build based on fe509e7

dev/.documenter-siteinfo.json

@@ -1 +1 @@
-{"documenter":{"julia_version":"1.10.3","generation_timestamp":"2024-05-23T02:37:05","documenter_version":"1.4.1"}}
+{"documenter":{"julia_version":"1.10.3","generation_timestamp":"2024-05-24T00:19:27","documenter_version":"1.4.1"}}

dev/howtos/1_parameters/index.html

@@ -67,4 +67,4 @@
    2 │ β           2.0            2.0  d                false
    3 │ γ           3.0            3.0  km                true</span></span></code></pre><p>And then vectorizing the parameters</p><pre><code class="language-julia hljs">vec(p)</code></pre><pre class="documenter-example-output"><code class="nohighlight hljs ansi">2-element Vector{Float64}:
     1.0
- 3000.0</code></pre><p>Note how <code>γ</code> (the third parameter, but the second flattenable one), is converted to meters.</p><h2 id="Other-features"><a class="docs-heading-anchor" href="#Other-features">Other features</a><a id="Other-features-1"></a><a class="docs-heading-anchor-permalink" href="#Other-features" title="Permalink"></a></h2><p>Coming soon!</p><hr/><p><em>This page was generated using <a href="https://github.com/fredrikekre/Literate.jl">Literate.jl</a>.</em></p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../../tutorials/6_groundwater_discharge/">« Groundwater discharge</a><a class="docs-footer-nextpage" href="../2_plot/">Plot basic things »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.4.1 on <span class="colophon-date" title="Thursday 23 May 2024 02:37">Thursday 23 May 2024</span>. Using Julia version 1.10.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+ 3000.0</code></pre><p>Note how <code>γ</code> (the third parameter, but the second flattenable one), is converted to meters.</p><h2 id="Other-features"><a class="docs-heading-anchor" href="#Other-features">Other features</a><a id="Other-features-1"></a><a class="docs-heading-anchor-permalink" href="#Other-features" title="Permalink"></a></h2><p>Coming soon!</p><hr/><p><em>This page was generated using <a href="https://github.com/fredrikekre/Literate.jl">Literate.jl</a>.</em></p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../../tutorials/6_groundwater_discharge/">« Groundwater discharge</a><a class="docs-footer-nextpage" href="../2_plot/">Plot basic things »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.4.1 on <span class="colophon-date" title="Friday 24 May 2024 00:19">Friday 24 May 2024</span>. Using Julia version 1.10.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/howtos/2_plot/index.html

@@ -22,10 +22,10 @@
  0.8688879687250066
  0.9154080085253663
  0.9009688679024191
- 0.8854560256532099</code></pre><h2 id="horizontal-plots"><a class="docs-heading-anchor" href="#horizontal-plots">Horizontal plots</a><a id="horizontal-plots-1"></a><a class="docs-heading-anchor-permalink" href="#horizontal-plots" title="Permalink"></a></h2><h3 id="Horizontal-slice"><a class="docs-heading-anchor" href="#Horizontal-slice">Horizontal slice</a><a id="Horizontal-slice-1"></a><a class="docs-heading-anchor-permalink" href="#Horizontal-slice" title="Permalink"></a></h3><p>The most common thing you plot after a simulation of marine tracers is a horizontal slice. In this case, you just need to provide the tracer (<code>dummy</code> here), the grid object <code>grd</code>, and the depth at which you want to plot.</p><pre><code class="language-julia hljs">plothorizontalslice(dummy, grd, depth=10)</code></pre><img src="64fb1778.svg" alt="Example block output"/><p>You can supply units for the depth at which you want to see the horizontal slice.</p><pre><code class="language-julia hljs">plothorizontalslice(dummy, grd, depth=10u&quot;m&quot;)</code></pre><img src="edd49955.svg" alt="Example block output"/><p>And the units should be understood under the hood.</p><pre><code class="language-julia hljs">plothorizontalslice(dummy, grd, depth=3u&quot;km&quot;)</code></pre><img src="69dee1ef.svg" alt="Example block output"/><p>If your tracer is supplied with units, those will show in the colorbar label</p><pre><code class="language-julia hljs">plothorizontalslice(dummy * u&quot;mol/m^3&quot;, grd, depth=10u&quot;m&quot;)</code></pre><img src="cac1988d.svg" alt="Example block output"/><p>The advantage of Plots.jl recipes like this one is that you can specify other pieces of the plot as you would with built-in functions. The advantage of Plots.jl recipes like this one is that you can specify other pieces of the plot as you would with built-in functions. For example, you can chose the colormap with the <code>color</code> keyword argument.</p><pre><code class="language-julia hljs">dummy .*= cosd.(lonvec(grd))
-plt = plothorizontalslice(dummy, grd, depth=100, color=:balance)</code></pre><img src="d86250f7.svg" alt="Example block output"/><p>And you can finetune attributes after the plot is created.</p><pre><code class="language-julia hljs">plot!(plt, xlabel=&quot;Lon&quot;, ylabel=&quot;Lat&quot;, colorbar_title=&quot;dummy value&quot;, title=&quot;The pacific as a whole&quot;)</code></pre><img src="de63abaa.svg" alt="Example block output"/><h2 id="vertical-plots"><a class="docs-heading-anchor" href="#vertical-plots">Vertical plots</a><a id="vertical-plots-1"></a><a class="docs-heading-anchor-permalink" href="#vertical-plots" title="Permalink"></a></h2><p>Exploring the vertical distribution of tracers is important after all.</p><h3 id="Zonal-slices"><a class="docs-heading-anchor" href="#Zonal-slices">Zonal slices</a><a id="Zonal-slices-1"></a><a class="docs-heading-anchor-permalink" href="#Zonal-slices" title="Permalink"></a></h3><p>You must specify the longitude</p><pre><code class="language-julia hljs">dummy = cosd.(latvec(grd))
+ 0.8854560256532099</code></pre><h2 id="horizontal-plots"><a class="docs-heading-anchor" href="#horizontal-plots">Horizontal plots</a><a id="horizontal-plots-1"></a><a class="docs-heading-anchor-permalink" href="#horizontal-plots" title="Permalink"></a></h2><h3 id="Horizontal-slice"><a class="docs-heading-anchor" href="#Horizontal-slice">Horizontal slice</a><a id="Horizontal-slice-1"></a><a class="docs-heading-anchor-permalink" href="#Horizontal-slice" title="Permalink"></a></h3><p>The most common thing you plot after a simulation of marine tracers is a horizontal slice. In this case, you just need to provide the tracer (<code>dummy</code> here), the grid object <code>grd</code>, and the depth at which you want to plot.</p><pre><code class="language-julia hljs">plothorizontalslice(dummy, grd, depth=10)</code></pre><img src="becf78e6.svg" alt="Example block output"/><p>You can supply units for the depth at which you want to see the horizontal slice.</p><pre><code class="language-julia hljs">plothorizontalslice(dummy, grd, depth=10u&quot;m&quot;)</code></pre><img src="edb424f6.svg" alt="Example block output"/><p>And the units should be understood under the hood.</p><pre><code class="language-julia hljs">plothorizontalslice(dummy, grd, depth=3u&quot;km&quot;)</code></pre><img src="731d1ce3.svg" alt="Example block output"/><p>If your tracer is supplied with units, those will show in the colorbar label</p><pre><code class="language-julia hljs">plothorizontalslice(dummy * u&quot;mol/m^3&quot;, grd, depth=10u&quot;m&quot;)</code></pre><img src="7114a3b3.svg" alt="Example block output"/><p>The advantage of Plots.jl recipes like this one is that you can specify other pieces of the plot as you would with built-in functions. The advantage of Plots.jl recipes like this one is that you can specify other pieces of the plot as you would with built-in functions. For example, you can chose the colormap with the <code>color</code> keyword argument.</p><pre><code class="language-julia hljs">dummy .*= cosd.(lonvec(grd))
+plt = plothorizontalslice(dummy, grd, depth=100, color=:balance)</code></pre><img src="61b31757.svg" alt="Example block output"/><p>And you can finetune attributes after the plot is created.</p><pre><code class="language-julia hljs">plot!(plt, xlabel=&quot;Lon&quot;, ylabel=&quot;Lat&quot;, colorbar_title=&quot;dummy value&quot;, title=&quot;The pacific as a whole&quot;)</code></pre><img src="a3099642.svg" alt="Example block output"/><h2 id="vertical-plots"><a class="docs-heading-anchor" href="#vertical-plots">Vertical plots</a><a id="vertical-plots-1"></a><a class="docs-heading-anchor-permalink" href="#vertical-plots" title="Permalink"></a></h2><p>Exploring the vertical distribution of tracers is important after all.</p><h3 id="Zonal-slices"><a class="docs-heading-anchor" href="#Zonal-slices">Zonal slices</a><a id="Zonal-slices-1"></a><a class="docs-heading-anchor-permalink" href="#Zonal-slices" title="Permalink"></a></h3><p>You must specify the longitude</p><pre><code class="language-julia hljs">dummy = cosd.(latvec(grd))
 dummy .+= sqrt.(depthvec(grd)) / 30
-plotmeridionalslice(dummy, grd, lon=330)</code></pre><img src="5896a8a8.svg" alt="Example block output"/><h3 id="Zonal-averages"><a class="docs-heading-anchor" href="#Zonal-averages">Zonal averages</a><a id="Zonal-averages-1"></a><a class="docs-heading-anchor-permalink" href="#Zonal-averages" title="Permalink"></a></h3><h4 id="Global-zonal-average"><a class="docs-heading-anchor" href="#Global-zonal-average">Global zonal average</a><a id="Global-zonal-average-1"></a><a class="docs-heading-anchor-permalink" href="#Global-zonal-average" title="Permalink"></a></h4><pre><code class="language-julia hljs">zonalaverage(dummy, grd)</code></pre><pre class="documenter-example-output"><code class="nohighlight hljs ansi">91×24 Matrix{Float64}:
+plotmeridionalslice(dummy, grd, lon=330)</code></pre><img src="a220ec3c.svg" alt="Example block output"/><h3 id="Zonal-averages"><a class="docs-heading-anchor" href="#Zonal-averages">Zonal averages</a><a id="Zonal-averages-1"></a><a class="docs-heading-anchor-permalink" href="#Zonal-averages" title="Permalink"></a></h3><h4 id="Global-zonal-average"><a class="docs-heading-anchor" href="#Global-zonal-average">Global zonal average</a><a id="Global-zonal-average-1"></a><a class="docs-heading-anchor-permalink" href="#Global-zonal-average" title="Permalink"></a></h4><pre><code class="language-julia hljs">zonalaverage(dummy, grd)</code></pre><pre class="documenter-example-output"><code class="nohighlight hljs ansi">91×24 Matrix{Float64}:
  NaN         NaN         NaN         …  NaN        NaN        NaN  NaN  NaN
  NaN         NaN         NaN            NaN        NaN        NaN  NaN  NaN
  NaN         NaN         NaN            NaN        NaN        NaN  NaN  NaN
@@ -48,5 +48,5 @@
  NaN         NaN         NaN         …  NaN        NaN        NaN  NaN  NaN</code></pre><p>If you want a zonal average over a specific region, you can just mask it out</p><h4 id="Basin-zonal-average"><a class="docs-heading-anchor" href="#Basin-zonal-average">Basin zonal average</a><a id="Basin-zonal-average-1"></a><a class="docs-heading-anchor-permalink" href="#Basin-zonal-average" title="Permalink"></a></h4><p>This is experimental at this stage and relies on <a href="https://github.com/briochemc/OceanBasins.jl">OceanBasins.jl</a>. You can create basin masks using this package with</p><pre><code class="language-julia hljs">using OceanBasins
 OCEANS = oceanpolygons()
 basins = sum(i*isbasin(latvec(grd), lonvec(grd), OCEANS) for (i,isbasin) in enumerate([isindian2, ispacific2, isatlantic2, isantarctic]))
-plothorizontalslice(basins, grd, depth=0, seriestype=:heatmap, color=:lightrainbow)</code></pre><img src="8dea8ff4.svg" alt="Example block output"/><p>and you can mask a specific region with the <code>mask</code> keyword argument</p><pre><code class="language-julia hljs">mPAC = ispacific(latvec(grd), lonvec(grd), OCEANS)
-plotzonalaverage(dummy, grd, mask=mPAC)</code></pre><img src="9719ce08.svg" alt="Example block output"/><h3 id="Meridional-slices"><a class="docs-heading-anchor" href="#Meridional-slices">Meridional slices</a><a id="Meridional-slices-1"></a><a class="docs-heading-anchor-permalink" href="#Meridional-slices" title="Permalink"></a></h3><p>Just as you should expect at this stage, you can plot a meridional slice with</p><pre><code class="language-julia hljs">plotmeridionalslice(dummy, grd, lon=-30)</code></pre><img src="9fb34b5a.svg" alt="Example block output"/><h2 id="profile-plots"><a class="docs-heading-anchor" href="#profile-plots">Depth profiles</a><a id="profile-plots-1"></a><a class="docs-heading-anchor-permalink" href="#profile-plots" title="Permalink"></a></h2><p>Sometimes you want a profile at a given station or location</p><pre><code class="language-julia hljs">plotdepthprofile(dummy, grd, lonlat=(-30,30))</code></pre><img src="4bf29ae8.svg" alt="Example block output"/><hr/><p><em>This page was generated using <a href="https://github.com/fredrikekre/Literate.jl">Literate.jl</a>.</em></p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../1_parameters/">« Parameters guide</a><a class="docs-footer-nextpage" href="../3_cruiseplot/">Plot transect/cruise data »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.4.1 on <span class="colophon-date" title="Thursday 23 May 2024 02:37">Thursday 23 May 2024</span>. Using Julia version 1.10.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+plothorizontalslice(basins, grd, depth=0, seriestype=:heatmap, color=:lightrainbow)</code></pre><img src="6a46f36c.svg" alt="Example block output"/><p>and you can mask a specific region with the <code>mask</code> keyword argument</p><pre><code class="language-julia hljs">mPAC = ispacific(latvec(grd), lonvec(grd), OCEANS)
+plotzonalaverage(dummy, grd, mask=mPAC)</code></pre><img src="b5d8b579.svg" alt="Example block output"/><h3 id="Meridional-slices"><a class="docs-heading-anchor" href="#Meridional-slices">Meridional slices</a><a id="Meridional-slices-1"></a><a class="docs-heading-anchor-permalink" href="#Meridional-slices" title="Permalink"></a></h3><p>Just as you should expect at this stage, you can plot a meridional slice with</p><pre><code class="language-julia hljs">plotmeridionalslice(dummy, grd, lon=-30)</code></pre><img src="306e9487.svg" alt="Example block output"/><h2 id="profile-plots"><a class="docs-heading-anchor" href="#profile-plots">Depth profiles</a><a id="profile-plots-1"></a><a class="docs-heading-anchor-permalink" href="#profile-plots" title="Permalink"></a></h2><p>Sometimes you want a profile at a given station or location</p><pre><code class="language-julia hljs">plotdepthprofile(dummy, grd, lonlat=(-30,30))</code></pre><img src="8b8730c8.svg" alt="Example block output"/><hr/><p><em>This page was generated using <a href="https://github.com/fredrikekre/Literate.jl">Literate.jl</a>.</em></p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../1_parameters/">« Parameters guide</a><a class="docs-footer-nextpage" href="../3_cruiseplot/">Plot transect/cruise data »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.4.1 on <span class="colophon-date" title="Friday 24 May 2024 00:19">Friday 24 May 2024</span>. Using Julia version 1.10.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>