deploy: 1d215ac

full-documentation/index.html

@@ -471,30 +471,30 @@ <h2 id="review-status">Review status</h2>
 <table>
 <thead>
 <tr>
-<th align="left">Reviewer/Editor and Date (copy from screen)</th>
-<th align="left">Comments</th>
+<th style="text-align: left;">Reviewer/Editor and Date (copy from screen)</th>
+<th style="text-align: left;">Comments</th>
 </tr>
 </thead>
 <tbody>
 <tr>
-<td align="left">Main.GiovanniPetrucciani - 14-Dec-2010</td>
-<td align="left">created template page</td>
+<td style="text-align: left;">Main.GiovanniPetrucciani - 14-Dec-2010</td>
+<td style="text-align: left;">created template page</td>
 </tr>
 <tr>
-<td align="left">Main.GiovanniPetrucciani - 21-Mar-2011</td>
-<td align="left">new tag</td>
+<td style="text-align: left;">Main.GiovanniPetrucciani - 21-Mar-2011</td>
+<td style="text-align: left;">new tag</td>
 </tr>
 <tr>
-<td align="left">Main.LucaLista - 04-May-2011</td>
-<td align="left">added CRAB submission</td>
+<td style="text-align: left;">Main.LucaLista - 04-May-2011</td>
+<td style="text-align: left;">added CRAB submission</td>
 </tr>
 <tr>
-<td align="left">Main.GiovanniPetrucciani - 10-Jun-2011</td>
-<td align="left">Frequentist limits</td>
+<td style="text-align: left;">Main.GiovanniPetrucciani - 10-Jun-2011</td>
+<td style="text-align: left;">Frequentist limits</td>
 </tr>
 <tr>
-<td align="left">Main.GiovanniPetrucciani - 10-Jun-2011</td>
-<td align="left">Frequentist grids and expected limits</td>
+<td style="text-align: left;">Main.GiovanniPetrucciani - 10-Jun-2011</td>
+<td style="text-align: left;">Frequentist grids and expected limits</td>
 </tr>
 </tbody>
 </table>

index.html

@@ -490,6 +490,6 @@ <h4 class="modal-title" id="keyboardModalLabel">Keyboard Shortcuts</h4>
 </html>
 
 <!--
-MkDocs version : 1.4.3
-Build Date UTC : 2023-07-26 10:12:06.732893+00:00
+MkDocs version : 1.5.0
+Build Date UTC : 2023-07-27 20:36:12.554551+00:00
 -->

part2/settinguptheanalysis/index.html

@@ -332,7 +332,7 @@ <h3 id="binned-shape-analysis">Binned shape analysis</h3>
 <p>The combine tool can take as input histograms saved as TH1, as RooAbsHist in a RooFit workspace (an example of how to create a RooFit workspace and save histograms is available in <a href="https://github.com/cms-analysis/HiggsAnalysis-CombinedLimit/blob/main/data/benchmarks/shapes/make_simple_shapes.cxx">github</a>), or from a pandas dataframe (<a href="https://github.com/cms-analysis/HiggsAnalysis-CombinedLimit/blob/main/data/tutorials/shapes/simple-shapes-df.txt">example</a>)</p>
 <p>The block of lines defining the mapping (first block in the datacard) contains one or more rows in the form</p>
 <ul>
-<li><strong>shapes <em>process</em> <em>channel</em> <em>file</em> <em>histogram</em> <em>[histogram_with_systematics]</em> </strong></li>
+<li><em><em>shapes </em>process</em> <em>channel</em> <em>file</em> <em>histogram</em> <em>[histogram_with_systematics]</em> **</li>
 </ul>
 <p>In this line</p>
 <ul>
@@ -359,7 +359,7 @@ <h4 id="template-shape-uncertainties">Template shape uncertainties</h4>
 <p>For each shape uncertainty and process/channel affected by it, two additional input shapes have to be provided, obtained shifting that parameter up and down by one standard deviation. When building the likelihood, each shape uncertainty is associated to a nuisance parameter taken from a unit gaussian distribution, which is used to interpolate or extrapolate using the specified histograms.</p>
 <p>For each given source of shape uncertainty, in the part of the datacard containing shape uncertainties (last block), there must be a row</p>
 <ul>
-<li><strong> <em>name</em> <em>shape</em> <em>effect_for_each_process_and_channel</em> </strong></li>
+<li>** <em>name</em> <em>shape</em> <em>effect_for_each_process_and_channel</em> **</li>
 </ul>
 <p>The effect can be "-" or 0 for no effect, 1 for normal effect, and possibly something different from 1 to test larger or smaller effects (in that case, the unit gaussian is scaled by that factor before using it as parameter for the interpolation)</p>
 <p>The datacard in <a href="https://github.com/cms-analysis/HiggsAnalysis-CombinedLimit/blob/main/data/tutorials/shapes/simple-shapes-TH1.txt">data/tutorials/shapes/simple-shapes-TH1.txt</a> is a clear example of how to include shapes in the datacard. In the first block the following line specifies the shape mapping:</p>
@@ -394,42 +394,42 @@ <h4 id="template-shape-uncertainties">Template shape uncertainties</h4>
 <table>
 <thead>
 <tr>
-<th align="left">histogram</th>
-<th align="left">meaning</th>
+<th style="text-align: left;">histogram</th>
+<th style="text-align: left;">meaning</th>
 </tr>
 </thead>
 <tbody>
 <tr>
-<td align="left"><code>e/data_obs</code></td>
-<td align="left">observed data in electron channel</td>
+<td style="text-align: left;"><code>e/data_obs</code></td>
+<td style="text-align: left;">observed data in electron channel</td>
 </tr>
 <tr>
-<td align="left"><code>e/higgs</code></td>
-<td align="left">expected shape for higgs in electron channel</td>
+<td style="text-align: left;"><code>e/higgs</code></td>
+<td style="text-align: left;">expected shape for higgs in electron channel</td>
 </tr>
 <tr>
-<td align="left"><code>e/zz</code></td>
-<td align="left">expected shape for ZZ in electron channel</td>
+<td style="text-align: left;"><code>e/zz</code></td>
+<td style="text-align: left;">expected shape for ZZ in electron channel</td>
 </tr>
 <tr>
-<td align="left"><code>e/top</code></td>
-<td align="left">expected shape for top in electron channel</td>
+<td style="text-align: left;"><code>e/top</code></td>
+<td style="text-align: left;">expected shape for top in electron channel</td>
 </tr>
 <tr>
-<td align="left"><code>mu/data_obs</code></td>
-<td align="left">observed data in muon channel</td>
+<td style="text-align: left;"><code>mu/data_obs</code></td>
+<td style="text-align: left;">observed data in muon channel</td>
 </tr>
 <tr>
-<td align="left"><code>mu/higgs</code></td>
-<td align="left">expected shape for higgs in muon channel</td>
+<td style="text-align: left;"><code>mu/higgs</code></td>
+<td style="text-align: left;">expected shape for higgs in muon channel</td>
 </tr>
 <tr>
-<td align="left"><code>mu/zz</code></td>
-<td align="left">expected shape for ZZ in muon channel</td>
+<td style="text-align: left;"><code>mu/zz</code></td>
+<td style="text-align: left;">expected shape for ZZ in muon channel</td>
 </tr>
 <tr>
-<td align="left"><code>mu/top</code></td>
-<td align="left">expected shape for top in muon channel</td>
+<td style="text-align: left;"><code>mu/top</code></td>
+<td style="text-align: left;">expected shape for top in muon channel</td>
 </tr>
 </tbody>
 </table>
@@ -492,7 +492,7 @@ <h3 id="unbinned-or-parametric-shape-analysis">Unbinned or parametric shape anal
 <p>meaning there is a parameter already contained in the input workspace called <strong><code>sigma</code></strong> which should be <em>constrained</em> with a Gaussian centered at 1.0 with a width of 0.1. Note that, the exact interpretation (i.e all combine knows is that 1.0 should be the most likely value and 0.1 is its 1σ uncertainy) of these parameters is left to the user since the signal pdf is constructed externally by you. Asymmetric uncertainties are written as with <code>lnN</code> using the syntax <strong>-1σ/+1σ</strong> in the datacard.</p>
 <p>If one wants to specify a parameter that is freely floating across its given range, and not gaussian constrained, the following syntax is used:</p>
 <ul>
-<li><strong>name <em>flatParam</em> </strong></li>
+<li><em><em>name </em>flatParam</em> **</li>
 </ul>
 <p>Though this is <em>not strictly necessary</em> in frequentist methods using profiled likelihoods as combine will still profile these nuisances when performing fits (as is the case for the <code>simple-shapes-parametric.txt</code> datacard).</p>
 <div class="admonition warning">

part3/nonstandard/index.html

@@ -687,8 +687,8 @@ <h2 id="roomultipdf-conventional-bias-studies">RooMultiPdf conventional bias stu
 
 
    // Save to a new workspace
-   TFile *fout = new TFile(&quot;workspace.root&quot;,&quot;RECREATE&quot;);
-   RooWorkspace wout(&quot;workspace&quot;,&quot;workspaace&quot;);
+   TFile *fout = new TFile(&quot;toyhgg_in.root&quot;,&quot;RECREATE&quot;);
+   RooWorkspace wout(&quot;multipdf&quot;,&quot;multipdf&quot;);
 
    data-&gt;SetName(&quot;data&quot;);
    wout.import(*data);

part5/longexercise/index.html

@@ -759,7 +759,7 @@ <h3 id="e-signal-strength-measurement-and-uncertainty-breakdown">E: Signal stren
 <p>While it is perfectly fine to just list the relevant nuisance parameters in the <code>--freezeParameters</code> argument for the <span class="arithmatex"><span class="MathJax_Preview">\sigma_{\text{fr.theory}}</span><script type="math/tex">\sigma_{\text{fr.theory}}</script></span> scan, a convenient way can be to define a named group of parameters in the text datacard and then freeze all parameters in this group with <code>--freezeNuisanceGroups</code>. The syntax for defining a group is:</p>
 <pre><code class="language-shell">[group name] group = uncertainty_1 uncertainty_2 ... uncertainty_N
 </code></pre>
-<p><strong> Tasks and questions: </strong></p>
+<p>** Tasks and questions: **</p>
 <ul>
 <li>Take our stat+syst split one step further and separate the systematic part into two: one part for hadronic tau uncertainties and one for all others.</li>
 <li>Do this by defining a <code>tauID</code> group in the datacard including the following parameters: <code>CMS_eff_t</code>, <code>CMS_eff_t_highpt</code>, and the three <code>CMS_scale_t_X</code> uncertainties.</li>

part5/longexerciseanswers/index.html

@@ -475,7 +475,7 @@ <h3 id="d-calculating-the-significance">D: Calculating the significance</h3>
 </details>
 
 <h3 id="e-signal-strength-measurement-and-uncertainty-breakdown">E: Signal strength measurement and uncertainty breakdown</h3>
-<p><strong> Tasks and questions: </strong></p>
+<p>** Tasks and questions: **</p>
 <ul>
 <li>Take our stat+syst split one step further and separate the systematic part into two: one part for hadronic tau uncertainties and one for all others. Do this by defining a <code>tauID</code> group in the datacard including the following parameters: <code>CMS_eff_t</code>, <code>CMS_eff_t_highpt</code>, and the three <code>CMS_scale_t_X</code> uncertainties.</li>
 </ul>

part5/roofit/index.html

@@ -821,7 +821,7 @@ <h1 id="likelihoods-and-fitting-to-data">Likelihoods and Fitting to data</h1>
 <p>This is exactly what needs to be done when you want to use shape based datacards in combine with parametric models.</p>
 <h2 id="a-likelihood-for-a-counting-experiment">A likelihood for a counting experiment</h2>
 <p>An introductory presentation about likelihoods and interval estimation is available <a href="https://indico.cern.ch/event/976099/contributions/4138517/">here</a>.</p>
-<p><strong>Note: We will use python syntax in this section; you should use a .py script. Make sure to do <code>import ROOT</code> at the top of your script </strong></p>
+<p>**Note: We will use python syntax in this section; you should use a .py script. Make sure to do <code>import ROOT</code> at the top of your script **</p>
 <p>We've seen how to create variables and pdfs, and how to fit a pdf to data. But what if we have a counting experiment, or a histogram template shape? And what about systematic uncertainties?  Let's build a likelihood
 for this:</p>
 <p><span class="arithmatex"><span class="MathJax_Preview">\mathcal{L} \propto p(\text{data}|\text{parameters})</span><script type="math/tex">\mathcal{L} \propto p(\text{data}|\text{parameters})</script></span></p>

tutorials-part-2/index.html

@@ -307,42 +307,42 @@ <h5 id="not-parametric-shapes-and-uncertainties">Not parametric shapes and uncer
 <table>
 <thead>
 <tr>
-<th align="left">histogram</th>
-<th align="left">meaning</th>
+<th style="text-align: left;">histogram</th>
+<th style="text-align: left;">meaning</th>
 </tr>
 </thead>
 <tbody>
 <tr>
-<td align="left"><code>e/data_obs</code></td>
-<td align="left">observed data in electron channel</td>
+<td style="text-align: left;"><code>e/data_obs</code></td>
+<td style="text-align: left;">observed data in electron channel</td>
 </tr>
 <tr>
-<td align="left"><code>e/higgs</code></td>
-<td align="left">expected shape for higgs in electron channel</td>
+<td style="text-align: left;"><code>e/higgs</code></td>
+<td style="text-align: left;">expected shape for higgs in electron channel</td>
 </tr>
 <tr>
-<td align="left"><code>e/zz</code></td>
-<td align="left">expected shape for ZZ in electron channel</td>
+<td style="text-align: left;"><code>e/zz</code></td>
+<td style="text-align: left;">expected shape for ZZ in electron channel</td>
 </tr>
 <tr>
-<td align="left"><code>e/top</code></td>
-<td align="left">expected shape for top in electron channel</td>
+<td style="text-align: left;"><code>e/top</code></td>
+<td style="text-align: left;">expected shape for top in electron channel</td>
 </tr>
 <tr>
-<td align="left"><code>mu/data_obs</code></td>
-<td align="left">observed data in muon channel</td>
+<td style="text-align: left;"><code>mu/data_obs</code></td>
+<td style="text-align: left;">observed data in muon channel</td>
 </tr>
 <tr>
-<td align="left"><code>mu/higgs</code></td>
-<td align="left">expected shape for higgs in muon channel</td>
+<td style="text-align: left;"><code>mu/higgs</code></td>
+<td style="text-align: left;">expected shape for higgs in muon channel</td>
 </tr>
 <tr>
-<td align="left"><code>mu/zz</code></td>
-<td align="left">expected shape for ZZ in muon channel</td>
+<td style="text-align: left;"><code>mu/zz</code></td>
+<td style="text-align: left;">expected shape for ZZ in muon channel</td>
 </tr>
 <tr>
-<td align="left"><code>mu/top</code></td>
-<td align="left">expected shape for top in muon channel</td>
+<td style="text-align: left;"><code>mu/top</code></td>
+<td style="text-align: left;">expected shape for top in muon channel</td>
 </tr>
 </tbody>
 </table>