Merge pull request #461 from jakobrunge/developer

updated docs

Author: jakobrunge

docs/_build/.doctrees/environment.pickle

@@ -618,7 +618,7 @@ <h1><code class="xref py py-mod docutils literal notranslate"><span class="pre">
 Must be greater zero.</p></li>
 <li><p><strong>tau_max</strong> (<em>int</em><em>, </em><em>default: 1</em>) – Maximum time lag. Must be larger or equal to tau_min.</p></li>
 <li><p><strong>save_iterations</strong> (<em>bool</em><em>, </em><em>default: False</em>) – Whether to save iteration step results such as conditions used.</p></li>
-<li><p><strong>pc_alpha</strong> (<em>float</em><em> or </em><em>list</em><em> of </em><em>floats</em><em>, </em><em>default:</em><em> [</em><em>0.05</em><em>, </em><em>0.1</em><em>, </em><em>0.2</em><em>, </em><em>...</em><em>, </em><em>0.5</em><em>]</em>) – Significance level in algorithm. If a list or None is passed, the
+<li><p><strong>pc_alpha</strong> (<em>float</em><em> or </em><em>list</em><em> of </em><em>floats</em><em>, </em><em>default: 0.2</em>) – Significance level in algorithm. If a list or None is passed, the
 pc_alpha level is optimized for every variable across the given
 pc_alpha values using the score computed in
 cond_ind_test.get_model_selection_criterion().</p></li>
@@ -743,7 +743,7 @@ <h1><code class="xref py py-mod docutils literal notranslate"><span class="pre">
 
 <dl class="py method">
 <dt class="sig sig-object py" id="tigramite.pcmci.PCMCI.run_pcmci">
-<span class="sig-name descname"><span class="pre">run_pcmci</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">selected_links</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">link_assumptions</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tau_min</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tau_max</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">save_iterations</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pc_alpha</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.05</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_conds_dim</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_combinations</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_conds_py</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_conds_px</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">alpha_level</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.05</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fdr_method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'none'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/tigramite/pcmci.html#PCMCI.run_pcmci"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#tigramite.pcmci.PCMCI.run_pcmci" title="Link to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">run_pcmci</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">selected_links</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">link_assumptions</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tau_min</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tau_max</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">save_iterations</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pc_alpha</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_conds_dim</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_combinations</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_conds_py</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_conds_px</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">alpha_level</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.05</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fdr_method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'none'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/tigramite/pcmci.html#PCMCI.run_pcmci"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#tigramite.pcmci.PCMCI.run_pcmci" title="Link to this definition">¶</a></dt>
 <dd><p>Runs PCMCI time-lagged causal discovery for time series.</p>
 <p>Wrapper around PC-algorithm function and MCI function.</p>
 <p class="rubric">Notes</p>
@@ -849,7 +849,7 @@ <h1><code class="xref py py-mod docutils literal notranslate"><span class="pre">
 <li><p><strong>tau_min</strong> (<em>int</em><em>, </em><em>optional</em><em> (</em><em>default: 0</em><em>)</em>) – Minimum time lag to test. Note that zero-lags are undirected.</p></li>
 <li><p><strong>tau_max</strong> (<em>int</em><em>, </em><em>optional</em><em> (</em><em>default: 1</em><em>)</em>) – Maximum time lag. Must be larger or equal to tau_min.</p></li>
 <li><p><strong>save_iterations</strong> (<em>bool</em><em>, </em><em>optional</em><em> (</em><em>default: False</em><em>)</em>) – Whether to save iteration step results such as conditions used.</p></li>
-<li><p><strong>pc_alpha</strong> (<em>float</em><em>, </em><em>optional</em><em> (</em><em>default: 0.05</em><em>)</em>) – Significance level in algorithm.</p></li>
+<li><p><strong>pc_alpha</strong> (<em>float</em><em>, </em><em>optional</em><em> (</em><em>default: 0.2</em><em>)</em>) – Significance level in PC1 algorithm.</p></li>
 <li><p><strong>max_conds_dim</strong> (<em>int</em><em>, </em><em>optional</em><em> (</em><em>default: None</em><em>)</em>) – Maximum number of conditions to test. If None is passed, this number
 is unrestricted.</p></li>
 <li><p><strong>max_combinations</strong> (<em>int</em><em>, </em><em>optional</em><em> (</em><em>default: 1</em><em>)</em>) – Maximum number of combinations of conditions of current cardinality

docs/_build/.doctrees/index.doctree

@@ -61,7 +61,7 @@ def run(self):
 # Run the setup
 setup(
     name="tigramite",
-    version="5.2.8.1",
+    version="5.2.8.2",
     packages=["tigramite", "tigramite.independence_tests", "tigramite.toymodels"],
     license="GNU General Public License v3.0",
     description="Tigramite causal inference for time series",