Deploy documentation

config/index.html

@@ -33,4 +33,4 @@
     }</code></pre><p>In particular, you can set <code>&quot;correlated&quot;: true</code> if you want to use one variable to correlate the nuisance parameters (eg to speed up the computation times), and <code>&quot;fixed&quot;: false</code> if you want to include a prior for nuisance parameters (otherwise these parameters they will be fixed to their partition value and not constrained).</p><p>If a variable is correlated (either <code>energy_scale</code> or <code>efficiency</code>), the code will search for a field in the <code>fit_groups</code> block of the partitions JSON file to use a correlated variable per each fit group.  In particular, the field has to be specified as:</p><ul><li><code>&quot;efficiency_group_name&quot;: &quot;...&quot;</code></li><li><code>&quot;energy_scale_group_name&quot;: &quot;...&quot;</code></li></ul><div class="admonition is-info"><header class="admonition-header">Note</header><div class="admonition-body"><p>If the key doesn&#39;t exist, this defaults to &quot;all&quot;</p></div></div><p>Parameters are then added to the model called <code>αr_\$name</code> (for resolution), <code>αe_\$name</code> for efficiency and <code>αb_\$name</code> for bias.</p><div class="admonition is-warning"><header class="admonition-header">Warning</header><div class="admonition-body"><p>The <span>$\alpha$</span> parameter names default to <code>_all</code>, if you want one different per experiment this must be explicitly specified in the fit groups entry</p></div></div><h2 id="Background-shape-and-correlation"><a class="docs-heading-anchor" href="#Background-shape-and-correlation">Background shape and correlation</a><a id="Background-shape-and-correlation-1"></a><a class="docs-heading-anchor-permalink" href="#Background-shape-and-correlation" title="Permalink"></a></h2><p>There are several options to control the background in more detail. These can be added to the &quot;bkg&quot; section of the config: In particular:</p><ul><li>&quot;correlated&quot; adds a hierarchical (correlated) background to the model, this key should have a dictionary giving details on the prior shape and ranges for example:</li></ul><pre><code class="language-json hljs">&quot;correlated&quot;:{&quot;mode&quot;:&quot;lognormal&quot;,&quot;range&quot;:[0,0.1]}</code></pre><p>The three options for the mode are &#39;lognormal&#39;, &#39;normal&#39; or &#39;none&#39;. While the range gives the range of the uniform prior on the <code>\sigma_B</code> parameter.</p><ul><li>&quot;shape&quot; changes the shape of the background from uniform. The user should provide a dictionary giving details on the shape:</li></ul><p>for example:</p><pre><code class="language-json hljs">&quot;shape&quot;:{
             &quot;name&quot;:&quot;exponential&quot;,
             &quot;pars&quot;:{&quot;slope&quot;:[-10,10]}
-        },</code></pre><p>The &quot;pars&quot; subdictionary describes the range of the priors on the parameters of the model, currently implemented shapes are &quot;uniform&quot;, &quot;linear&quot; and &quot;exponential&quot;. These names correspond to functions in <code>fitting.jl</code> and logical conditions in <code>get_bkg_pdf</code> in <code>likelihood.jl</code>.</p><p>This will add parameters <code>${bkg_name}_slope</code> or similar to the model (and then call them). This names therefore must correspond to the names in the functions in <code>fitting.jl</code>. To add a new shape simply define a new method in <code>fitting.jl</code> and a new logical condition in <code>get_bkg_pdf</code> in <code>likelihood.jl</code>.</p><div class="admonition is-info"><header class="admonition-header">Note</header><div class="admonition-body"><p>If these keys are not provided the model defaults to a uniform uncorrelated background.</p></div></div><h2 id="Signal-shape"><a class="docs-heading-anchor" href="#Signal-shape">Signal shape</a><a id="Signal-shape-1"></a><a class="docs-heading-anchor-permalink" href="#Signal-shape" title="Permalink"></a></h2><p>The signal shape can be specified in the partition JSON file in order to have a different signal shape for different partitions. An example is given by the combined fit of GERDA/LEGEND and MAJORANA DEMONSTRATOR (MJD) partitions where for the first one we want to model the signal with a simple gaussian function while we want to model data from MJD accounting for an additional tail at the low-energy side of the gaussian. See the &quot;Partitions and events&quot; documentation.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../installation/">« First steps</a><a class="docs-footer-nextpage" href="../inputs/">Partitions and events »</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><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.8.0 on <span class="colophon-date" title="Wednesday 27 November 2024 03:47">Wednesday 27 November 2024</span>. Using Julia version 1.11.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+        },</code></pre><p>The &quot;pars&quot; subdictionary describes the range of the priors on the parameters of the model, currently implemented shapes are &quot;uniform&quot;, &quot;linear&quot; and &quot;exponential&quot;. These names correspond to functions in <code>fitting.jl</code> and logical conditions in <code>get_bkg_pdf</code> in <code>likelihood.jl</code>.</p><p>This will add parameters <code>${bkg_name}_slope</code> or similar to the model (and then call them). This names therefore must correspond to the names in the functions in <code>fitting.jl</code>. To add a new shape simply define a new method in <code>fitting.jl</code> and a new logical condition in <code>get_bkg_pdf</code> in <code>likelihood.jl</code>.</p><div class="admonition is-info"><header class="admonition-header">Note</header><div class="admonition-body"><p>If these keys are not provided the model defaults to a uniform uncorrelated background.</p></div></div><h2 id="Signal-shape"><a class="docs-heading-anchor" href="#Signal-shape">Signal shape</a><a id="Signal-shape-1"></a><a class="docs-heading-anchor-permalink" href="#Signal-shape" title="Permalink"></a></h2><p>The signal shape can be specified in the partition JSON file in order to have a different signal shape for different partitions. An example is given by the combined fit of GERDA/LEGEND and MAJORANA DEMONSTRATOR (MJD) partitions where for the first one we want to model the signal with a simple gaussian function while we want to model data from MJD accounting for an additional tail at the low-energy side of the gaussian. See the &quot;Partitions and events&quot; documentation.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../installation/">« First steps</a><a class="docs-footer-nextpage" href="../inputs/">Partitions and events »</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><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.8.0 on <span class="colophon-date" title="Friday 6 December 2024 07:06">Friday 6 December 2024</span>. Using Julia version 1.11.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

inputs/index.html

@@ -35,4 +35,4 @@
             "energy": 2069.420,
             "timestamp": 1755109448,
             "detector": "DET_0"
-        },</code></pre><p>The timestamp and detector are used to extract which partition this event corresponds to. To convert to this format from the standard GERDA and LEGEND files, there are tools available in https://github.com/tdixon97/legend-0vbb-config.</p><p>It is possible to supply a list of partition and event files in this case the list of fit groups and events are concatenated.</p><div class="admonition is-warning"><header class="admonition-header">Warning</header><div class="admonition-body"><p>If multiple files are provided <code>fit_group</code> must still be unique.</p></div></div></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../config/">« Configuration file</a><a class="docs-footer-nextpage" href="../toys/">Generating toys »</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><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.8.0 on <span class="colophon-date" title="Wednesday 27 November 2024 03:47">Wednesday 27 November 2024</span>. Using Julia version 1.11.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+        },</code></pre><p>The timestamp and detector are used to extract which partition this event corresponds to. To convert to this format from the standard GERDA and LEGEND files, there are tools available in https://github.com/tdixon97/legend-0vbb-config.</p><p>It is possible to supply a list of partition and event files in this case the list of fit groups and events are concatenated.</p><div class="admonition is-warning"><header class="admonition-header">Warning</header><div class="admonition-body"><p>If multiple files are provided <code>fit_group</code> must still be unique.</p></div></div></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../config/">« Configuration file</a><a class="docs-footer-nextpage" href="../toys/">Generating toys »</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><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.8.0 on <span class="colophon-date" title="Friday 6 December 2024 07:06">Friday 6 December 2024</span>. Using Julia version 1.11.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>