build based on cbfa7d8

dev/.documenter-siteinfo.json

@@ -1 +1 @@
-{"documenter":{"julia_version":"1.9.3","generation_timestamp":"2023-10-25T10:12:57","documenter_version":"1.1.2"}}
+{"documenter":{"julia_version":"1.9.3","generation_timestamp":"2023-10-30T10:10:50","documenter_version":"1.1.2"}}

dev/generated/reference/positions/index.html

@@ -3,7 +3,7 @@
 using CairoMakie
 using TopoPlots
 using PyMNE</code></pre><pre class="documenter-example-output"><code class="nohighlight hljs ansi">    CondaPkg Found dependencies: /home/runner/.julia/packages/PyMNE/HGgbW/CondaPkg.toml
-    CondaPkg Found dependencies: /home/runner/.julia/packages/PythonCall/qTEA1/CondaPkg.toml
+    CondaPkg Found dependencies: /home/runner/.julia/packages/PythonCall/wXfah/CondaPkg.toml
     CondaPkg Dependencies already up to date</code></pre><h1 id="get-MNE-positions"><a class="docs-heading-anchor" href="#get-MNE-positions">get MNE-positions</a><a id="get-MNE-positions-1"></a><a class="docs-heading-anchor-permalink" href="#get-MNE-positions" title="Permalink"></a></h1><p>Generate a fake MNE structure <a href="https://mne.tools/0.24/auto_examples/visualization/eeglab_head_sphere.html">taken from mne documentation</a></p><pre><code class="language-julia hljs">biosemi_montage = PyMNE.channels.make_standard_montage(&quot;biosemi64&quot;)
 n_channels = length(biosemi_montage.ch_names)
 fake_info = PyMNE.create_info(ch_names=biosemi_montage.ch_names, sfreq=250.,
@@ -13,21 +13,21 @@
 fake_evoked.set_montage(biosemi_montage)
 
 pos = to_positions(fake_evoked)</code></pre><pre class="documenter-example-output"><code class="nohighlight hljs ansi">64-element Vector{Point2{Float64}}:
- [0.34935274876763384, 0.8914697618166454]
+ [0.34935274876763395, 0.8914697618166454]
  [0.2285454515991697, 0.8299153694246765]
- [0.3239207434789678, 0.8210416675361911]
+ [0.323920743478968, 0.8210416675361911]
  [0.38009721906796695, 0.7346772379558053]
  [0.28116929732806945, 0.7288908776450373]
- [0.19598811803244962, 0.729048111114921]
+ [0.19598811803244956, 0.729048111114921]
  [0.13267223773863893, 0.7340421555641459]
  [0.07111784534666996, 0.6132348583956815]
- [0.1381378125628734, 0.6118022611559795]
+ [0.13813781256287347, 0.6118022611559794]
  [0.2400936018380034, 0.6086174147856195]
  ⋮
  [0.612772564740614, 0.34981504242270145]
- [0.5864401194985318, 0.2239606378043266]
+ [0.5864401194985319, 0.2239606378043266]
  [0.6853680412384293, 0.2297469981150946]
- [0.7705492205340492, 0.22958976464521094]
+ [0.7705492205340493, 0.22958976464521094]
  [0.8338651008278599, 0.22459572019598625]
  [0.8710458357539724, 0.19758233504967118]
  [0.7379918869673291, 0.12872250633545543]
@@ -39,4 +39,4 @@
 f = Figure(resolution=(600,300))
 scatter(f[1,1],pos3d[1:2,:])
 scatter(f[1,2],pos2)
-f</code></pre><img src="a31d64a3.png" alt="Example block output"/><p>as one can see, the &quot;naive&quot; transform of just dropping the third dimension doesnt really work (left). We rather have to project the chanels to a sphere and unfold it (right)</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="../../../how_to/show_oob_labels/">« Show out of Bounds Label</a><a class="docs-footer-nextpage" href="../../../api/">API »</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="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="auto">Automatic (OS)</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.1.2 on <span class="colophon-date" title="Wednesday 25 October 2023 10:12">Wednesday 25 October 2023</span>. Using Julia version 1.9.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+f</code></pre><img src="a31d64a3.png" alt="Example block output"/><p>as one can see, the &quot;naive&quot; transform of just dropping the third dimension doesnt really work (left). We rather have to project the chanels to a sphere and unfold it (right)</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="../../../how_to/show_oob_labels/">« Show out of Bounds Label</a><a class="docs-footer-nextpage" href="../../../api/">API »</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="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="auto">Automatic (OS)</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.1.2 on <span class="colophon-date" title="Monday 30 October 2023 10:10">Monday 30 October 2023</span>. Using Julia version 1.9.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/generated/tutorials/circTopo/index.html

@@ -21,4 +21,4 @@
     axis = (; label = "Time?!"),
     predictor = :time,
     predictorBounds = [80, 320],
-)</code></pre><img src="5b95213d.png" 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="../../../tutorials/topoplotseries/">« Topo Plot Series</a><a class="docs-footer-nextpage" href="../../../how_to/position2color/">Butterfly Colormap »</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="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="auto">Automatic (OS)</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.1.2 on <span class="colophon-date" title="Wednesday 25 October 2023 10:12">Wednesday 25 October 2023</span>. Using Julia version 1.9.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+)</code></pre><img src="5b95213d.png" 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="../../../tutorials/topoplotseries/">« Topo Plot Series</a><a class="docs-footer-nextpage" href="../../../how_to/position2color/">Butterfly Colormap »</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="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="auto">Automatic (OS)</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.1.2 on <span class="colophon-date" title="Monday 30 October 2023 10:10">Monday 30 October 2023</span>. Using Julia version 1.9.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/generated/tutorials/erp/index.html

@@ -19,7 +19,7 @@
 )
 results = coeftable(m)
 res_effects = effects(Dict(:continuous =&gt; -5:0.5:5), m);</code></pre><pre class="documenter-example-output"><code class="nohighlight hljs ansi">┌ Warning: Autocorrelation was NOT taken into account. Therefore SE are UNRELIABLE. Use at your own discretion
-└ @ Unfold ~/.julia/packages/Unfold/AF2na/src/solver.jl:75</code></pre><h2 id="Plot-the-results"><a class="docs-heading-anchor" href="#Plot-the-results">Plot the results</a><a id="Plot-the-results-1"></a><a class="docs-heading-anchor-permalink" href="#Plot-the-results" title="Permalink"></a></h2><pre><code class="language-julia hljs">plot_erp(results; :stderror =&gt; true,)</code></pre><img src="1013426e.png" alt="Example block output"/><h2 id="Column-Mappings-for-Line-Plots"><a class="docs-heading-anchor" href="#Column-Mappings-for-Line-Plots">Column Mappings for Line Plots</a><a id="Column-Mappings-for-Line-Plots-1"></a><a class="docs-heading-anchor-permalink" href="#Column-Mappings-for-Line-Plots" title="Permalink"></a></h2><p><code>plot_erp</code> use a <code>DataFrame</code> as an input, the library needs to know the names of the columns used for plotting.</p><p>There are multiple default values, that are checked in that order if they exist in the <code>DataFrame</code>, a custom name can be chosen using <code>plot_erp(...;mapping=(; :y=:myEstimate)</code></p><p>:x Default is <code>(:x, :time)</code>. :y Default is <code>(:y, :estimate, :yhat)</code>. :color Default is <code>(:color, :coefname)</code>.</p><h1 id="Configuration-for-Line-Plots"><a class="docs-heading-anchor" href="#Configuration-for-Line-Plots">Configuration for Line Plots</a><a id="Configuration-for-Line-Plots-1"></a><a class="docs-heading-anchor-permalink" href="#Configuration-for-Line-Plots" title="Permalink"></a></h1><h2 id="key-values"><a class="docs-heading-anchor" href="#key-values">key values</a><a id="key-values-1"></a><a class="docs-heading-anchor-permalink" href="#key-values" title="Permalink"></a></h2><p><code>plot_erp(...; &lt;name&gt;=&lt;value&gt;,...)</code>.</p><ul><li>categoricalColor (boolean, true) - in case of numeric <code>:color</code> column, is color a continuous or categorical variable?</li><li>categoricalGroup (boolean, true) - in case of numeric <code>:group</code> column, treat <code>:group</code> as categorical variable by default</li><li>stderror (boolean, false) - add an error-ribbon based on the <code>:stderror</code> column</li><li>pvalue (see below)</li></ul><p>Using some general configurations we can pretty up the default visualization. Here we use the following configuration:</p><pre><code class="language-julia hljs">plot_erp(
+└ @ Unfold ~/.julia/packages/Unfold/LwbaS/src/solver.jl:75</code></pre><h2 id="Plot-the-results"><a class="docs-heading-anchor" href="#Plot-the-results">Plot the results</a><a id="Plot-the-results-1"></a><a class="docs-heading-anchor-permalink" href="#Plot-the-results" title="Permalink"></a></h2><pre><code class="language-julia hljs">plot_erp(results; :stderror =&gt; true,)</code></pre><img src="1013426e.png" alt="Example block output"/><h2 id="Column-Mappings-for-Line-Plots"><a class="docs-heading-anchor" href="#Column-Mappings-for-Line-Plots">Column Mappings for Line Plots</a><a id="Column-Mappings-for-Line-Plots-1"></a><a class="docs-heading-anchor-permalink" href="#Column-Mappings-for-Line-Plots" title="Permalink"></a></h2><p><code>plot_erp</code> use a <code>DataFrame</code> as an input, the library needs to know the names of the columns used for plotting.</p><p>There are multiple default values, that are checked in that order if they exist in the <code>DataFrame</code>, a custom name can be chosen using <code>plot_erp(...;mapping=(; :y=:myEstimate)</code></p><p>:x Default is <code>(:x, :time)</code>. :y Default is <code>(:y, :estimate, :yhat)</code>. :color Default is <code>(:color, :coefname)</code>.</p><h1 id="Configuration-for-Line-Plots"><a class="docs-heading-anchor" href="#Configuration-for-Line-Plots">Configuration for Line Plots</a><a id="Configuration-for-Line-Plots-1"></a><a class="docs-heading-anchor-permalink" href="#Configuration-for-Line-Plots" title="Permalink"></a></h1><h2 id="key-values"><a class="docs-heading-anchor" href="#key-values">key values</a><a id="key-values-1"></a><a class="docs-heading-anchor-permalink" href="#key-values" title="Permalink"></a></h2><p><code>plot_erp(...; &lt;name&gt;=&lt;value&gt;,...)</code>.</p><ul><li>categoricalColor (boolean, true) - in case of numeric <code>:color</code> column, is color a continuous or categorical variable?</li><li>categoricalGroup (boolean, true) - in case of numeric <code>:group</code> column, treat <code>:group</code> as categorical variable by default</li><li>stderror (boolean, false) - add an error-ribbon based on the <code>:stderror</code> column</li><li>pvalue (see below)</li></ul><p>Using some general configurations we can pretty up the default visualization. Here we use the following configuration:</p><pre><code class="language-julia hljs">plot_erp(
     res_effects;
     mapping = (; y = :yhat, color = :continuous, group = :continuous),
     legend = (; nbanks = 2),
@@ -30,4 +30,4 @@
 #		coefname=[&quot;(Intercept)&quot;,&quot;condition: face&quot;] # if coefname not specified, line should be black
 #	)</code></pre><p>plot_erp(results; :pvalue=&gt;pvals)</p><h3 id="stderror-(boolean)"><a class="docs-heading-anchor" href="#stderror-(boolean)">stderror (boolean)</a><a id="stderror-(boolean)-1"></a><a class="docs-heading-anchor-permalink" href="#stderror-(boolean)" title="Permalink"></a></h3><p>Indicating whether the plot should show a colored band showing lower and higher estimates based on the stderror. Default is <code>false</code>.</p><p>previously we showed <code>:stderror</code>- but low/high is possible as well`</p><pre><code class="language-julia hljs">results.se_low = results.estimate .- 0.5
 results.se_high = results.estimate .+ 0.15
-plot_erp(select(results, Not(:stderror)); stderror = true)</code></pre><img src="b1b2cf75.png" alt="Example block output"/><div class="admonition is-info"><header class="admonition-header">Note</header><div class="admonition-body"><p>as in the above code,<code>:stderror</code> has precedence over <code>:se_low</code>/<code>:se_high</code></p></div></div><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="../../../">« UnfoldMakie Documentation</a><a class="docs-footer-nextpage" href="../../../tutorials/butterfly/">Butterfly Plot »</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="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="auto">Automatic (OS)</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.1.2 on <span class="colophon-date" title="Wednesday 25 October 2023 10:12">Wednesday 25 October 2023</span>. Using Julia version 1.9.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+plot_erp(select(results, Not(:stderror)); stderror = true)</code></pre><img src="b1b2cf75.png" alt="Example block output"/><div class="admonition is-info"><header class="admonition-header">Note</header><div class="admonition-body"><p>as in the above code,<code>:stderror</code> has precedence over <code>:se_low</code>/<code>:se_high</code></p></div></div><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="../../../">« UnfoldMakie Documentation</a><a class="docs-footer-nextpage" href="../../../tutorials/butterfly/">Butterfly Plot »</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="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="auto">Automatic (OS)</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.1.2 on <span class="colophon-date" title="Monday 30 October 2023 10:10">Monday 30 October 2023</span>. Using Julia version 1.9.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>