization-and-localization-i18n-l18n">Contributing to Internationalization and Localization (i18n/l18n)</a></li><li><a href="#releases-amp-versioning">Releases &amp; versioning</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 24/03/2020</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/releases/v2"><span class="arrow-prev"></span><span>Auspice Version 2.0</span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#contributing-code">Contributing code</a><ul class="toc-headings"><li><a href="#make-sure-tests-are-passing">Make sure tests are passing</a></li></ul></li><li><a href="#contributing-to-documentation">Contributing to Documentation</a></li><li><a href="#contributing-to-internationalization-and-localization-i18n-l18n">Contributing to Internationalization and Localization (i18n/l18n)</a></li><li><a href="#releases-amp-versioning">Releases &amp; versioning</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>

22
docs/contributing/overview/index.html

@ -64,9 +64,25 @@
<p>Code contributions are welcomed! <a href="https://nextstrain.github.io/auspice/introduction/install">Please see the main auspice docs</a> for details on how to install and run auspice from source.</p>
<p>Please comment on an open issue if you are working on it.
For changes unrelated to an open issue, please make an issue outlining what you would like to change/add.</p>
<p>Please ensure there are no <strong>linting</strong> errors by running <code>npm run lint</code> (which uses <a href="https://eslint.org/">eslint</a>).
In the future we will make this a requirement for PRs or commits.</p>
<p>Where possible, <strong>please rebase</strong> your work onto master rather than merging changes from master into your PR.</p>
<h3><a class="anchor" aria-hidden="true" id="make-sure-tests-are-passing"></a><a href="#make-sure-tests-are-passing" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>Make sure tests are passing</h3>
<p>When you submit a pull request to the auspice repository, a variety of integration and unit tests will need to pass before it can be merged.</p>
<p>You will likely want to run these tests locally before submitting:</p>
<p>First, install the dependencies with <code>npm i</code>, then:</p>
<h4><a class="anchor" aria-hidden="true" id="for-unit-tests"></a><a href="#for-unit-tests" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>For unit tests:</h4>
<p>Run <code>npm test</code>.</p>
<h4><a class="anchor" aria-hidden="true" id="for-linting"></a><a href="#for-linting" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>For linting:</h4>
<p>Run <code>npm run lint</code>. If there are issues run <code>npm run lint:fix</code>.</p>
<h4><a class="anchor" aria-hidden="true" id="for-integration-tests"></a><a href="#for-integration-tests" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>For integration tests:</h4>
<ol>
<li>Fetch the datasets with <code>npm run get-data</code> and <code>npm run get-narratives</code>.</li>
<li>Ensure you are <strong>not</strong> currently running the site locally, then run <code>npm run integration-test:ci</code>.</li>
</ol>
<h4><a class="anchor" aria-hidden="true" id="for-smoke-tests"></a><a href="#for-smoke-tests" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>For smoke tests:</h4>
<ol>
<li>Fetch the datasets with <code>npm run get-data</code> and <code>npm run get-narratives</code>.</li>
<li>Ensure you are <strong>not</strong> currently running the site locally, then run <code>npm run smoke-test:ci</code>.</li>
</ol>
<h2><a class="anchor" aria-hidden="true" id="contributing-to-documentation"></a><a href="#contributing-to-documentation" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>Contributing to Documentation</h2>
<p>Nextstrain documentation is available at <a href="https://nextstrain.github.io/auspice/">nextstrain.github.io/auspice/</a>.</p>
<p>This documentation is built from files contained within the Auspice GitHub repo -- see the <a href="https://github.com/nextstrain/auspice/tree/master/docs-src">docs-src/README</a> within the <code>docs-src</code> directory for more details and instructions on how to contribute.</p>
@ -107,4 +123,4 @@ This will display the strings which:</p>
</ol>
<h2><a class="anchor" aria-hidden="true" id="releases-versioning"></a><a href="#releases-versioning" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>Releases &amp; versioning</h2>
<p>New versions are released via the <code>./releaseNewVersion.sh</code> script from an up-to-date <code>master</code> branch. It will prompt you for the version number increase, push changes to the <code>release</code> branch and, as long as Travis-CI is successful then a new version will be automatically published to <a href="https://www.npmjs.com/package/auspice">npm</a>.</p>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 3/24/2020</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/releases/v2"><span class="arrow-prev"></span><span>Auspice Version 2.0</span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#contributing-code">Contributing code</a></li><li><a href="#contributing-to-documentation">Contributing to Documentation</a></li><li><a href="#contributing-to-internationalization-and-localization-i18n-l18n">Contributing to Internationalization and Localization (i18n/l18n)</a></li><li><a href="#releases-amp-versioning">Releases &amp; versioning</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 24/03/2020</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/releases/v2"><span class="arrow-prev"></span><span>Auspice Version 2.0</span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#contributing-code">Contributing code</a><ul class="toc-headings"><li><a href="#make-sure-tests-are-passing">Make sure tests are passing</a></li></ul></li><li><a href="#contributing-to-documentation">Contributing to Documentation</a></li><li><a href="#contributing-to-internationalization-and-localization-i18n-l18n">Contributing to Internationalization and Localization (i18n/l18n)</a></li><li><a href="#releases-amp-versioning">Releases &amp; versioning</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>

2
docs/customise-client/api.html

@ -163,4 +163,4 @@ This can be changed by specifying <code>serverAddress</code> in the customisatio
<p>Note that currently you can't specify a different domain due to CORS headers.
This may well be a simple fix -- please get in touch if you can help here!</p>
</blockquote>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 3/22/2020</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/customise-client/introduction"><span class="arrow-prev"></span><span>Customising Auspice</span></a><a class="docs-next button" href="/auspice/customise-client/requests"><span>Requests Made from the Client</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#available-customisations">Available Customisations</a></li><li><a href="#sidebar-theme">Sidebar Theme</a></li><li><a href="#nav-bar-component">Nav-bar Component</a></li><li><a href="#splash-component">Splash component</a></li><li><a href="#specifying-the-api-server-address">Specifying the API server address</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 22/03/2020</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/customise-client/introduction"><span class="arrow-prev"></span><span>Customising Auspice</span></a><a class="docs-next button" href="/auspice/customise-client/requests"><span>Requests Made from the Client</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#available-customisations">Available Customisations</a></li><li><a href="#sidebar-theme">Sidebar Theme</a></li><li><a href="#nav-bar-component">Nav-bar Component</a></li><li><a href="#splash-component">Splash component</a></li><li><a href="#specifying-the-api-server-address">Specifying the API server address</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>

2
docs/customise-client/api/index.html

@ -163,4 +163,4 @@ This can be changed by specifying <code>serverAddress</code> in the customisatio
<p>Note that currently you can't specify a different domain due to CORS headers.
This may well be a simple fix -- please get in touch if you can help here!</p>
</blockquote>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 3/22/2020</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/customise-client/introduction"><span class="arrow-prev"></span><span>Customising Auspice</span></a><a class="docs-next button" href="/auspice/customise-client/requests"><span>Requests Made from the Client</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#available-customisations">Available Customisations</a></li><li><a href="#sidebar-theme">Sidebar Theme</a></li><li><a href="#nav-bar-component">Nav-bar Component</a></li><li><a href="#splash-component">Splash component</a></li><li><a href="#specifying-the-api-server-address">Specifying the API server address</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 22/03/2020</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/customise-client/introduction"><span class="arrow-prev"></span><span>Customising Auspice</span></a><a class="docs-next button" href="/auspice/customise-client/requests"><span>Requests Made from the Client</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#available-customisations">Available Customisations</a></li><li><a href="#sidebar-theme">Sidebar Theme</a></li><li><a href="#nav-bar-component">Nav-bar Component</a></li><li><a href="#splash-component">Splash component</a></li><li><a href="#specifying-the-api-server-address">Specifying the API server address</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>

2
docs/customise-client/introduction.html

@ -63,4 +63,4 @@ This is how Auspice running locally and nextstrain.org look different, despite b
</code></pre>
<p><a href="https://github.com/nextstrain/nextstrain.org/blob/master/auspice-client/customisations/config.json">Here's</a> the file used by nextstrain.org to change the appearance of Auspice in the above image.</p>
<p>See the <a href="/auspice/customise-client/api">client customisation API</a> for the available options.</p>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 3/22/2020</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/advanced-functionality/misc"><span class="arrow-prev"></span><span>Miscellaneous</span></a><a class="docs-next button" href="/auspice/customise-client/api"><span>Client Customisation API</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 22/03/2020</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/advanced-functionality/misc"><span class="arrow-prev"></span><span>Miscellaneous</span></a><a class="docs-next button" href="/auspice/customise-client/api"><span>Client Customisation API</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>

2
docs/customise-client/introduction/index.html

@ -63,4 +63,4 @@ This is how Auspice running locally and nextstrain.org look different, despite b
</code></pre>
<p><a href="https://github.com/nextstrain/nextstrain.org/blob/master/auspice-client/customisations/config.json">Here's</a> the file used by nextstrain.org to change the appearance of Auspice in the above image.</p>
<p>See the <a href="/auspice/customise-client/api">client customisation API</a> for the available options.</p>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 3/22/2020</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/advanced-functionality/misc"><span class="arrow-prev"></span><span>Miscellaneous</span></a><a class="docs-next button" href="/auspice/customise-client/api"><span>Client Customisation API</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 22/03/2020</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/advanced-functionality/misc"><span class="arrow-prev"></span><span>Miscellaneous</span></a><a class="docs-next button" href="/auspice/customise-client/api"><span>Client Customisation API</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>

2
docs/customise-client/requests.html

@ -87,4 +87,4 @@ These are requested using our hardcoded access key, however this may change to a
<p>Auspice has the potential to include Google Analytics in a limited fashion.
See <a href="/auspice/customise-client/api#available-customisations">the client customisation API documentation</a> for how to set this.
Note that these requests are only made if you specify a Google Analytics key during build-time customisation of the client.</p>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 11/15/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/customise-client/api"><span class="arrow-prev"></span><span>Client Customisation API</span></a><a class="docs-next button" href="/auspice/server/introduction"><span>Auspice servers</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#requests-to-the-auspice-server">Requests to the Auspice Server</a><ul class="toc-headings"><li><a href="#auspice-client-javascript-code">Auspice Client JavaScript Code</a></li><li><a href="#quot-charon-quot-get-requests">&quot;Charon&quot; GET requests</a></li><li><a href="#image-requests">Image Requests</a></li></ul></li><li><a href="#external-requests">External Requests</a><ul class="toc-headings"><li><a href="#fonts">Fonts</a></li><li><a href="#leaflet">Leaflet</a></li><li><a href="#google-analytics-optional">Google Analytics (Optional)</a></li></ul></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 15/11/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/customise-client/api"><span class="arrow-prev"></span><span>Client Customisation API</span></a><a class="docs-next button" href="/auspice/server/introduction"><span>Auspice servers</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#requests-to-the-auspice-server">Requests to the Auspice Server</a><ul class="toc-headings"><li><a href="#auspice-client-javascript-code">Auspice Client JavaScript Code</a></li><li><a href="#quot-charon-quot-get-requests">&quot;Charon&quot; GET requests</a></li><li><a href="#image-requests">Image Requests</a></li></ul></li><li><a href="#external-requests">External Requests</a><ul class="toc-headings"><li><a href="#fonts">Fonts</a></li><li><a href="#leaflet">Leaflet</a></li><li><a href="#google-analytics-optional">Google Analytics (Optional)</a></li></ul></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>

2
docs/customise-client/requests/index.html

@ -87,4 +87,4 @@ These are requested using our hardcoded access key, however this may change to a
<p>Auspice has the potential to include Google Analytics in a limited fashion.
See <a href="/auspice/customise-client/api#available-customisations">the client customisation API documentation</a> for how to set this.
Note that these requests are only made if you specify a Google Analytics key during build-time customisation of the client.</p>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 11/15/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/customise-client/api"><span class="arrow-prev"></span><span>Client Customisation API</span></a><a class="docs-next button" href="/auspice/server/introduction"><span>Auspice servers</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#requests-to-the-auspice-server">Requests to the Auspice Server</a><ul class="toc-headings"><li><a href="#auspice-client-javascript-code">Auspice Client JavaScript Code</a></li><li><a href="#quot-charon-quot-get-requests">&quot;Charon&quot; GET requests</a></li><li><a href="#image-requests">Image Requests</a></li></ul></li><li><a href="#external-requests">External Requests</a><ul class="toc-headings"><li><a href="#fonts">Fonts</a></li><li><a href="#leaflet">Leaflet</a></li><li><a href="#google-analytics-optional">Google Analytics (Optional)</a></li></ul></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 15/11/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/customise-client/api"><span class="arrow-prev"></span><span>Client Customisation API</span></a><a class="docs-next button" href="/auspice/server/introduction"><span>Auspice servers</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#requests-to-the-auspice-server">Requests to the Auspice Server</a><ul class="toc-headings"><li><a href="#auspice-client-javascript-code">Auspice Client JavaScript Code</a></li><li><a href="#quot-charon-quot-get-requests">&quot;Charon&quot; GET requests</a></li><li><a href="#image-requests">Image Requests</a></li></ul></li><li><a href="#external-requests">External Requests</a><ul class="toc-headings"><li><a href="#fonts">Fonts</a></li><li><a href="#leaflet">Leaflet</a></li><li><a href="#google-analytics-optional">Google Analytics (Optional)</a></li></ul></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>

2
docs/introduction/how-to-run.html

@ -133,4 +133,4 @@ Using BEAST trees is possible, but you have to use Augur to convert them first.<
<li>You can download the narrative Markdown files by running <a href="https://github.com/nextstrain/auspice/blob/master/scripts/get-narratives.sh">this script</a> which will create a <code>./narratives</code> directory for you.</li>
</ul>
<p>You can then run <code>auspice view --datasetDir data --narrativeDir narratives</code> to visualise all of the <a href="https://nextstrain.org">nextstrain.org</a> datasets locally.</p>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 3/22/2020</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/introduction/install"><span class="arrow-prev"></span><span>Install Auspice</span></a><a class="docs-next button" href="/auspice/advanced-functionality/second-trees"><span>Displaying multiple trees</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#how-to-get-an-example-dataset-up-and-running">How to Get an Example Dataset Up and Running</a></li><li><a href="#auspice-view"><code>auspice view</code></a></li><li><a href="#auspice-build"><code>auspice build</code></a></li><li><a href="#auspice-develop"><code>auspice develop</code></a></li><li><a href="#auspice-convert"><code>auspice convert</code></a></li><li><a href="#input-file-formats">Input File Formats</a><ul class="toc-headings"><li><a href="#dataset-jsons">Dataset JSONs</a></li><li><a href="#narratives">Narratives</a></li></ul></li><li><a href="#obtaining-a-set-of-input-files">Obtaining a Set of Input Files</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 22/03/2020</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/introduction/install"><span class="arrow-prev"></span><span>Install Auspice</span></a><a class="docs-next button" href="/auspice/advanced-functionality/second-trees"><span>Displaying multiple trees</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#how-to-get-an-example-dataset-up-and-running">How to Get an Example Dataset Up and Running</a></li><li><a href="#auspice-view"><code>auspice view</code></a></li><li><a href="#auspice-build"><code>auspice build</code></a></li><li><a href="#auspice-develop"><code>auspice develop</code></a></li><li><a href="#auspice-convert"><code>auspice convert</code></a></li><li><a href="#input-file-formats">Input File Formats</a><ul class="toc-headings"><li><a href="#dataset-jsons">Dataset JSONs</a></li><li><a href="#narratives">Narratives</a></li></ul></li><li><a href="#obtaining-a-set-of-input-files">Obtaining a Set of Input Files</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>

2
docs/introduction/how-to-run/index.html

@ -133,4 +133,4 @@ Using BEAST trees is possible, but you have to use Augur to convert them first.<
<li>You can download the narrative Markdown files by running <a href="https://github.com/nextstrain/auspice/blob/master/scripts/get-narratives.sh">this script</a> which will create a <code>./narratives</code> directory for you.</li>
</ul>
<p>You can then run <code>auspice view --datasetDir data --narrativeDir narratives</code> to visualise all of the <a href="https://nextstrain.org">nextstrain.org</a> datasets locally.</p>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 3/22/2020</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/introduction/install"><span class="arrow-prev"></span><span>Install Auspice</span></a><a class="docs-next button" href="/auspice/advanced-functionality/second-trees"><span>Displaying multiple trees</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#how-to-get-an-example-dataset-up-and-running">How to Get an Example Dataset Up and Running</a></li><li><a href="#auspice-view"><code>auspice view</code></a></li><li><a href="#auspice-build"><code>auspice build</code></a></li><li><a href="#auspice-develop"><code>auspice develop</code></a></li><li><a href="#auspice-convert"><code>auspice convert</code></a></li><li><a href="#input-file-formats">Input File Formats</a><ul class="toc-headings"><li><a href="#dataset-jsons">Dataset JSONs</a></li><li><a href="#narratives">Narratives</a></li></ul></li><li><a href="#obtaining-a-set-of-input-files">Obtaining a Set of Input Files</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 22/03/2020</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/introduction/install"><span class="arrow-prev"></span><span>Install Auspice</span></a><a class="docs-next button" href="/auspice/advanced-functionality/second-trees"><span>Displaying multiple trees</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#how-to-get-an-example-dataset-up-and-running">How to Get an Example Dataset Up and Running</a></li><li><a href="#auspice-view"><code>auspice view</code></a></li><li><a href="#auspice-build"><code>auspice build</code></a></li><li><a href="#auspice-develop"><code>auspice develop</code></a></li><li><a href="#auspice-convert"><code>auspice convert</code></a></li><li><a href="#input-file-formats">Input File Formats</a><ul class="toc-headings"><li><a href="#dataset-jsons">Dataset JSONs</a></li><li><a href="#narratives">Narratives</a></li></ul></li><li><a href="#obtaining-a-set-of-input-files">Obtaining a Set of Input Files</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>

2
docs/introduction/install.html

@ -105,4 +105,4 @@ npm run get-narratives
</code></pre>
<p>Updating Auspice should only require pulling the new version from GitHub -- it shouldn't require any <code>npm</code> commands.
You will, however, have to re-build Auspice whenever the client-related code has changed, via <code>auspice build</code>.</p>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 3/28/2020</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/introduction/overview"><span class="arrow-prev"></span><span>Overview</span></a><a class="docs-next button" href="/auspice/introduction/how-to-run"><span>How to Run Auspice</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#prerequisites">Prerequisites</a></li><li><a href="#create-a-conda-environment">Create a Conda Environment</a></li><li><a href="#install-auspice-from-npm">Install Auspice from npm</a></li><li><a href="#installing-from-source">Installing from Source</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 28/03/2020</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/introduction/overview"><span class="arrow-prev"></span><span>Overview</span></a><a class="docs-next button" href="/auspice/introduction/how-to-run"><span>How to Run Auspice</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#prerequisites">Prerequisites</a></li><li><a href="#create-a-conda-environment">Create a Conda Environment</a></li><li><a href="#install-auspice-from-npm">Install Auspice from npm</a></li><li><a href="#installing-from-source">Installing from Source</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>

2
docs/introduction/install/index.html

@ -105,4 +105,4 @@ npm run get-narratives
</code></pre>
<p>Updating Auspice should only require pulling the new version from GitHub -- it shouldn't require any <code>npm</code> commands.
You will, however, have to re-build Auspice whenever the client-related code has changed, via <code>auspice build</code>.</p>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 3/28/2020</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/introduction/overview"><span class="arrow-prev"></span><span>Overview</span></a><a class="docs-next button" href="/auspice/introduction/how-to-run"><span>How to Run Auspice</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#prerequisites">Prerequisites</a></li><li><a href="#create-a-conda-environment">Create a Conda Environment</a></li><li><a href="#install-auspice-from-npm">Install Auspice from npm</a></li><li><a href="#installing-from-source">Installing from Source</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 28/03/2020</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/introduction/overview"><span class="arrow-prev"></span><span>Overview</span></a><a class="docs-next button" href="/auspice/introduction/how-to-run"><span>How to Run Auspice</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#prerequisites">Prerequisites</a></li><li><a href="#create-a-conda-environment">Create a Conda Environment</a></li><li><a href="#install-auspice-from-npm">Install Auspice from npm</a></li><li><a href="#installing-from-source">Installing from Source</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>

2
docs/introduction/overview.html

@ -69,4 +69,4 @@ It allows easy customisation of aesthetics and functionality, and powers the vis
<h2><a class="anchor" aria-hidden="true" id="license-and-copyright"></a><a href="#license-and-copyright" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>License and Copyright</h2>
<p>Copyright © 2014-2020 Trevor Bedford and Richard Neher.</p>
<p>Source code to Nextstrain is made available under the terms of the <a href="LICENSE.txt">GNU Affero General Public License</a> (AGPL). Nextstrain is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.</p>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 3/24/2020</em></div><div class="docs-prevnext"><a class="docs-next button" href="/auspice/introduction/install"><span>Install Auspice</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#license-and-copyright">License and Copyright</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 24/03/2020</em></div><div class="docs-prevnext"><a class="docs-next button" href="/auspice/introduction/install"><span>Install Auspice</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#license-and-copyright">License and Copyright</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>

2
docs/introduction/overview/index.html

@ -69,4 +69,4 @@ It allows easy customisation of aesthetics and functionality, and powers the vis
<h2><a class="anchor" aria-hidden="true" id="license-and-copyright"></a><a href="#license-and-copyright" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>License and Copyright</h2>
<p>Copyright © 2014-2020 Trevor Bedford and Richard Neher.</p>
<p>Source code to Nextstrain is made available under the terms of the <a href="LICENSE.txt">GNU Affero General Public License</a> (AGPL). Nextstrain is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.</p>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 3/24/2020</em></div><div class="docs-prevnext"><a class="docs-next button" href="/auspice/introduction/install"><span>Install Auspice</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#license-and-copyright">License and Copyright</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 24/03/2020</em></div><div class="docs-prevnext"><a class="docs-next button" href="/auspice/introduction/install"><span>Install Auspice</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#license-and-copyright">License and Copyright</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>

2
docs/narratives/create-pdf.html

@ -95,4 +95,4 @@ decktape generic --load-pause 3000 --key ArrowDown --size 1600x900 \
</code></pre>
<p>You'll see a lot of bad-looking warning messages printed in the terminal 😱, but as long as you see &quot;Printed 11 slides&quot; or similar then the command has worked.
You should now be able to view a static PDF of the narrative, in this case at <code>example.pdf</code>.</p>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 11/15/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/narratives/how-to-write"><span class="arrow-prev"></span><span>Writing a Narrative</span></a><a class="docs-next button" href="/auspice/releases/changelog"><span>Changelog</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#prerequisites">Prerequisites</a></li><li><a href="#saving-an-online-narrative-to-pdf">Saving an online narrative to PDF</a></li><li><a href="#saving-a-local-narrative-to-pdf">Saving a local narrative to PDF</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 15/11/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/narratives/how-to-write"><span class="arrow-prev"></span><span>Writing a Narrative</span></a><a class="docs-next button" href="/auspice/releases/changelog"><span>Changelog</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#prerequisites">Prerequisites</a></li><li><a href="#saving-an-online-narrative-to-pdf">Saving an online narrative to PDF</a></li><li><a href="#saving-a-local-narrative-to-pdf">Saving a local narrative to PDF</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>

2
docs/narratives/create-pdf/index.html

@ -95,4 +95,4 @@ decktape generic --load-pause 3000 --key ArrowDown --size 1600x900 \
</code></pre>
<p>You'll see a lot of bad-looking warning messages printed in the terminal 😱, but as long as you see &quot;Printed 11 slides&quot; or similar then the command has worked.
You should now be able to view a static PDF of the narrative, in this case at <code>example.pdf</code>.</p>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 11/15/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/narratives/how-to-write"><span class="arrow-prev"></span><span>Writing a Narrative</span></a><a class="docs-next button" href="/auspice/releases/changelog"><span>Changelog</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#prerequisites">Prerequisites</a></li><li><a href="#saving-an-online-narrative-to-pdf">Saving an online narrative to PDF</a></li><li><a href="#saving-a-local-narrative-to-pdf">Saving a local narrative to PDF</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 15/11/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/narratives/how-to-write"><span class="arrow-prev"></span><span>Writing a Narrative</span></a><a class="docs-next button" href="/auspice/releases/changelog"><span>Changelog</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#prerequisites">Prerequisites</a></li><li><a href="#saving-an-online-narrative-to-pdf">Saving an online narrative to PDF</a></li><li><a href="#saving-a-local-narrative-to-pdf">Saving a local narrative to PDF</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>

2
docs/narratives/how-to-write.html

@ -151,4 +151,4 @@ For instance, let's assume your GitHub username is &quot;yourname&quot; and your
</code></pre>
<p>Then, by uploading the repo to GitHub it will be available to everyone at nextstrain.org/narratives/yourname/auspice-narrative-example.</p>
<p>This is how the narrative file at <a href="https://github.com/emmahodcroft/tb/blob/master/narratives/tb_crispell.md">GitHub &gt; emmahodcroft &gt; tb &gt; narratives</a> can be accessed via <a href="https://nextstrain.org/community/narratives/emmahodcroft/tb/crispell">nextstrain.org/community/narratives/emmahodcroft/tb/crispell</a>.</p>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 11/15/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/narratives/introduction"><span class="arrow-prev"></span><span>Communicating Results Using Narratives</span></a><a class="docs-next button" href="/auspice/narratives/create-pdf"><span>Converting a narrative to PDF</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#step-1-get-the-underlying-datasets">Step 1: Get the Underlying Datasets</a></li><li><a href="#step-2-start-a-simple-narrative">Step 2: Start a Simple Narrative</a></li><li><a href="#step-3-view-the-narrative-so-far">Step 3: View the Narrative so Far</a></li><li><a href="#step-4-adding-a-paragraph">Step 4: Adding a Paragraph</a></li><li><a href="#step-5-adding-more-paragraphs">Step 5: Adding More Paragraphs</a></li><li><a href="#step-6-upload-your-example-to-the-nextstrain-community-to-share-with-everyone">Step 6: Upload Your Example to the Nextstrain Community to Share with Everyone</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 15/11/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/narratives/introduction"><span class="arrow-prev"></span><span>Communicating Results Using Narratives</span></a><a class="docs-next button" href="/auspice/narratives/create-pdf"><span>Converting a narrative to PDF</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#step-1-get-the-underlying-datasets">Step 1: Get the Underlying Datasets</a></li><li><a href="#step-2-start-a-simple-narrative">Step 2: Start a Simple Narrative</a></li><li><a href="#step-3-view-the-narrative-so-far">Step 3: View the Narrative so Far</a></li><li><a href="#step-4-adding-a-paragraph">Step 4: Adding a Paragraph</a></li><li><a href="#step-5-adding-more-paragraphs">Step 5: Adding More Paragraphs</a></li><li><a href="#step-6-upload-your-example-to-the-nextstrain-community-to-share-with-everyone">Step 6: Upload Your Example to the Nextstrain Community to Share with Everyone</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>

2
docs/narratives/how-to-write/index.html

@ -151,4 +151,4 @@ For instance, let's assume your GitHub username is &quot;yourname&quot; and your
</code></pre>
<p>Then, by uploading the repo to GitHub it will be available to everyone at nextstrain.org/narratives/yourname/auspice-narrative-example.</p>
<p>This is how the narrative file at <a href="https://github.com/emmahodcroft/tb/blob/master/narratives/tb_crispell.md">GitHub &gt; emmahodcroft &gt; tb &gt; narratives</a> can be accessed via <a href="https://nextstrain.org/community/narratives/emmahodcroft/tb/crispell">nextstrain.org/community/narratives/emmahodcroft/tb/crispell</a>.</p>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 11/15/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/narratives/introduction"><span class="arrow-prev"></span><span>Communicating Results Using Narratives</span></a><a class="docs-next button" href="/auspice/narratives/create-pdf"><span>Converting a narrative to PDF</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#step-1-get-the-underlying-datasets">Step 1: Get the Underlying Datasets</a></li><li><a href="#step-2-start-a-simple-narrative">Step 2: Start a Simple Narrative</a></li><li><a href="#step-3-view-the-narrative-so-far">Step 3: View the Narrative so Far</a></li><li><a href="#step-4-adding-a-paragraph">Step 4: Adding a Paragraph</a></li><li><a href="#step-5-adding-more-paragraphs">Step 5: Adding More Paragraphs</a></li><li><a href="#step-6-upload-your-example-to-the-nextstrain-community-to-share-with-everyone">Step 6: Upload Your Example to the Nextstrain Community to Share with Everyone</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 15/11/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/narratives/introduction"><span class="arrow-prev"></span><span>Communicating Results Using Narratives</span></a><a class="docs-next button" href="/auspice/narratives/create-pdf"><span>Converting a narrative to PDF</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#step-1-get-the-underlying-datasets">Step 1: Get the Underlying Datasets</a></li><li><a href="#step-2-start-a-simple-narrative">Step 2: Start a Simple Narrative</a></li><li><a href="#step-3-view-the-narrative-so-far">Step 3: View the Narrative so Far</a></li><li><a href="#step-4-adding-a-paragraph">Step 4: Adding a Paragraph</a></li><li><a href="#step-5-adding-more-paragraphs">Step 5: Adding More Paragraphs</a></li><li><a href="#step-6-upload-your-example-to-the-nextstrain-community-to-share-with-everyone">Step 6: Upload Your Example to the Nextstrain Community to Share with Everyone</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>

2
docs/narratives/introduction.html

@ -96,4 +96,4 @@ This limits what views can be defined by paragraphs in the narratives.</p></li>
<li><p>The frontmatter parsing will be extended to allow arrays of authors (etc).</p></li>
</ul>
<p>Take a look at the <a href="https://github.com/nextstrain/auspice/labels/narratives">GitHub issues tagged as related to narrative functionality</a> for a potentially more up-to-date list of these.</p>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 10/17/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/server/authentication"><span class="arrow-prev"></span><span>Authentication</span></a><a class="docs-next button" href="/auspice/narratives/how-to-write"><span>Writing a Narrative</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#examples">Examples</a></li><li><a href="#how-to-write-a-narrative">How to Write a Narrative</a></li><li><a href="#sharing-narratives">Sharing Narratives</a></li><li><a href="#known-bugs-limitations">Known Bugs / Limitations</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 17/10/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/server/authentication"><span class="arrow-prev"></span><span>Authentication</span></a><a class="docs-next button" href="/auspice/narratives/how-to-write"><span>Writing a Narrative</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#examples">Examples</a></li><li><a href="#how-to-write-a-narrative">How to Write a Narrative</a></li><li><a href="#sharing-narratives">Sharing Narratives</a></li><li><a href="#known-bugs-limitations">Known Bugs / Limitations</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>

2
docs/narratives/introduction/index.html

@ -96,4 +96,4 @@ This limits what views can be defined by paragraphs in the narratives.</p></li>
<li><p>The frontmatter parsing will be extended to allow arrays of authors (etc).</p></li>
</ul>
<p>Take a look at the <a href="https://github.com/nextstrain/auspice/labels/narratives">GitHub issues tagged as related to narrative functionality</a> for a potentially more up-to-date list of these.</p>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 10/17/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/server/authentication"><span class="arrow-prev"></span><span>Authentication</span></a><a class="docs-next button" href="/auspice/narratives/how-to-write"><span>Writing a Narrative</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#examples">Examples</a></li><li><a href="#how-to-write-a-narrative">How to Write a Narrative</a></li><li><a href="#sharing-narratives">Sharing Narratives</a></li><li><a href="#known-bugs-limitations">Known Bugs / Limitations</a></li></ul></nav></div