From eb275a72d93be94b14f1498eacb08766541cf827 Mon Sep 17 00:00:00 2001
From: binho <binho@binhos-MacBook-Pro.local>
Date: Tue, 13 Feb 2024 15:01:00 -0600
Subject: [PATCH] Cleaning examples, add tree dist doc

---
 docs/build/doctrees/environment.pickle     | Bin 3556047 -> 3583592 bytes
 docs/build/html/pjdoc/index.html           |  73 ++++++++++++++-------
 docs/build/html/searchindex.js             |   2 +-
 examples/birthdeath_incomplete_sampling.pj |  20 ++++++
 examples/birthdeath_timehet.pj             |   3 +-
 examples/bisse.pj                          |   5 +-
 examples/bisse_timehet.pj                  |   4 +-
 examples/fbd.pj                            |   5 +-
 examples/geosse.pj                         |   5 +-
 examples/geosse_timehet.pj                 |   8 ++-
 examples/yule.pj                           |   3 +-
 examples/yule_incomplete_sampling.pj       |  27 --------
 12 files changed, 90 insertions(+), 65 deletions(-)
 create mode 100644 examples/birthdeath_incomplete_sampling.pj
 delete mode 100644 examples/yule_incomplete_sampling.pj

diff --git a/docs/build/doctrees/environment.pickle b/docs/build/doctrees/environment.pickle
index 6fd4317485dd94bc50ac7c4d71184850ad5aaf48..16051f109fd23523a144e668bc02b23c406c4dc9 100644
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diff --git a/docs/build/html/pjdoc/index.html b/docs/build/html/pjdoc/index.html
index a08f972..f65c4fa 100644
--- a/docs/build/html/pjdoc/index.html
+++ b/docs/build/html/pjdoc/index.html
@@ -118,43 +118,43 @@
 <h1>Documentation<a class="headerlink" href="#documentation" title="Link to this heading"></a></h1>
 <nav class="contents local" id="contents">
 <ul class="simple">
-<li><p><a class="reference internal" href="#overview" id="id17">Overview</a></p>
+<li><p><a class="reference internal" href="#overview" id="id18">Overview</a></p>
 <ul>
-<li><p><a class="reference internal" href="#origins-and-design" id="id18">Origins and design</a></p></li>
-<li><p><a class="reference internal" href="#graphical-models" id="id19">Graphical models</a></p>
+<li><p><a class="reference internal" href="#origins-and-design" id="id19">Origins and design</a></p></li>
+<li><p><a class="reference internal" href="#graphical-models" id="id20">Graphical models</a></p>
 <ul>
-<li><p><a class="reference internal" href="#how-to-read-a-dag" id="id20">How to read a DAG?</a></p></li>
+<li><p><a class="reference internal" href="#how-to-read-a-dag" id="id21">How to read a DAG?</a></p></li>
 </ul>
 </li>
-<li><p><a class="reference internal" href="#specifying-a-model-an-example" id="id21">Specifying a model (an example)</a></p>
+<li><p><a class="reference internal" href="#specifying-a-model-an-example" id="id22">Specifying a model (an example)</a></p>
 <ul>
-<li><p><a class="reference internal" href="#multiple-samples-and-replicates" id="id22">Multiple samples and replicates</a></p></li>
+<li><p><a class="reference internal" href="#multiple-samples-and-replicates" id="id23">Multiple samples and replicates</a></p></li>
 </ul>
 </li>
 </ul>
 </li>
-<li><p><a class="reference internal" href="#graphical-user-interface-gui" id="id23">Graphical user interface (GUI)</a></p>
+<li><p><a class="reference internal" href="#graphical-user-interface-gui" id="id24">Graphical user interface (GUI)</a></p>
 <ul>
-<li><p><a class="reference internal" href="#implementation-comparison" id="id24">Implementation comparison</a></p></li>
-<li><p><a class="reference internal" href="#coverage-validation" id="id25">Coverage validation</a></p></li>
+<li><p><a class="reference internal" href="#implementation-comparison" id="id25">Implementation comparison</a></p></li>
+<li><p><a class="reference internal" href="#coverage-validation" id="id26">Coverage validation</a></p></li>
 </ul>
 </li>
-<li><p><a class="reference internal" href="#command-line-interface-cli" id="id26">Command-line interface (CLI)</a></p></li>
-<li><p><a class="reference internal" href="#bypassing-the-interfaces" id="id27">Bypassing the interfaces</a></p></li>
-<li><p><a class="reference internal" href="#lexicon" id="id28">Lexicon</a></p>
+<li><p><a class="reference internal" href="#command-line-interface-cli" id="id27">Command-line interface (CLI)</a></p></li>
+<li><p><a class="reference internal" href="#bypassing-the-interfaces" id="id28">Bypassing the interfaces</a></p></li>
+<li><p><a class="reference internal" href="#lexicon" id="id29">Lexicon</a></p>
 <ul>
-<li><p><a class="reference internal" href="#parametric-distributions" id="id29">Parametric distributions</a></p>
+<li><p><a class="reference internal" href="#parametric-distributions" id="id30">Parametric distributions</a></p>
 <ul>
-<li><p><a class="reference internal" href="#uniform" id="id30">Uniform</a></p></li>
-<li><p><a class="reference internal" href="#exponential" id="id31">Exponential</a></p></li>
-<li><p><a class="reference internal" href="#gamma" id="id32">Gamma</a></p></li>
-<li><p><a class="reference internal" href="#normal" id="id33">Normal</a></p></li>
-<li><p><a class="reference internal" href="#log-normal" id="id34">Log-normal</a></p></li>
+<li><p><a class="reference internal" href="#uniform" id="id31">Uniform</a></p></li>
+<li><p><a class="reference internal" href="#exponential" id="id32">Exponential</a></p></li>
+<li><p><a class="reference internal" href="#gamma" id="id33">Gamma</a></p></li>
+<li><p><a class="reference internal" href="#normal" id="id34">Normal</a></p></li>
+<li><p><a class="reference internal" href="#log-normal" id="id35">Log-normal</a></p></li>
 </ul>
 </li>
-<li><p><a class="reference internal" href="#tree-distributions" id="id35">Tree distributions</a></p>
+<li><p><a class="reference internal" href="#tree-distributions" id="id36">Tree distributions</a></p>
 <ul>
-<li><p><a class="reference internal" href="#discrete-sse" id="id36">Discrete SSE</a></p></li>
+<li><p><a class="reference internal" href="#discrete-sse" id="id37">Discrete SSE</a></p></li>
 </ul>
 </li>
 </ul>
@@ -594,7 +594,7 @@ <h4>Discrete SSE<a class="headerlink" href="#discrete-sse" title="Link to this h
 <p>The discrete SSE model in PhyloJunction supports not only state-dependent rates, but also state-dependent sampling probabilities.
 Specifying SSE probabilities can be done like so:</p>
 <div class="literal-block-wrapper docutils container" id="id15">
-<div class="code-block-caption"><span class="caption-text"><strong>Script excerpt 2.</strong> Command in <em>phylojunction</em> to add a sampling probability parameter (deterministic node) to the DAG.</span><a class="headerlink" href="#id15" title="Link to this code"></a></div>
+<div class="code-block-caption"><span class="caption-text"><strong>Script excerpt 2.</strong> Command in the <em>phylojunction</em> language to add a sampling probability parameter (deterministic node) to the DAG.</span><a class="headerlink" href="#id15" title="Link to this code"></a></div>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">det_sampling_prob</span> <span class="o">:=</span> <span class="n">sse_prob</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="s2">&quot;rho&quot;</span><span class="p">,</span> <span class="n">value</span><span class="o">=</span><span class="mf">1.0</span><span class="p">,</span> <span class="n">state</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
 <span class="c1"># by setting the value to 1.0, we assume complete sampling!</span>
 </pre></div>
@@ -627,9 +627,9 @@ <h4>Discrete SSE<a class="headerlink" href="#discrete-sse" title="Link to this h
 In the presence of time-heterogeneity, these parameters are assumed to vary according to a user-defined piecewise constant function (this is coded into the model via the <code class="docutils literal notranslate"><span class="pre">value</span></code> and <code class="docutils literal notranslate"><span class="pre">epoch</span></code> parameters of <code class="docutils literal notranslate"><span class="pre">sse_rate</span></code> and <code class="docutils literal notranslate"><span class="pre">sse_prob</span></code>).
 The limits of each “piece” of that function are given by the argument to <code class="docutils literal notranslate"><span class="pre">epoch_age_ends</span></code> (see above).</p>
 <div class="literal-block-wrapper docutils container" id="id16">
-<div class="code-block-caption"><span class="caption-text"><strong>Script excerpt 3.</strong> Command in <em>phylojunction</em> to organize rate and probability parameters into a stash (a deterministic node in the DAG).</span><a class="headerlink" href="#id16" title="Link to this code"></a></div>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">det_birth_rate1</span> <span class="o">:=</span> <span class="n">sse_rate</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="s2">&quot;lambda1&quot;</span><span class="p">,</span> <span class="n">value</span><span class="o">=</span><span class="mf">1.0</span><span class="p">,</span> <span class="n">event</span><span class="o">=</span><span class="s2">&quot;speciation&quot;</span><span class="p">)</span>
-<span class="n">det_birth_rate2</span> <span class="o">:=</span> <span class="n">sse_rate</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="s2">&quot;lambda2&quot;</span><span class="p">,</span> <span class="n">value</span><span class="o">=</span><span class="mf">2.0</span><span class="p">,</span> <span class="n">event</span><span class="o">=</span><span class="s2">&quot;speciation&quot;</span><span class="p">)</span>
+<div class="code-block-caption"><span class="caption-text"><strong>Script excerpt 3.</strong> Command in the <em>phylojunction</em> language to organize rate and probability parameters into a stash (a deterministic node in the DAG).</span><a class="headerlink" href="#id16" title="Link to this code"></a></div>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">det_birth_rate1</span> <span class="o">:=</span> <span class="n">sse_rate</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="s2">&quot;lambda1&quot;</span><span class="p">,</span> <span class="n">value</span><span class="o">=</span><span class="mf">1.0</span><span class="p">,</span> <span class="n">event</span><span class="o">=</span><span class="s2">&quot;speciation&quot;</span><span class="p">,</span> <span class="n">epoch</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
+<span class="n">det_birth_rate2</span> <span class="o">:=</span> <span class="n">sse_rate</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="s2">&quot;lambda2&quot;</span><span class="p">,</span> <span class="n">value</span><span class="o">=</span><span class="mf">2.0</span><span class="p">,</span> <span class="n">event</span><span class="o">=</span><span class="s2">&quot;speciation&quot;</span><span class="p">,</span> <span class="n">epoch</span><span class="o">=</span><span class="mi">2</span><span class="p">)</span>
 
 <span class="n">stash</span> <span class="o">:=</span> <span class="n">sse_stash</span><span class="p">(</span><span class="n">flat_rate_mat</span><span class="o">=</span><span class="p">[</span><span class="n">det_birth_rate1</span><span class="p">,</span> <span class="n">det_birth_rate2</span><span class="p">],</span> <span class="n">n_epochs</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span> <span class="n">seed_age</span><span class="o">=</span><span class="mf">2.0</span><span class="p">,</span> <span class="n">epoch_age_ends</span><span class="o">=</span><span class="p">[</span><span class="mf">1.0</span><span class="p">])</span>
 <span class="c1"># there are two epochs, the oldest one ends at age 1.0, the youngest one ends at the present</span>
@@ -658,6 +658,31 @@ <h4>Discrete SSE<a class="headerlink" href="#discrete-sse" title="Link to this h
 <div class="line"><code class="docutils literal notranslate"><span class="pre">runtime_limit</span></code> (positive integer, optional): Maximum number of minutes to wait until all samples are drawn. Sampling is aborted at this point. Defaults to 5.</div>
 </div>
 </div></blockquote>
+<p>Below, an example of assigning a discrete SSE to a stochastic DAG node representing phylogenetic tree samples:</p>
+<div class="literal-block-wrapper docutils container" id="id17">
+<div class="code-block-caption"><span class="caption-text"><strong>Script excerpt 4.</strong> Commands in <em>phylojunction</em> to build a discrete SSE distribution and assign it to a stochastic DAG node.</span><a class="headerlink" href="#id17" title="Link to this code"></a></div>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">det_birth_rate1</span> <span class="o">:=</span> <span class="n">sse_rate</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="s2">&quot;lambda1&quot;</span><span class="p">,</span> <span class="n">value</span><span class="o">=</span><span class="mf">1.0</span><span class="p">,</span> <span class="n">event</span><span class="o">=</span><span class="s2">&quot;speciation&quot;</span><span class="p">,</span> <span class="n">epoch</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
+<span class="n">det_birth_rate2</span> <span class="o">:=</span> <span class="n">sse_rate</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="s2">&quot;lambda2&quot;</span><span class="p">,</span> <span class="n">value</span><span class="o">=</span><span class="mf">2.0</span><span class="p">,</span> <span class="n">event</span><span class="o">=</span><span class="s2">&quot;speciation&quot;</span><span class="p">,</span> <span class="n">epoch</span><span class="o">=</span><span class="mi">2</span><span class="p">)</span>
+
+<span class="n">stash</span> <span class="o">:=</span> <span class="n">sse_stash</span><span class="p">(</span><span class="n">flat_rate_mat</span><span class="o">=</span><span class="p">[</span><span class="n">det_birth_rate1</span><span class="p">,</span> <span class="n">det_birth_rate2</span><span class="p">],</span> <span class="n">n_epochs</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span> <span class="n">seed_age</span><span class="o">=</span><span class="mf">2.0</span><span class="p">,</span> <span class="n">epoch_age_ends</span><span class="o">=</span><span class="p">[</span><span class="mf">1.0</span><span class="p">])</span>
+
+<span class="n">trs</span> <span class="o">~</span> <span class="n">discrete_sse</span><span class="p">(</span><span class="n">n</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span> <span class="n">stash</span><span class="o">=</span><span class="n">stash</span><span class="p">,</span> <span class="n">start_state</span><span class="o">=</span><span class="p">[</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">],</span> <span class="n">stop</span><span class="o">=</span><span class="s2">&quot;age&quot;</span><span class="p">,</span> <span class="n">stop_value</span><span class="o">=</span><span class="mf">2.0</span><span class="p">,</span> <span class="n">origin</span><span class="o">=</span><span class="s2">&quot;true&quot;</span><span class="p">)</span>
+</pre></div>
+</div>
+</div>
+<p>For examples of different models that can be simulated with <code class="docutils literal notranslate"><span class="pre">discrete_sse</span></code>, see:</p>
+<blockquote>
+<div><ol class="arabic simple">
+<li><p><a class="reference external" href="https://raw.githubusercontent.com/fkmendes/PhyloJunction/main/examples/yule.pj" rel="noopener noreferrer" target="_blank">Yule</a> (pure-birth) model;</p></li>
+<li><p><a class="reference external" href="https://raw.githubusercontent.com/fkmendes/PhyloJunction/main/examples/birthdeath.pj" rel="noopener noreferrer" target="_blank">Birth-death</a> model;</p></li>
+<li><p><a class="reference external" href="https://raw.githubusercontent.com/fkmendes/PhyloJunction/main/examples/birthdeath_incomplete_sampling.pj" rel="noopener noreferrer" target="_blank">Birth-death with incomplete sampling</a> model;</p></li>
+<li><p><a class="reference external" href="https://raw.githubusercontent.com/fkmendes/PhyloJunction/main/examples/fbd.pj" rel="noopener noreferrer" target="_blank">Fossilized birth-death</a> (FBD) model;</p></li>
+<li><p><a class="reference external" href="https://raw.githubusercontent.com/fkmendes/PhyloJunction/main/examples/birthdeath.pj" rel="noopener noreferrer" target="_blank">Binary state-dependent speciation and extinction</a> (BiSSE) model;</p></li>
+<li><p><a class="reference external" href="https://raw.githubusercontent.com/fkmendes/PhyloJunction/main/examples/birthdeath.pj" rel="noopener noreferrer" target="_blank">Time-heterogeneous binary state-dependent speciation and extinction</a> (skyline BiSSE) model;</p></li>
+<li><p><a class="reference external" href="https://raw.githubusercontent.com/fkmendes/PhyloJunction/main/examples/birthdeath.pj" rel="noopener noreferrer" target="_blank">Geographic state-dependent speciation and extinction</a> (GeoSSE) model;</p></li>
+<li><p><a class="reference external" href="https://raw.githubusercontent.com/fkmendes/PhyloJunction/main/examples/geosse_timehet.pj" rel="noopener noreferrer" target="_blank">Time-heterogeneous geographic state-dependent speciation and extinction</a> (skyline GeoSSE) model;</p></li>
+</ol>
+</div></blockquote>
 </section>
 </section>
 </section>
diff --git a/docs/build/html/searchindex.js b/docs/build/html/searchindex.js
index 8465ac1..b56aeee 100644
--- a/docs/build/html/searchindex.js
+++ b/docs/build/html/searchindex.js
@@ -1 +1 @@
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(phylojunction.distribution.dn_discrete_sse.dnsse attribute)": [[6, "phylojunction.distribution.dn_discrete_sse.DnSSE.runtime_limit"]], "seed_age (phylojunction.distribution.dn_discrete_sse.dnsse attribute)": [[6, "phylojunction.distribution.dn_discrete_sse.DnSSE.seed_age"]], "simulate() (phylojunction.distribution.dn_discrete_sse.dnsse method)": [[6, "phylojunction.distribution.dn_discrete_sse.DnSSE.simulate"]], "slice_t_ends (phylojunction.distribution.dn_discrete_sse.dnsse attribute)": [[6, "phylojunction.distribution.dn_discrete_sse.DnSSE.slice_t_ends"]], "sse_stash (phylojunction.distribution.dn_discrete_sse.dnsse attribute)": [[6, "phylojunction.distribution.dn_discrete_sse.DnSSE.sse_stash"]], "start_states (phylojunction.distribution.dn_discrete_sse.dnsse attribute)": [[6, "phylojunction.distribution.dn_discrete_sse.DnSSE.start_states"]], "state_count (phylojunction.distribution.dn_discrete_sse.dnsse attribute)": [[6, "phylojunction.distribution.dn_discrete_sse.DnSSE.state_count"]], "stop (phylojunction.distribution.dn_discrete_sse.dnsse attribute)": [[6, "phylojunction.distribution.dn_discrete_sse.DnSSE.stop"]], "stop_val (phylojunction.distribution.dn_discrete_sse.dnsse attribute)": [[6, "phylojunction.distribution.dn_discrete_sse.DnSSE.stop_val"]], "vectorized_params (phylojunction.distribution.dn_parametric.dnexponential attribute)": [[6, "phylojunction.distribution.dn_parametric.DnExponential.vectorized_params"]], "vectorized_params (phylojunction.distribution.dn_parametric.dngamma attribute)": [[6, "phylojunction.distribution.dn_parametric.DnGamma.vectorized_params"]], "vectorized_params (phylojunction.distribution.dn_parametric.dnlognormal attribute)": [[6, "phylojunction.distribution.dn_parametric.DnLogNormal.vectorized_params"]], "vectorized_params (phylojunction.distribution.dn_parametric.dnnormal attribute)": [[6, "phylojunction.distribution.dn_parametric.DnNormal.vectorized_params"]], "vectorized_params (phylojunction.distribution.dn_parametric.dnunif attribute)": [[6, "phylojunction.distribution.dn_parametric.DnUnif.vectorized_params"]], "with_origin (phylojunction.distribution.dn_discrete_sse.dnsse attribute)": [[6, "phylojunction.distribution.dn_discrete_sse.DnSSE.with_origin"]], "phylojunction.inference": [[7, "module-phylojunction.inference"]], "dag_obj_to_rev_inference_spec() (in module phylojunction.inference.revbayes.rb_inference)": [[8, "phylojunction.inference.revbayes.rb_inference.dag_obj_to_rev_inference_spec"]], "get_exponential_rev_inference_spec_info() (in module phylojunction.inference.revbayes.rb_dn_parametric)": [[8, "phylojunction.inference.revbayes.rb_dn_parametric.get_exponential_rev_inference_spec_info"]], "get_gamma_rev_inference_spec_info() (in module phylojunction.inference.revbayes.rb_dn_parametric)": [[8, "phylojunction.inference.revbayes.rb_dn_parametric.get_gamma_rev_inference_spec_info"]], "get_ln_rev_inference_spec_info() (in module phylojunction.inference.revbayes.rb_dn_parametric)": [[8, "phylojunction.inference.revbayes.rb_dn_parametric.get_ln_rev_inference_spec_info"]], "get_mcmc_logging_spec_list() (in module phylojunction.inference.revbayes.rb_inference)": [[8, "phylojunction.inference.revbayes.rb_inference.get_mcmc_logging_spec_list"]], "get_normal_rev_inference_spec_info() (in module phylojunction.inference.revbayes.rb_dn_parametric)": [[8, "phylojunction.inference.revbayes.rb_dn_parametric.get_normal_rev_inference_spec_info"]], "get_rev_str_from_dn_parametric_obj() (in module phylojunction.inference.revbayes.rb_dn_parametric)": [[8, "phylojunction.inference.revbayes.rb_dn_parametric.get_rev_str_from_dn_parametric_obj"]], "get_unif_rev_inference_spec_info() (in module phylojunction.inference.revbayes.rb_dn_parametric)": [[8, "phylojunction.inference.revbayes.rb_dn_parametric.get_unif_rev_inference_spec_info"]], "phylojunction.inference.revbayes": [[8, "module-phylojunction.inference.revbayes"]], "phylojunction.inference.revbayes.rb_dn_parametric": [[8, "module-phylojunction.inference.revbayes.rb_dn_parametric"]], "phylojunction.inference.revbayes.rb_inference": [[8, "module-phylojunction.inference.revbayes.rb_inference"]], "phylojunction.interface": [[9, "module-phylojunction.interface"]], "phylojunction.interface.pj_sandbox": [[9, "module-phylojunction.interface.pj_sandbox"]], "run_example_manual_incomplete_sampling_bisse() (in module phylojunction.interface.pj_sandbox)": [[9, "phylojunction.interface.pj_sandbox.run_example_manual_incomplete_sampling_bisse"]], "run_example_manual_tree_building() (in module phylojunction.interface.pj_sandbox)": [[9, "phylojunction.interface.pj_sandbox.run_example_manual_tree_building"]], "run_example_read_tree_function() (in module phylojunction.interface.pj_sandbox)": [[9, "phylojunction.interface.pj_sandbox.run_example_read_tree_function"]], "run_example_yule_file() (in module phylojunction.interface.pj_sandbox)": [[9, "phylojunction.interface.pj_sandbox.run_example_yule_file"]], "run_example_yule_string() (in module phylojunction.interface.pj_sandbox)": [[9, "phylojunction.interface.pj_sandbox.run_example_yule_string"]], "cmdline2dag() (in module phylojunction.interface.cmdbox.cmd_parse)": [[10, "phylojunction.interface.cmdbox.cmd_parse.cmdline2dag"]], "parse_deterministic_function_assignment() (in module phylojunction.interface.cmdbox.cmd_parse)": [[10, "phylojunction.interface.cmdbox.cmd_parse.parse_deterministic_function_assignment"]], "parse_samp_dn_assignment() (in module phylojunction.interface.cmdbox.cmd_parse)": [[10, "phylojunction.interface.cmdbox.cmd_parse.parse_samp_dn_assignment"]], "parse_spec() (in module phylojunction.interface.cmdbox.cmd_parse_utils)": [[10, "phylojunction.interface.cmdbox.cmd_parse_utils.parse_spec"]], "parse_val_vector() (in module phylojunction.interface.cmdbox.cmd_parse_utils)": [[10, "phylojunction.interface.cmdbox.cmd_parse_utils.parse_val_vector"]], "parse_variable_assignment() (in module phylojunction.interface.cmdbox.cmd_parse)": [[10, "phylojunction.interface.cmdbox.cmd_parse.parse_variable_assignment"]], "phylojunction.interface.cmdbox": [[10, "module-phylojunction.interface.cmdbox"]], "phylojunction.interface.cmdbox.cmd_parse": [[10, "module-phylojunction.interface.cmdbox.cmd_parse"]], "phylojunction.interface.cmdbox.cmd_parse_utils": [[10, "module-phylojunction.interface.cmdbox.cmd_parse_utils"]], "script2dag() (in module phylojunction.interface.cmdbox.cmd_parse)": [[10, "phylojunction.interface.cmdbox.cmd_parse.script2dag"]], "tokenize_fn_spec() (in module phylojunction.interface.cmdbox.cmd_parse_utils)": [[10, "phylojunction.interface.cmdbox.cmd_parse_utils.tokenize_fn_spec"]], "val_or_obj() (in module phylojunction.interface.cmdbox.cmd_parse_utils)": [[10, "phylojunction.interface.cmdbox.cmd_parse_utils.val_or_obj"]], "pjctfngrammar (class in phylojunction.interface.grammar.ct_fn_grammar)": [[11, "phylojunction.interface.grammar.ct_fn_grammar.PJCtFnGrammar"]], "pjdetfngrammar (class in phylojunction.interface.grammar.det_fn_grammar)": [[11, "phylojunction.interface.grammar.det_fn_grammar.PJDetFnGrammar"]], "pjdngrammar (class in phylojunction.interface.grammar.dn_grammar)": [[11, "phylojunction.interface.grammar.dn_grammar.PJDnGrammar"]], "create_ct_fn_obj() (phylojunction.interface.grammar.ct_fn_grammar.pjctfngrammar class method)": [[11, "phylojunction.interface.grammar.ct_fn_grammar.PJCtFnGrammar.create_ct_fn_obj"]], "create_det_fn_obj() (phylojunction.interface.grammar.det_fn_grammar.pjdetfngrammar class method)": [[11, "phylojunction.interface.grammar.det_fn_grammar.PJDetFnGrammar.create_det_fn_obj"]], "create_dn_obj() (phylojunction.interface.grammar.dn_grammar.pjdngrammar class method)": [[11, "phylojunction.interface.grammar.dn_grammar.PJDnGrammar.create_dn_obj"]], "ct_fn_grammar_dict (phylojunction.interface.grammar.ct_fn_grammar.pjctfngrammar attribute)": [[11, "phylojunction.interface.grammar.ct_fn_grammar.PJCtFnGrammar.ct_fn_grammar_dict"]], "det_fn_grammar_dict (phylojunction.interface.grammar.det_fn_grammar.pjdetfngrammar attribute)": [[11, "phylojunction.interface.grammar.det_fn_grammar.PJDetFnGrammar.det_fn_grammar_dict"]], "dn_grammar_dict (phylojunction.interface.grammar.dn_grammar.pjdngrammar attribute)": [[11, "phylojunction.interface.grammar.dn_grammar.PJDnGrammar.dn_grammar_dict"]], "extract_value_from_dagnodes() (in module phylojunction.interface.grammar.det_fn_discrete_sse_makers)": [[11, "phylojunction.interface.grammar.det_fn_discrete_sse_makers.extract_value_from_dagnodes"]], "grammar_check() (phylojunction.interface.grammar.ct_fn_grammar.pjctfngrammar class method)": [[11, "phylojunction.interface.grammar.ct_fn_grammar.PJCtFnGrammar.grammar_check"]], "grammar_check() (phylojunction.interface.grammar.det_fn_grammar.pjdetfngrammar class method)": [[11, "phylojunction.interface.grammar.det_fn_grammar.PJDetFnGrammar.grammar_check"]], "grammar_check() (phylojunction.interface.grammar.dn_grammar.pjdngrammar class method)": [[11, "phylojunction.interface.grammar.dn_grammar.PJDnGrammar.grammar_check"]], "init_return_ann_tr() (phylojunction.interface.grammar.ct_fn_grammar.pjctfngrammar class method)": [[11, "phylojunction.interface.grammar.ct_fn_grammar.PJCtFnGrammar.init_return_ann_tr"]], "init_return_discrete_sse_dn() (phylojunction.interface.grammar.dn_grammar.pjdngrammar class method)": [[11, "phylojunction.interface.grammar.dn_grammar.PJDnGrammar.init_return_discrete_SSE_dn"]], "init_return_parametric_dn() (phylojunction.interface.grammar.dn_grammar.pjdngrammar class method)": [[11, "phylojunction.interface.grammar.dn_grammar.PJDnGrammar.init_return_parametric_dn"]], "init_return_sse_stash() (phylojunction.interface.grammar.det_fn_grammar.pjdetfngrammar class method)": [[11, "phylojunction.interface.grammar.det_fn_grammar.PJDetFnGrammar.init_return_sse_stash"]], "init_return_state_dep_prob() (phylojunction.interface.grammar.det_fn_grammar.pjdetfngrammar class method)": [[11, "phylojunction.interface.grammar.det_fn_grammar.PJDetFnGrammar.init_return_state_dep_prob"]], "init_return_state_dep_rate() (phylojunction.interface.grammar.det_fn_grammar.pjdetfngrammar class method)": [[11, "phylojunction.interface.grammar.det_fn_grammar.PJDetFnGrammar.init_return_state_dep_rate"]], "init_return_tree_mapped_with_attr() (phylojunction.interface.grammar.det_fn_grammar.pjdetfngrammar class method)": [[11, "phylojunction.interface.grammar.det_fn_grammar.PJDetFnGrammar.init_return_tree_mapped_with_attr"]], "make_discretestatedependentprobability() (in module phylojunction.interface.grammar.det_fn_discrete_sse_makers)": [[11, "phylojunction.interface.grammar.det_fn_discrete_sse_makers.make_DiscreteStateDependentProbability"]], "make_discretestatedependentrate() (in module 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"phylojunction.interface.grammar.ct_fn_grammar": [[11, "module-phylojunction.interface.grammar.ct_fn_grammar"]], "phylojunction.interface.grammar.ct_fn_treereader_makers": [[11, "module-phylojunction.interface.grammar.ct_fn_treereader_makers"]], "phylojunction.interface.grammar.det_fn_discrete_sse_makers": [[11, "module-phylojunction.interface.grammar.det_fn_discrete_sse_makers"]], "phylojunction.interface.grammar.det_fn_grammar": [[11, "module-phylojunction.interface.grammar.det_fn_grammar"]], "phylojunction.interface.grammar.det_fn_map_attribute": [[11, "module-phylojunction.interface.grammar.det_fn_map_attribute"]], "phylojunction.interface.grammar.dn_discrete_sse_makers": [[11, "module-phylojunction.interface.grammar.dn_discrete_sse_makers"]], "phylojunction.interface.grammar.dn_grammar": [[11, "module-phylojunction.interface.grammar.dn_grammar"]], "ct_fn_name (phylojunction.pgm.pgm.constantfn property)": [[12, "phylojunction.pgm.pgm.ConstantFn.CT_FN_NAME"]], "constantfn (class in phylojunction.pgm.pgm)": [[12, "phylojunction.pgm.pgm.ConstantFn"]], "dn_name (phylojunction.pgm.pgm.distrforsampling property)": [[12, "phylojunction.pgm.pgm.DistrForSampling.DN_NAME"]], "deterministicnodedag (class in phylojunction.pgm.pgm)": [[12, "phylojunction.pgm.pgm.DeterministicNodeDAG"]], "directedacyclicgraph (class in phylojunction.pgm.pgm)": [[12, "phylojunction.pgm.pgm.DirectedAcyclicGraph"]], "distrforsampling (class in phylojunction.pgm.pgm)": [[12, "phylojunction.pgm.pgm.DistrForSampling"]], "nodedag (class in phylojunction.pgm.pgm)": [[12, "phylojunction.pgm.pgm.NodeDAG"]], "stochasticnodedag (class in phylojunction.pgm.pgm)": [[12, "phylojunction.pgm.pgm.StochasticNodeDAG"]], "valuegenerator (class in phylojunction.pgm.pgm)": [[12, "phylojunction.pgm.pgm.ValueGenerator"]], "abstract_attribute() (in module phylojunction.pgm.pgm)": [[12, "phylojunction.pgm.pgm.abstract_attribute"]], "add_node() (phylojunction.pgm.pgm.directedacyclicgraph method)": [[12, "phylojunction.pgm.pgm.DirectedAcyclicGraph.add_node"]], "call_order_idx (phylojunction.pgm.pgm.nodedag attribute)": [[12, "phylojunction.pgm.pgm.NodeDAG.call_order_idx"]], "constant_fn (phylojunction.pgm.pgm.stochasticnodedag attribute)": [[12, "phylojunction.pgm.pgm.StochasticNodeDAG.constant_fn"]], "extract_vals_as_str_from_node_dag() (in module phylojunction.pgm.pgm)": [[12, "phylojunction.pgm.pgm.extract_vals_as_str_from_node_dag"]], "generate() (phylojunction.pgm.pgm.valuegenerator method)": [[12, "phylojunction.pgm.pgm.ValueGenerator.generate"]], "generate_value() (phylojunction.pgm.pgm.stochasticnodedag method)": [[12, "phylojunction.pgm.pgm.StochasticNodeDAG.generate_value"]], "get_display_str_by_name() (phylojunction.pgm.pgm.directedacyclicgraph method)": [[12, "phylojunction.pgm.pgm.DirectedAcyclicGraph.get_display_str_by_name"]], "get_node_dag_by_name() (phylojunction.pgm.pgm.directedacyclicgraph method)": [[12, "phylojunction.pgm.pgm.DirectedAcyclicGraph.get_node_dag_by_name"]], "get_node_stats_str() (phylojunction.pgm.pgm.deterministicnodedag method)": [[12, "phylojunction.pgm.pgm.DeterministicNodeDAG.get_node_stats_str"]], "get_node_stats_str() (phylojunction.pgm.pgm.nodedag method)": [[12, "phylojunction.pgm.pgm.NodeDAG.get_node_stats_str"]], "get_node_stats_str() (phylojunction.pgm.pgm.stochasticnodedag method)": [[12, "phylojunction.pgm.pgm.StochasticNodeDAG.get_node_stats_str"]], "get_rev_inference_spec_info() (phylojunction.pgm.pgm.valuegenerator method)": [[12, "phylojunction.pgm.pgm.ValueGenerator.get_rev_inference_spec_info"]], "get_sorted_node_dag_list() (phylojunction.pgm.pgm.directedacyclicgraph method)": [[12, "phylojunction.pgm.pgm.DirectedAcyclicGraph.get_sorted_node_dag_list"]], "get_start2end_str() (phylojunction.pgm.pgm.nodedag method)": [[12, "phylojunction.pgm.pgm.NodeDAG.get_start2end_str"]], "init_check_vectorize_sample_size() (phylojunction.pgm.pgm.valuegenerator method)": [[12, "phylojunction.pgm.pgm.ValueGenerator.init_check_vectorize_sample_size"]], "is_clamped (phylojunction.pgm.pgm.nodedag attribute)": [[12, "phylojunction.pgm.pgm.NodeDAG.is_clamped"]], "is_deterministic (phylojunction.pgm.pgm.nodedag attribute)": [[12, "phylojunction.pgm.pgm.NodeDAG.is_deterministic"]], "is_sampled (phylojunction.pgm.pgm.nodedag attribute)": [[12, "phylojunction.pgm.pgm.NodeDAG.is_sampled"]], "n_nodes (phylojunction.pgm.pgm.directedacyclicgraph attribute)": [[12, "phylojunction.pgm.pgm.DirectedAcyclicGraph.n_nodes"]], "n_repl() (phylojunction.pgm.pgm.valuegenerator method)": [[12, "phylojunction.pgm.pgm.ValueGenerator.n_repl"]], "n_samples() (phylojunction.pgm.pgm.valuegenerator method)": [[12, "phylojunction.pgm.pgm.ValueGenerator.n_samples"]], "name_node_dict (phylojunction.pgm.pgm.directedacyclicgraph attribute)": [[12, "phylojunction.pgm.pgm.DirectedAcyclicGraph.name_node_dict"]], "node_name (phylojunction.pgm.pgm.nodedag attribute)": [[12, "phylojunction.pgm.pgm.NodeDAG.node_name"]], "node_val_dict (phylojunction.pgm.pgm.directedacyclicgraph attribute)": [[12, "phylojunction.pgm.pgm.DirectedAcyclicGraph.node_val_dict"]], "operator_weight (phylojunction.pgm.pgm.stochasticnodedag attribute)": [[12, "phylojunction.pgm.pgm.StochasticNodeDAG.operator_weight"]], "parent_nd_list (phylojunction.pgm.pgm.nodedag attribute)": [[12, "phylojunction.pgm.pgm.NodeDAG.parent_nd_list"]], "phylojunction.pgm": [[12, "module-phylojunction.pgm"]], "phylojunction.pgm.pgm": [[12, "module-phylojunction.pgm.pgm"]], "plot_blank() (in module phylojunction.pgm.pgm)": [[12, "phylojunction.pgm.pgm.plot_blank"]], "plot_node() (phylojunction.pgm.pgm.deterministicnodedag method)": [[12, "phylojunction.pgm.pgm.DeterministicNodeDAG.plot_node"]], "plot_node() (phylojunction.pgm.pgm.nodedag method)": [[12, "phylojunction.pgm.pgm.NodeDAG.plot_node"]], "plot_node() (phylojunction.pgm.pgm.stochasticnodedag method)": [[12, "phylojunction.pgm.pgm.StochasticNodeDAG.plot_node"]], "plot_node_histogram() (in module phylojunction.pgm.pgm)": [[12, "phylojunction.pgm.pgm.plot_node_histogram"]], "populate_operator_weight() (phylojunction.pgm.pgm.deterministicnodedag method)": [[12, "phylojunction.pgm.pgm.DeterministicNodeDAG.populate_operator_weight"]], "populate_operator_weight() (phylojunction.pgm.pgm.nodedag method)": [[12, "phylojunction.pgm.pgm.NodeDAG.populate_operator_weight"]], "populate_operator_weight() (phylojunction.pgm.pgm.stochasticnodedag method)": [[12, "phylojunction.pgm.pgm.StochasticNodeDAG.populate_operator_weight"]], "random_seed (phylojunction.pgm.pgm.directedacyclicgraph property)": [[12, "phylojunction.pgm.pgm.DirectedAcyclicGraph.random_seed"]], "repl_size (phylojunction.pgm.pgm.nodedag property)": [[12, "phylojunction.pgm.pgm.NodeDAG.repl_size"]], "sample_size (phylojunction.pgm.pgm.directedacyclicgraph attribute)": [[12, "phylojunction.pgm.pgm.DirectedAcyclicGraph.sample_size"]], "sample_size (phylojunction.pgm.pgm.nodedag property)": [[12, "phylojunction.pgm.pgm.NodeDAG.sample_size"]], "sampling_dn (phylojunction.pgm.pgm.stochasticnodedag attribute)": [[12, "phylojunction.pgm.pgm.StochasticNodeDAG.sampling_dn"]], "value (phylojunction.pgm.pgm.nodedag property)": [[12, "phylojunction.pgm.pgm.NodeDAG.value"]], "add_within_hpd_col() (in module phylojunction.plotting.pj_organize)": [[13, "phylojunction.plotting.pj_organize.add_within_hpd_col"]], "join_dataframes() (in module phylojunction.plotting.pj_organize)": [[13, "phylojunction.plotting.pj_organize.join_dataframes"]], "phylojunction.plotting": [[13, "module-phylojunction.plotting"]], "phylojunction.plotting.pj_draw": [[13, "module-phylojunction.plotting.pj_draw"]], "phylojunction.plotting.pj_organize": [[13, "module-phylojunction.plotting.pj_organize"]], "phylojunction.plotting.pj_seeing_colors": [[13, "module-phylojunction.plotting.pj_seeing_colors"]], "phylojunction.plotting.pj_testing_tree_plotting": [[13, "module-phylojunction.plotting.pj_testing_tree_plotting"]], "plot_intervals() (in module phylojunction.plotting.pj_draw)": [[13, "phylojunction.plotting.pj_draw.plot_intervals"]], "plot_violins() (in module phylojunction.plotting.pj_draw)": [[13, "phylojunction.plotting.pj_draw.plot_violins"]], "truncate_colormap() (in module phylojunction.plotting.pj_seeing_colors)": [[13, "phylojunction.plotting.pj_seeing_colors.truncate_colormap"]], "dump_pgm_data() (in module phylojunction.readwrite.pj_write)": [[14, "phylojunction.readwrite.pj_write.dump_pgm_data"]], "dump_serialized_pgm() (in module phylojunction.readwrite.pj_write)": [[14, "phylojunction.readwrite.pj_write.dump_serialized_pgm"]], "get_write_inference_rev_scripts() (in module phylojunction.readwrite.pj_write)": [[14, "phylojunction.readwrite.pj_write.get_write_inference_rev_scripts"]], "initialize_scalar_dataframe() (in module phylojunction.readwrite.pj_write)": [[14, "phylojunction.readwrite.pj_write.initialize_scalar_dataframe"]], "initialize_tree_dataframe() (in module phylojunction.readwrite.pj_write)": [[14, "phylojunction.readwrite.pj_write.initialize_tree_dataframe"]], "is_csv() (in module phylojunction.readwrite.pj_read)": [[14, "phylojunction.readwrite.pj_read.is_csv"]], "is_tsv() (in module phylojunction.readwrite.pj_read)": [[14, "phylojunction.readwrite.pj_read.is_tsv"]], "parse_cli_str_write_fig() (in module phylojunction.readwrite.pj_read)": [[14, "phylojunction.readwrite.pj_read.parse_cli_str_write_fig"]], "phylojunction.readwrite": [[14, "module-phylojunction.readwrite"]], "phylojunction.readwrite.pj_read": [[14, "module-phylojunction.readwrite.pj_read"]], "phylojunction.readwrite.pj_write": [[14, "module-phylojunction.readwrite.pj_write"]], "prep_data_df() (in module phylojunction.readwrite.pj_write)": [[14, "phylojunction.readwrite.pj_write.prep_data_df"]], "prep_data_filepaths_dfs() (in module phylojunction.readwrite.pj_write)": [[14, "phylojunction.readwrite.pj_write.prep_data_filepaths_dfs"]], "read_csv_tsv_into_dataframe() (in module phylojunction.readwrite.pj_read)": [[14, "phylojunction.readwrite.pj_read.read_csv_tsv_into_dataframe"]], "read_node_attr_update_tree() (in module phylojunction.readwrite.pj_read)": [[14, "phylojunction.readwrite.pj_read.read_node_attr_update_tree"]], "read_nwk_tree_str() (in module phylojunction.readwrite.pj_read)": [[14, "phylojunction.readwrite.pj_read.read_nwk_tree_str"]], "read_serialized_pgm() (in module phylojunction.readwrite.pj_read)": [[14, "phylojunction.readwrite.pj_read.read_serialized_pgm"]], "read_text_file() (in module phylojunction.readwrite.pj_read)": [[14, "phylojunction.readwrite.pj_read.read_text_file"]], "write_data_df() (in module phylojunction.readwrite.pj_write)": [[14, "phylojunction.readwrite.pj_write.write_data_df"]], "write_fig_to_file() (in module phylojunction.readwrite.pj_write)": [[14, "phylojunction.readwrite.pj_write.write_fig_to_file"]], "write_str_list() (in module phylojunction.readwrite.pj_write)": [[14, "phylojunction.readwrite.pj_write.write_str_list"]], "annotatedtreeincorrectannotationerror": [[15, "phylojunction.utility.exception_classes.AnnotatedTreeIncorrectAnnotationError"]], "annotatedtreemissingnodename": [[15, "phylojunction.utility.exception_classes.AnnotatedTreeMissingNodeName"]], "annotatedtreemisspecerror": [[15, "phylojunction.utility.exception_classes.AnnotatedTreeMisspecError"]], "annotatedtreenodemissingattrerror": [[15, "phylojunction.utility.exception_classes.AnnotatedTreeNodeMissingAttrError"]], "dagcannotaddnodeerror": [[15, "phylojunction.utility.exception_classes.DAGCannotAddNodeError"]], "dagcannotinitialize": [[15, "phylojunction.utility.exception_classes.DAGCannotInitialize"]], "dimensionalityerror": [[15, "phylojunction.utility.exception_classes.DimensionalityError"]], "dimensionalitywarning": [[15, "phylojunction.utility.exception_classes.DimensionalityWarning"]], "functionargsmismatcherror": [[15, "phylojunction.utility.exception_classes.FunctionArgsMismatchError"]], "generatefailerror": [[15, "phylojunction.utility.exception_classes.GenerateFailError"]], "incorrectdimensionerror": [[15, "phylojunction.utility.exception_classes.IncorrectDimensionError"]], "inexistentvariableerror": [[15, "phylojunction.utility.exception_classes.InexistentVariableError"]], "invalidmcmcchainlength": [[15, "phylojunction.utility.exception_classes.InvalidMCMCChainLength"]], "missingcolumnname": [[15, "phylojunction.utility.exception_classes.MissingColumnName"]], "noplatingallowederror": [[15, "phylojunction.utility.exception_classes.NoPlatingAllowedError"]], "nodedagstatcantfloaterror": [[15, "phylojunction.utility.exception_classes.NodeDAGStatCantFloatError"]], "nodeinferencedimensionalityerror": [[15, "phylojunction.utility.exception_classes.NodeInferenceDimensionalityError"]], "notbetweenzeroandoneerror": [[15, "phylojunction.utility.exception_classes.NotBetweenZeroAndOneError"]], "objinitincorrectdimensionerror": [[15, "phylojunction.utility.exception_classes.ObjInitIncorrectDimensionError"]], "objinitinvalidargerror": [[15, "phylojunction.utility.exception_classes.ObjInitInvalidArgError"]], "objinitmissingparametererror": [[15, "phylojunction.utility.exception_classes.ObjInitMissingParameterError"]], "objinitmissingstatedependentparametererror": [[15, "phylojunction.utility.exception_classes.ObjInitMissingStateDependentParameterError"]], "objinitrepeatedstatedependentparametererror": [[15, "phylojunction.utility.exception_classes.ObjInitRepeatedStateDependentParameterError"]], "objinitrequirenonzerostatedependentparametererror": [[15, "phylojunction.utility.exception_classes.ObjInitRequireNonZeroStateDependentParameterError"]], "objinitrequiresameparametertypeerror": [[15, "phylojunction.utility.exception_classes.ObjInitRequireSameParameterTypeError"]], "pjcliinvalidinputerror": [[15, "phylojunction.utility.exception_classes.PJCLIInvalidInputError"]], "pjclisampleoutofrangeerror": [[15, "phylojunction.utility.exception_classes.PJCLISampleOutOfRangeError"]], "pjiofiledoesnotexisterror": [[15, "phylojunction.utility.exception_classes.PJIOFileDoesNotExistError"]], "parsectfninitfailerror": [[15, "phylojunction.utility.exception_classes.ParseCtFnInitFailError"]], "parsedetfninitfailerror": [[15, "phylojunction.utility.exception_classes.ParseDetFnInitFailError"]], "parsedninitfailerror": [[15, "phylojunction.utility.exception_classes.ParseDnInitFailError"]], "parsefunctionargerror": [[15, "phylojunction.utility.exception_classes.ParseFunctionArgError"]], "parseinvalidargumenterror": [[15, "phylojunction.utility.exception_classes.ParseInvalidArgumentError"]], "parseinvalidnewickstringerror": [[15, "phylojunction.utility.exception_classes.ParseInvalidNewickStringError"]], "parsemissingargumenterror": [[15, "phylojunction.utility.exception_classes.ParseMissingArgumentError"]], "parsemissingparametererror": [[15, "phylojunction.utility.exception_classes.ParseMissingParameterError"]], "parsemissingspecificationerror": [[15, "phylojunction.utility.exception_classes.ParseMissingSpecificationError"]], "parsemutuallyexclusiveparameterserror": [[15, "phylojunction.utility.exception_classes.ParseMutuallyExclusiveParametersError"]], "parsenotaparametererror": [[15, "phylojunction.utility.exception_classes.ParseNotAParameterError"]], "parsepathdoesnotexisterror": [[15, "phylojunction.utility.exception_classes.ParsePathDoesNotExistError"]], "parserequireintegererror": [[15, "phylojunction.utility.exception_classes.ParseRequireIntegerError"]], "parserequirenumericerror": [[15, "phylojunction.utility.exception_classes.ParseRequireNumericError"]], "parserequirepositiveintegererror": [[15, "phylojunction.utility.exception_classes.ParseRequirePositiveIntegerError"]], "parserequiresinglevalueerror": [[15, "phylojunction.utility.exception_classes.ParseRequireSingleValueError"]], "replicatenumbererror": [[15, "phylojunction.utility.exception_classes.ReplicateNumberError"]], "runtimelimit": [[15, "phylojunction.utility.exception_classes.RunTimeLimit"]], "ssestashmisspec": [[15, "phylojunction.utility.exception_classes.SSEStashMisspec"]], "scriptsyntaxerror": [[15, "phylojunction.utility.exception_classes.ScriptSyntaxError"]], "statedependentparametermisspec": [[15, "phylojunction.utility.exception_classes.StateDependentParameterMisspec"]], "variableassignmenterror": [[15, "phylojunction.utility.exception_classes.VariableAssignmentError"]], "variablemisspec": [[15, "phylojunction.utility.exception_classes.VariableMisspec"]], "at_least (phylojunction.utility.exception_classes.objinitincorrectdimensionerror attribute)": [[15, "phylojunction.utility.exception_classes.ObjInitIncorrectDimensionError.at_least"]], "autovivify() (in module phylojunction.utility.helper_functions)": [[15, "phylojunction.utility.helper_functions.autovivify"]], "check_and_vectorize_if_must() (in module phylojunction.utility.helper_functions)": [[15, "phylojunction.utility.helper_functions.check_and_vectorize_if_must"]], "cmd_line (phylojunction.utility.exception_classes.scriptsyntaxerror attribute)": [[15, "phylojunction.utility.exception_classes.ScriptSyntaxError.cmd_line"]], "container_name (phylojunction.utility.exception_classes.incorrectdimensionerror attribute)": [[15, "phylojunction.utility.exception_classes.IncorrectDimensionError.container_name"]], "create_str_defaultdict() (in module phylojunction.utility.helper_functions)": [[15, "phylojunction.utility.helper_functions.create_str_defaultdict"]], "ct_fn_name (phylojunction.utility.exception_classes.parsectfninitfailerror attribute)": [[15, "phylojunction.utility.exception_classes.ParseCtFnInitFailError.ct_fn_name"]], "det_fn_name (phylojunction.utility.exception_classes.parsedetfninitfailerror attribute)": [[15, "phylojunction.utility.exception_classes.ParseDetFnInitFailError.det_fn_name"]], "det_name (phylojunction.utility.exception_classes.noplatingallowederror attribute)": [[15, "phylojunction.utility.exception_classes.NoPlatingAllowedError.det_name"]], "dn_name (phylojunction.utility.exception_classes.dimensionalityerror attribute)": [[15, "phylojunction.utility.exception_classes.DimensionalityError.dn_name"]], "dn_name (phylojunction.utility.exception_classes.dimensionalitywarning attribute)": [[15, "phylojunction.utility.exception_classes.DimensionalityWarning.dn_name"]], "dn_name (phylojunction.utility.exception_classes.parsedninitfailerror attribute)": [[15, "phylojunction.utility.exception_classes.ParseDnInitFailError.dn_name"]], "exp_len (phylojunction.utility.exception_classes.incorrectdimensionerror attribute)": [[15, "phylojunction.utility.exception_classes.IncorrectDimensionError.exp_len"]], "exp_len (phylojunction.utility.exception_classes.objinitincorrectdimensionerror attribute)": [[15, "phylojunction.utility.exception_classes.ObjInitIncorrectDimensionError.exp_len"]], "fn_name (phylojunction.utility.exception_classes.functionargsmismatcherror attribute)": [[15, "phylojunction.utility.exception_classes.FunctionArgsMismatchError.fn_name"]], "get_covg() (in module phylojunction.utility.helper_functions)": [[15, "phylojunction.utility.helper_functions.get_covg"]], "get_ellapsed_time_in_minutes() (in module phylojunction.utility.helper_functions)": [[15, "phylojunction.utility.helper_functions.get_ellapsed_time_in_minutes"]], "is_val_in_interval() (in module phylojunction.utility.helper_functions)": [[15, "phylojunction.utility.helper_functions.is_val_in_interval"]], "message (phylojunction.utility.exception_classes.annotatedtreeincorrectannotationerror attribute)": [[15, "phylojunction.utility.exception_classes.AnnotatedTreeIncorrectAnnotationError.message"]], "message (phylojunction.utility.exception_classes.annotatedtreemissingnodename attribute)": [[15, "phylojunction.utility.exception_classes.AnnotatedTreeMissingNodeName.message"]], "message (phylojunction.utility.exception_classes.annotatedtreemisspecerror attribute)": [[15, "phylojunction.utility.exception_classes.AnnotatedTreeMisspecError.message"]], "message (phylojunction.utility.exception_classes.annotatedtreenodemissingattrerror attribute)": [[15, "phylojunction.utility.exception_classes.AnnotatedTreeNodeMissingAttrError.message"]], "message (phylojunction.utility.exception_classes.dagcannotaddnodeerror attribute)": [[15, "phylojunction.utility.exception_classes.DAGCannotAddNodeError.message"]], "message (phylojunction.utility.exception_classes.dagcannotinitialize attribute)": [[15, "phylojunction.utility.exception_classes.DAGCannotInitialize.message"]], "message (phylojunction.utility.exception_classes.dimensionalityerror attribute)": [[15, "phylojunction.utility.exception_classes.DimensionalityError.message"]], "message (phylojunction.utility.exception_classes.dimensionalitywarning attribute)": [[15, "phylojunction.utility.exception_classes.DimensionalityWarning.message"]], "message (phylojunction.utility.exception_classes.functionargsmismatcherror attribute)": [[15, "phylojunction.utility.exception_classes.FunctionArgsMismatchError.message"]], "message (phylojunction.utility.exception_classes.generatefailerror attribute)": [[15, "phylojunction.utility.exception_classes.GenerateFailError.message"]], "message (phylojunction.utility.exception_classes.incorrectdimensionerror attribute)": [[15, "phylojunction.utility.exception_classes.IncorrectDimensionError.message"]], "message (phylojunction.utility.exception_classes.inexistentvariableerror attribute)": [[15, "phylojunction.utility.exception_classes.InexistentVariableError.message"]], "message (phylojunction.utility.exception_classes.invalidmcmcchainlength attribute)": [[15, "phylojunction.utility.exception_classes.InvalidMCMCChainLength.message"]], "message (phylojunction.utility.exception_classes.missingcolumnname attribute)": [[15, "phylojunction.utility.exception_classes.MissingColumnName.message"]], "message (phylojunction.utility.exception_classes.noplatingallowederror attribute)": [[15, "phylojunction.utility.exception_classes.NoPlatingAllowedError.message"]], "message (phylojunction.utility.exception_classes.nodedagstatcantfloaterror attribute)": [[15, "phylojunction.utility.exception_classes.NodeDAGStatCantFloatError.message"]], "message (phylojunction.utility.exception_classes.nodeinferencedimensionalityerror attribute)": [[15, "phylojunction.utility.exception_classes.NodeInferenceDimensionalityError.message"]], "message (phylojunction.utility.exception_classes.notbetweenzeroandoneerror attribute)": [[15, "phylojunction.utility.exception_classes.NotBetweenZeroAndOneError.message"]], "message (phylojunction.utility.exception_classes.objinitincorrectdimensionerror attribute)": [[15, "phylojunction.utility.exception_classes.ObjInitIncorrectDimensionError.message"]], "message (phylojunction.utility.exception_classes.objinitinvalidargerror attribute)": [[15, "phylojunction.utility.exception_classes.ObjInitInvalidArgError.message"]], "message (phylojunction.utility.exception_classes.objinitmissingparametererror attribute)": [[15, "phylojunction.utility.exception_classes.ObjInitMissingParameterError.message"]], "message (phylojunction.utility.exception_classes.objinitmissingstatedependentparametererror attribute)": [[15, "phylojunction.utility.exception_classes.ObjInitMissingStateDependentParameterError.message"]], "message (phylojunction.utility.exception_classes.objinitrepeatedstatedependentparametererror attribute)": [[15, "phylojunction.utility.exception_classes.ObjInitRepeatedStateDependentParameterError.message"]], "message (phylojunction.utility.exception_classes.objinitrequirenonzerostatedependentparametererror attribute)": [[15, "phylojunction.utility.exception_classes.ObjInitRequireNonZeroStateDependentParameterError.message"]], "message (phylojunction.utility.exception_classes.objinitrequiresameparametertypeerror attribute)": [[15, "phylojunction.utility.exception_classes.ObjInitRequireSameParameterTypeError.message"]], "message (phylojunction.utility.exception_classes.pjcliinvalidinputerror attribute)": [[15, "phylojunction.utility.exception_classes.PJCLIInvalidInputError.message"]], "message (phylojunction.utility.exception_classes.parsectfninitfailerror attribute)": [[15, "phylojunction.utility.exception_classes.ParseCtFnInitFailError.message"]], "message (phylojunction.utility.exception_classes.parsedetfninitfailerror attribute)": [[15, "phylojunction.utility.exception_classes.ParseDetFnInitFailError.message"]], "message (phylojunction.utility.exception_classes.parsedninitfailerror attribute)": [[15, "phylojunction.utility.exception_classes.ParseDnInitFailError.message"]], "message (phylojunction.utility.exception_classes.parsefunctionargerror attribute)": [[15, "phylojunction.utility.exception_classes.ParseFunctionArgError.message"]], "message (phylojunction.utility.exception_classes.parseinvalidargumenterror attribute)": [[15, "phylojunction.utility.exception_classes.ParseInvalidArgumentError.message"]], "message (phylojunction.utility.exception_classes.parseinvalidnewickstringerror attribute)": [[15, "phylojunction.utility.exception_classes.ParseInvalidNewickStringError.message"]], "message (phylojunction.utility.exception_classes.parsemissingargumenterror attribute)": [[15, "phylojunction.utility.exception_classes.ParseMissingArgumentError.message"]], "message (phylojunction.utility.exception_classes.parsemissingparametererror attribute)": [[15, "phylojunction.utility.exception_classes.ParseMissingParameterError.message"]], "message (phylojunction.utility.exception_classes.parsemissingspecificationerror attribute)": [[15, "phylojunction.utility.exception_classes.ParseMissingSpecificationError.message"]], "message (phylojunction.utility.exception_classes.parsemutuallyexclusiveparameterserror attribute)": [[15, "phylojunction.utility.exception_classes.ParseMutuallyExclusiveParametersError.message"]], "message (phylojunction.utility.exception_classes.parsenotaparametererror attribute)": [[15, "phylojunction.utility.exception_classes.ParseNotAParameterError.message"]], "message (phylojunction.utility.exception_classes.parsepathdoesnotexisterror attribute)": [[15, "phylojunction.utility.exception_classes.ParsePathDoesNotExistError.message"]], "message (phylojunction.utility.exception_classes.parserequireintegererror attribute)": [[15, "phylojunction.utility.exception_classes.ParseRequireIntegerError.message"]], "message (phylojunction.utility.exception_classes.parserequirenumericerror attribute)": [[15, "phylojunction.utility.exception_classes.ParseRequireNumericError.message"]], "message (phylojunction.utility.exception_classes.parserequirepositiveintegererror attribute)": [[15, "phylojunction.utility.exception_classes.ParseRequirePositiveIntegerError.message"]], "message (phylojunction.utility.exception_classes.parserequiresinglevalueerror attribute)": [[15, "phylojunction.utility.exception_classes.ParseRequireSingleValueError.message"]], "message (phylojunction.utility.exception_classes.replicatenumbererror attribute)": [[15, "phylojunction.utility.exception_classes.ReplicateNumberError.message"]], "message (phylojunction.utility.exception_classes.ssestashmisspec attribute)": [[15, "phylojunction.utility.exception_classes.SSEStashMisspec.message"]], "message (phylojunction.utility.exception_classes.scriptsyntaxerror attribute)": [[15, "phylojunction.utility.exception_classes.ScriptSyntaxError.message"]], "message (phylojunction.utility.exception_classes.statedependentparametermisspec attribute)": [[15, "phylojunction.utility.exception_classes.StateDependentParameterMisspec.message"]], "message (phylojunction.utility.exception_classes.variableassignmenterror attribute)": [[15, "phylojunction.utility.exception_classes.VariableAssignmentError.message"]], "message (phylojunction.utility.exception_classes.variablemisspec attribute)": [[15, "phylojunction.utility.exception_classes.VariableMisspec.message"]], "mutually_exclusive_par_name (phylojunction.utility.exception_classes.parsemutuallyexclusiveparameterserror attribute)": [[15, "phylojunction.utility.exception_classes.ParseMutuallyExclusiveParametersError.mutually_exclusive_par_name"]], "n_diff_par (phylojunction.utility.exception_classes.objinitrequiresameparametertypeerror attribute)": [[15, "phylojunction.utility.exception_classes.ObjInitRequireSameParameterTypeError.n_diff_par"]], "node_dag_name (phylojunction.utility.exception_classes.noplatingallowederror attribute)": [[15, "phylojunction.utility.exception_classes.NoPlatingAllowedError.node_dag_name"]], "node_name (phylojunction.utility.exception_classes.nodeinferencedimensionalityerror attribute)": [[15, "phylojunction.utility.exception_classes.NodeInferenceDimensionalityError.node_name"]], "node_name (phylojunction.utility.exception_classes.replicatenumbererror attribute)": [[15, "phylojunction.utility.exception_classes.ReplicateNumberError.node_name"]], "obj_name (phylojunction.utility.exception_classes.objinitincorrectdimensionerror attribute)": [[15, "phylojunction.utility.exception_classes.ObjInitIncorrectDimensionError.obj_name"]], "obj_name (phylojunction.utility.exception_classes.objinitinvalidargerror attribute)": [[15, "phylojunction.utility.exception_classes.ObjInitInvalidArgError.obj_name"]], "obj_name (phylojunction.utility.exception_classes.objinitmissingparametererror attribute)": [[15, "phylojunction.utility.exception_classes.ObjInitMissingParameterError.obj_name"]], "obj_name (phylojunction.utility.exception_classes.objinitrequirenonzerostatedependentparametererror attribute)": [[15, "phylojunction.utility.exception_classes.ObjInitRequireNonZeroStateDependentParameterError.obj_name"]], "obj_name (phylojunction.utility.exception_classes.objinitrequiresameparametertypeerror attribute)": [[15, "phylojunction.utility.exception_classes.ObjInitRequireSameParameterTypeError.obj_name"]], "obj_name (phylojunction.utility.exception_classes.parserequireintegererror attribute)": [[15, "phylojunction.utility.exception_classes.ParseRequireIntegerError.obj_name"]], "obj_name (phylojunction.utility.exception_classes.parserequirenumericerror attribute)": [[15, "phylojunction.utility.exception_classes.ParseRequireNumericError.obj_name"]], "obj_name (phylojunction.utility.exception_classes.parserequirepositiveintegererror attribute)": [[15, "phylojunction.utility.exception_classes.ParseRequirePositiveIntegerError.obj_name"]], "obj_name (phylojunction.utility.exception_classes.parserequiresinglevalueerror attribute)": [[15, "phylojunction.utility.exception_classes.ParseRequireSingleValueError.obj_name"]], "obs_len (phylojunction.utility.exception_classes.incorrectdimensionerror attribute)": [[15, "phylojunction.utility.exception_classes.IncorrectDimensionError.obs_len"]], "obs_len (phylojunction.utility.exception_classes.objinitincorrectdimensionerror attribute)": [[15, "phylojunction.utility.exception_classes.ObjInitIncorrectDimensionError.obs_len"]], "par_name (phylojunction.utility.exception_classes.dimensionalityerror attribute)": [[15, "phylojunction.utility.exception_classes.DimensionalityError.par_name"]], "par_name (phylojunction.utility.exception_classes.notbetweenzeroandoneerror attribute)": [[15, "phylojunction.utility.exception_classes.NotBetweenZeroAndOneError.par_name"]], "par_name (phylojunction.utility.exception_classes.pjcliinvalidinputerror attribute)": [[15, "phylojunction.utility.exception_classes.PJCLIInvalidInputError.par_name"]], "par_name (phylojunction.utility.exception_classes.parsefunctionargerror attribute)": [[15, "phylojunction.utility.exception_classes.ParseFunctionArgError.par_name"]], "par_name (phylojunction.utility.exception_classes.parseinvalidargumenterror attribute)": [[15, "phylojunction.utility.exception_classes.ParseInvalidArgumentError.par_name"]], "par_name (phylojunction.utility.exception_classes.parseinvalidnewickstringerror attribute)": [[15, "phylojunction.utility.exception_classes.ParseInvalidNewickStringError.par_name"]], "par_name (phylojunction.utility.exception_classes.parsemissingargumenterror attribute)": [[15, "phylojunction.utility.exception_classes.ParseMissingArgumentError.par_name"]], "par_name (phylojunction.utility.exception_classes.parsemissingparametererror attribute)": [[15, "phylojunction.utility.exception_classes.ParseMissingParameterError.par_name"]], "par_name (phylojunction.utility.exception_classes.parsemutuallyexclusiveparameterserror attribute)": [[15, "phylojunction.utility.exception_classes.ParseMutuallyExclusiveParametersError.par_name"]], "par_name (phylojunction.utility.exception_classes.parsenotaparametererror attribute)": [[15, "phylojunction.utility.exception_classes.ParseNotAParameterError.par_name"]], "par_name (phylojunction.utility.exception_classes.parsepathdoesnotexisterror attribute)": [[15, "phylojunction.utility.exception_classes.ParsePathDoesNotExistError.par_name"]], "path_str (phylojunction.utility.exception_classes.parsepathdoesnotexisterror attribute)": [[15, "phylojunction.utility.exception_classes.ParsePathDoesNotExistError.path_str"]], "phylojunction.utility": [[15, "module-phylojunction.utility"]], "phylojunction.utility.exception_classes": [[15, "module-phylojunction.utility.exception_classes"]], "phylojunction.utility.helper_functions": [[15, "module-phylojunction.utility.helper_functions"]], "print_progress() (in module phylojunction.utility.helper_functions)": [[15, "phylojunction.utility.helper_functions.print_progress"]], "rv_name (phylojunction.utility.exception_classes.dimensionalitywarning attribute)": [[15, "phylojunction.utility.exception_classes.DimensionalityWarning.rv_name"]], "rv_name (phylojunction.utility.exception_classes.inexistentvariableerror attribute)": [[15, "phylojunction.utility.exception_classes.InexistentVariableError.rv_name"]], "rv_name (phylojunction.utility.exception_classes.variableassignmenterror attribute)": [[15, "phylojunction.utility.exception_classes.VariableAssignmentError.rv_name"]], "rv_name (phylojunction.utility.exception_classes.variablemisspec attribute)": [[15, "phylojunction.utility.exception_classes.VariableMisspec.rv_name"]], "symmetric_diff_str (phylojunction.utility.exception_classes.objinitmissingstatedependentparametererror attribute)": [[15, 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\ No newline at end of file
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"n_extinct_terminal_nodes (phylojunction.data.tree.annotatedtree attribute)": [[5, "phylojunction.data.tree.AnnotatedTree.n_extinct_terminal_nodes"]], "n_sa_nodes (phylojunction.data.tree.annotatedtree attribute)": [[5, "phylojunction.data.tree.AnnotatedTree.n_sa_nodes"]], "node_ages_dict (phylojunction.data.tree.annotatedtree attribute)": [[5, "phylojunction.data.tree.AnnotatedTree.node_ages_dict"]], "node_attr_dict (phylojunction.data.tree.annotatedtree attribute)": [[5, "phylojunction.data.tree.AnnotatedTree.node_attr_dict"]], "node_heights_dict (phylojunction.data.tree.annotatedtree attribute)": [[5, "phylojunction.data.tree.AnnotatedTree.node_heights_dict"]], "origin_age (phylojunction.data.tree.annotatedtree attribute)": [[5, "phylojunction.data.tree.AnnotatedTree.origin_age"]], "origin_edge_length (phylojunction.data.tree.annotatedtree attribute)": [[5, "phylojunction.data.tree.AnnotatedTree.origin_edge_length"]], "origin_node (phylojunction.data.tree.annotatedtree attribute)": 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"phylojunction.pgm.pgm.DirectedAcyclicGraph.add_node"]], "call_order_idx (phylojunction.pgm.pgm.nodedag attribute)": [[12, "phylojunction.pgm.pgm.NodeDAG.call_order_idx"]], "constant_fn (phylojunction.pgm.pgm.stochasticnodedag attribute)": [[12, "phylojunction.pgm.pgm.StochasticNodeDAG.constant_fn"]], "extract_vals_as_str_from_node_dag() (in module phylojunction.pgm.pgm)": [[12, "phylojunction.pgm.pgm.extract_vals_as_str_from_node_dag"]], "generate() (phylojunction.pgm.pgm.valuegenerator method)": [[12, "phylojunction.pgm.pgm.ValueGenerator.generate"]], "generate_value() (phylojunction.pgm.pgm.stochasticnodedag method)": [[12, "phylojunction.pgm.pgm.StochasticNodeDAG.generate_value"]], "get_display_str_by_name() (phylojunction.pgm.pgm.directedacyclicgraph method)": [[12, "phylojunction.pgm.pgm.DirectedAcyclicGraph.get_display_str_by_name"]], "get_node_dag_by_name() (phylojunction.pgm.pgm.directedacyclicgraph method)": [[12, "phylojunction.pgm.pgm.DirectedAcyclicGraph.get_node_dag_by_name"]], "get_node_stats_str() (phylojunction.pgm.pgm.deterministicnodedag method)": [[12, "phylojunction.pgm.pgm.DeterministicNodeDAG.get_node_stats_str"]], "get_node_stats_str() (phylojunction.pgm.pgm.nodedag method)": [[12, "phylojunction.pgm.pgm.NodeDAG.get_node_stats_str"]], "get_node_stats_str() (phylojunction.pgm.pgm.stochasticnodedag method)": [[12, "phylojunction.pgm.pgm.StochasticNodeDAG.get_node_stats_str"]], "get_rev_inference_spec_info() (phylojunction.pgm.pgm.valuegenerator method)": [[12, "phylojunction.pgm.pgm.ValueGenerator.get_rev_inference_spec_info"]], "get_sorted_node_dag_list() (phylojunction.pgm.pgm.directedacyclicgraph method)": [[12, "phylojunction.pgm.pgm.DirectedAcyclicGraph.get_sorted_node_dag_list"]], "get_start2end_str() (phylojunction.pgm.pgm.nodedag method)": [[12, "phylojunction.pgm.pgm.NodeDAG.get_start2end_str"]], "init_check_vectorize_sample_size() (phylojunction.pgm.pgm.valuegenerator method)": [[12, "phylojunction.pgm.pgm.ValueGenerator.init_check_vectorize_sample_size"]], "is_clamped (phylojunction.pgm.pgm.nodedag attribute)": [[12, "phylojunction.pgm.pgm.NodeDAG.is_clamped"]], "is_deterministic (phylojunction.pgm.pgm.nodedag attribute)": [[12, "phylojunction.pgm.pgm.NodeDAG.is_deterministic"]], "is_sampled (phylojunction.pgm.pgm.nodedag attribute)": [[12, "phylojunction.pgm.pgm.NodeDAG.is_sampled"]], "n_nodes (phylojunction.pgm.pgm.directedacyclicgraph attribute)": [[12, "phylojunction.pgm.pgm.DirectedAcyclicGraph.n_nodes"]], "n_repl() (phylojunction.pgm.pgm.valuegenerator method)": [[12, "phylojunction.pgm.pgm.ValueGenerator.n_repl"]], "n_samples() (phylojunction.pgm.pgm.valuegenerator method)": [[12, "phylojunction.pgm.pgm.ValueGenerator.n_samples"]], "name_node_dict (phylojunction.pgm.pgm.directedacyclicgraph attribute)": [[12, "phylojunction.pgm.pgm.DirectedAcyclicGraph.name_node_dict"]], "node_name (phylojunction.pgm.pgm.nodedag attribute)": [[12, "phylojunction.pgm.pgm.NodeDAG.node_name"]], "node_val_dict (phylojunction.pgm.pgm.directedacyclicgraph attribute)": [[12, "phylojunction.pgm.pgm.DirectedAcyclicGraph.node_val_dict"]], "operator_weight (phylojunction.pgm.pgm.stochasticnodedag attribute)": [[12, "phylojunction.pgm.pgm.StochasticNodeDAG.operator_weight"]], "parent_nd_list (phylojunction.pgm.pgm.nodedag attribute)": [[12, "phylojunction.pgm.pgm.NodeDAG.parent_nd_list"]], "phylojunction.pgm": [[12, "module-phylojunction.pgm"]], "phylojunction.pgm.pgm": [[12, "module-phylojunction.pgm.pgm"]], "plot_blank() (in module phylojunction.pgm.pgm)": [[12, "phylojunction.pgm.pgm.plot_blank"]], "plot_node() (phylojunction.pgm.pgm.deterministicnodedag method)": [[12, "phylojunction.pgm.pgm.DeterministicNodeDAG.plot_node"]], "plot_node() (phylojunction.pgm.pgm.nodedag method)": [[12, "phylojunction.pgm.pgm.NodeDAG.plot_node"]], "plot_node() (phylojunction.pgm.pgm.stochasticnodedag method)": [[12, "phylojunction.pgm.pgm.StochasticNodeDAG.plot_node"]], "plot_node_histogram() (in module phylojunction.pgm.pgm)": [[12, "phylojunction.pgm.pgm.plot_node_histogram"]], "populate_operator_weight() (phylojunction.pgm.pgm.deterministicnodedag method)": [[12, "phylojunction.pgm.pgm.DeterministicNodeDAG.populate_operator_weight"]], "populate_operator_weight() (phylojunction.pgm.pgm.nodedag method)": [[12, "phylojunction.pgm.pgm.NodeDAG.populate_operator_weight"]], "populate_operator_weight() (phylojunction.pgm.pgm.stochasticnodedag method)": [[12, "phylojunction.pgm.pgm.StochasticNodeDAG.populate_operator_weight"]], "random_seed (phylojunction.pgm.pgm.directedacyclicgraph property)": [[12, "phylojunction.pgm.pgm.DirectedAcyclicGraph.random_seed"]], "repl_size (phylojunction.pgm.pgm.nodedag property)": [[12, "phylojunction.pgm.pgm.NodeDAG.repl_size"]], "sample_size (phylojunction.pgm.pgm.directedacyclicgraph attribute)": [[12, "phylojunction.pgm.pgm.DirectedAcyclicGraph.sample_size"]], "sample_size (phylojunction.pgm.pgm.nodedag property)": [[12, "phylojunction.pgm.pgm.NodeDAG.sample_size"]], "sampling_dn (phylojunction.pgm.pgm.stochasticnodedag attribute)": [[12, "phylojunction.pgm.pgm.StochasticNodeDAG.sampling_dn"]], "value (phylojunction.pgm.pgm.nodedag property)": [[12, "phylojunction.pgm.pgm.NodeDAG.value"]], "add_within_hpd_col() (in module phylojunction.plotting.pj_organize)": [[13, "phylojunction.plotting.pj_organize.add_within_hpd_col"]], "join_dataframes() (in module phylojunction.plotting.pj_organize)": [[13, "phylojunction.plotting.pj_organize.join_dataframes"]], "phylojunction.plotting": [[13, "module-phylojunction.plotting"]], "phylojunction.plotting.pj_draw": [[13, "module-phylojunction.plotting.pj_draw"]], "phylojunction.plotting.pj_organize": [[13, "module-phylojunction.plotting.pj_organize"]], "phylojunction.plotting.pj_seeing_colors": [[13, "module-phylojunction.plotting.pj_seeing_colors"]], "phylojunction.plotting.pj_testing_tree_plotting": [[13, "module-phylojunction.plotting.pj_testing_tree_plotting"]], "plot_intervals() (in module phylojunction.plotting.pj_draw)": [[13, "phylojunction.plotting.pj_draw.plot_intervals"]], "plot_violins() (in module phylojunction.plotting.pj_draw)": [[13, "phylojunction.plotting.pj_draw.plot_violins"]], "truncate_colormap() (in module phylojunction.plotting.pj_seeing_colors)": [[13, "phylojunction.plotting.pj_seeing_colors.truncate_colormap"]], "dump_pgm_data() (in module phylojunction.readwrite.pj_write)": [[14, "phylojunction.readwrite.pj_write.dump_pgm_data"]], "dump_serialized_pgm() (in module phylojunction.readwrite.pj_write)": [[14, "phylojunction.readwrite.pj_write.dump_serialized_pgm"]], "get_write_inference_rev_scripts() (in module phylojunction.readwrite.pj_write)": [[14, "phylojunction.readwrite.pj_write.get_write_inference_rev_scripts"]], "initialize_scalar_dataframe() (in module phylojunction.readwrite.pj_write)": [[14, "phylojunction.readwrite.pj_write.initialize_scalar_dataframe"]], "initialize_tree_dataframe() (in module phylojunction.readwrite.pj_write)": [[14, "phylojunction.readwrite.pj_write.initialize_tree_dataframe"]], "is_csv() (in module phylojunction.readwrite.pj_read)": [[14, "phylojunction.readwrite.pj_read.is_csv"]], "is_tsv() (in module phylojunction.readwrite.pj_read)": [[14, "phylojunction.readwrite.pj_read.is_tsv"]], "parse_cli_str_write_fig() (in module phylojunction.readwrite.pj_read)": [[14, "phylojunction.readwrite.pj_read.parse_cli_str_write_fig"]], "phylojunction.readwrite": [[14, "module-phylojunction.readwrite"]], "phylojunction.readwrite.pj_read": [[14, "module-phylojunction.readwrite.pj_read"]], "phylojunction.readwrite.pj_write": [[14, "module-phylojunction.readwrite.pj_write"]], "prep_data_df() (in module phylojunction.readwrite.pj_write)": [[14, "phylojunction.readwrite.pj_write.prep_data_df"]], "prep_data_filepaths_dfs() (in module phylojunction.readwrite.pj_write)": [[14, "phylojunction.readwrite.pj_write.prep_data_filepaths_dfs"]], "read_csv_tsv_into_dataframe() (in module phylojunction.readwrite.pj_read)": [[14, "phylojunction.readwrite.pj_read.read_csv_tsv_into_dataframe"]], "read_node_attr_update_tree() (in module phylojunction.readwrite.pj_read)": [[14, "phylojunction.readwrite.pj_read.read_node_attr_update_tree"]], "read_nwk_tree_str() (in module phylojunction.readwrite.pj_read)": [[14, "phylojunction.readwrite.pj_read.read_nwk_tree_str"]], "read_serialized_pgm() (in module phylojunction.readwrite.pj_read)": [[14, "phylojunction.readwrite.pj_read.read_serialized_pgm"]], "read_text_file() (in module phylojunction.readwrite.pj_read)": [[14, "phylojunction.readwrite.pj_read.read_text_file"]], "write_data_df() (in module phylojunction.readwrite.pj_write)": [[14, "phylojunction.readwrite.pj_write.write_data_df"]], "write_fig_to_file() (in module phylojunction.readwrite.pj_write)": [[14, "phylojunction.readwrite.pj_write.write_fig_to_file"]], "write_str_list() (in module phylojunction.readwrite.pj_write)": [[14, "phylojunction.readwrite.pj_write.write_str_list"]], "annotatedtreeincorrectannotationerror": [[15, "phylojunction.utility.exception_classes.AnnotatedTreeIncorrectAnnotationError"]], "annotatedtreemissingnodename": [[15, "phylojunction.utility.exception_classes.AnnotatedTreeMissingNodeName"]], "annotatedtreemisspecerror": [[15, "phylojunction.utility.exception_classes.AnnotatedTreeMisspecError"]], "annotatedtreenodemissingattrerror": [[15, "phylojunction.utility.exception_classes.AnnotatedTreeNodeMissingAttrError"]], "dagcannotaddnodeerror": [[15, "phylojunction.utility.exception_classes.DAGCannotAddNodeError"]], "dagcannotinitialize": [[15, "phylojunction.utility.exception_classes.DAGCannotInitialize"]], "dimensionalityerror": [[15, "phylojunction.utility.exception_classes.DimensionalityError"]], "dimensionalitywarning": [[15, "phylojunction.utility.exception_classes.DimensionalityWarning"]], "functionargsmismatcherror": [[15, "phylojunction.utility.exception_classes.FunctionArgsMismatchError"]], "generatefailerror": [[15, "phylojunction.utility.exception_classes.GenerateFailError"]], "incorrectdimensionerror": [[15, "phylojunction.utility.exception_classes.IncorrectDimensionError"]], "inexistentvariableerror": [[15, "phylojunction.utility.exception_classes.InexistentVariableError"]], "invalidmcmcchainlength": [[15, "phylojunction.utility.exception_classes.InvalidMCMCChainLength"]], "missingcolumnname": [[15, "phylojunction.utility.exception_classes.MissingColumnName"]], "noplatingallowederror": [[15, "phylojunction.utility.exception_classes.NoPlatingAllowedError"]], "nodedagstatcantfloaterror": [[15, "phylojunction.utility.exception_classes.NodeDAGStatCantFloatError"]], "nodeinferencedimensionalityerror": [[15, "phylojunction.utility.exception_classes.NodeInferenceDimensionalityError"]], "notbetweenzeroandoneerror": [[15, "phylojunction.utility.exception_classes.NotBetweenZeroAndOneError"]], "objinitincorrectdimensionerror": [[15, "phylojunction.utility.exception_classes.ObjInitIncorrectDimensionError"]], "objinitinvalidargerror": [[15, "phylojunction.utility.exception_classes.ObjInitInvalidArgError"]], "objinitmissingparametererror": [[15, "phylojunction.utility.exception_classes.ObjInitMissingParameterError"]], "objinitmissingstatedependentparametererror": [[15, "phylojunction.utility.exception_classes.ObjInitMissingStateDependentParameterError"]], "objinitrepeatedstatedependentparametererror": [[15, "phylojunction.utility.exception_classes.ObjInitRepeatedStateDependentParameterError"]], "objinitrequirenonzerostatedependentparametererror": [[15, "phylojunction.utility.exception_classes.ObjInitRequireNonZeroStateDependentParameterError"]], "objinitrequiresameparametertypeerror": [[15, "phylojunction.utility.exception_classes.ObjInitRequireSameParameterTypeError"]], "pjcliinvalidinputerror": [[15, "phylojunction.utility.exception_classes.PJCLIInvalidInputError"]], "pjclisampleoutofrangeerror": [[15, "phylojunction.utility.exception_classes.PJCLISampleOutOfRangeError"]], "pjiofiledoesnotexisterror": [[15, "phylojunction.utility.exception_classes.PJIOFileDoesNotExistError"]], "parsectfninitfailerror": [[15, "phylojunction.utility.exception_classes.ParseCtFnInitFailError"]], "parsedetfninitfailerror": [[15, "phylojunction.utility.exception_classes.ParseDetFnInitFailError"]], "parsedninitfailerror": [[15, "phylojunction.utility.exception_classes.ParseDnInitFailError"]], "parsefunctionargerror": [[15, "phylojunction.utility.exception_classes.ParseFunctionArgError"]], "parseinvalidargumenterror": [[15, "phylojunction.utility.exception_classes.ParseInvalidArgumentError"]], "parseinvalidnewickstringerror": [[15, "phylojunction.utility.exception_classes.ParseInvalidNewickStringError"]], "parsemissingargumenterror": [[15, "phylojunction.utility.exception_classes.ParseMissingArgumentError"]], "parsemissingparametererror": [[15, "phylojunction.utility.exception_classes.ParseMissingParameterError"]], "parsemissingspecificationerror": [[15, "phylojunction.utility.exception_classes.ParseMissingSpecificationError"]], "parsemutuallyexclusiveparameterserror": [[15, "phylojunction.utility.exception_classes.ParseMutuallyExclusiveParametersError"]], "parsenotaparametererror": [[15, "phylojunction.utility.exception_classes.ParseNotAParameterError"]], "parsepathdoesnotexisterror": [[15, "phylojunction.utility.exception_classes.ParsePathDoesNotExistError"]], "parserequireintegererror": [[15, "phylojunction.utility.exception_classes.ParseRequireIntegerError"]], "parserequirenumericerror": [[15, "phylojunction.utility.exception_classes.ParseRequireNumericError"]], "parserequirepositiveintegererror": [[15, "phylojunction.utility.exception_classes.ParseRequirePositiveIntegerError"]], "parserequiresinglevalueerror": [[15, "phylojunction.utility.exception_classes.ParseRequireSingleValueError"]], "replicatenumbererror": [[15, "phylojunction.utility.exception_classes.ReplicateNumberError"]], "runtimelimit": [[15, "phylojunction.utility.exception_classes.RunTimeLimit"]], "ssestashmisspec": [[15, "phylojunction.utility.exception_classes.SSEStashMisspec"]], "scriptsyntaxerror": [[15, "phylojunction.utility.exception_classes.ScriptSyntaxError"]], "statedependentparametermisspec": [[15, "phylojunction.utility.exception_classes.StateDependentParameterMisspec"]], "variableassignmenterror": [[15, "phylojunction.utility.exception_classes.VariableAssignmentError"]], "variablemisspec": [[15, "phylojunction.utility.exception_classes.VariableMisspec"]], "at_least (phylojunction.utility.exception_classes.objinitincorrectdimensionerror attribute)": [[15, "phylojunction.utility.exception_classes.ObjInitIncorrectDimensionError.at_least"]], "autovivify() (in module phylojunction.utility.helper_functions)": [[15, "phylojunction.utility.helper_functions.autovivify"]], "check_and_vectorize_if_must() (in module phylojunction.utility.helper_functions)": [[15, "phylojunction.utility.helper_functions.check_and_vectorize_if_must"]], "cmd_line (phylojunction.utility.exception_classes.scriptsyntaxerror attribute)": [[15, "phylojunction.utility.exception_classes.ScriptSyntaxError.cmd_line"]], "container_name (phylojunction.utility.exception_classes.incorrectdimensionerror attribute)": [[15, "phylojunction.utility.exception_classes.IncorrectDimensionError.container_name"]], "create_str_defaultdict() (in module phylojunction.utility.helper_functions)": [[15, "phylojunction.utility.helper_functions.create_str_defaultdict"]], "ct_fn_name (phylojunction.utility.exception_classes.parsectfninitfailerror attribute)": [[15, "phylojunction.utility.exception_classes.ParseCtFnInitFailError.ct_fn_name"]], "det_fn_name (phylojunction.utility.exception_classes.parsedetfninitfailerror attribute)": [[15, "phylojunction.utility.exception_classes.ParseDetFnInitFailError.det_fn_name"]], "det_name (phylojunction.utility.exception_classes.noplatingallowederror attribute)": [[15, "phylojunction.utility.exception_classes.NoPlatingAllowedError.det_name"]], "dn_name (phylojunction.utility.exception_classes.dimensionalityerror attribute)": [[15, "phylojunction.utility.exception_classes.DimensionalityError.dn_name"]], "dn_name (phylojunction.utility.exception_classes.dimensionalitywarning attribute)": [[15, "phylojunction.utility.exception_classes.DimensionalityWarning.dn_name"]], "dn_name (phylojunction.utility.exception_classes.parsedninitfailerror attribute)": [[15, "phylojunction.utility.exception_classes.ParseDnInitFailError.dn_name"]], "exp_len (phylojunction.utility.exception_classes.incorrectdimensionerror attribute)": [[15, "phylojunction.utility.exception_classes.IncorrectDimensionError.exp_len"]], "exp_len (phylojunction.utility.exception_classes.objinitincorrectdimensionerror attribute)": [[15, "phylojunction.utility.exception_classes.ObjInitIncorrectDimensionError.exp_len"]], "fn_name (phylojunction.utility.exception_classes.functionargsmismatcherror attribute)": [[15, "phylojunction.utility.exception_classes.FunctionArgsMismatchError.fn_name"]], "get_covg() (in module phylojunction.utility.helper_functions)": [[15, "phylojunction.utility.helper_functions.get_covg"]], "get_ellapsed_time_in_minutes() (in module phylojunction.utility.helper_functions)": [[15, "phylojunction.utility.helper_functions.get_ellapsed_time_in_minutes"]], "is_val_in_interval() (in module phylojunction.utility.helper_functions)": [[15, "phylojunction.utility.helper_functions.is_val_in_interval"]], "message (phylojunction.utility.exception_classes.annotatedtreeincorrectannotationerror attribute)": [[15, "phylojunction.utility.exception_classes.AnnotatedTreeIncorrectAnnotationError.message"]], "message (phylojunction.utility.exception_classes.annotatedtreemissingnodename attribute)": [[15, "phylojunction.utility.exception_classes.AnnotatedTreeMissingNodeName.message"]], "message (phylojunction.utility.exception_classes.annotatedtreemisspecerror attribute)": [[15, "phylojunction.utility.exception_classes.AnnotatedTreeMisspecError.message"]], "message (phylojunction.utility.exception_classes.annotatedtreenodemissingattrerror attribute)": [[15, "phylojunction.utility.exception_classes.AnnotatedTreeNodeMissingAttrError.message"]], "message (phylojunction.utility.exception_classes.dagcannotaddnodeerror attribute)": [[15, "phylojunction.utility.exception_classes.DAGCannotAddNodeError.message"]], "message (phylojunction.utility.exception_classes.dagcannotinitialize attribute)": [[15, "phylojunction.utility.exception_classes.DAGCannotInitialize.message"]], "message (phylojunction.utility.exception_classes.dimensionalityerror attribute)": [[15, "phylojunction.utility.exception_classes.DimensionalityError.message"]], "message (phylojunction.utility.exception_classes.dimensionalitywarning attribute)": [[15, "phylojunction.utility.exception_classes.DimensionalityWarning.message"]], "message (phylojunction.utility.exception_classes.functionargsmismatcherror attribute)": [[15, "phylojunction.utility.exception_classes.FunctionArgsMismatchError.message"]], "message (phylojunction.utility.exception_classes.generatefailerror attribute)": [[15, "phylojunction.utility.exception_classes.GenerateFailError.message"]], "message (phylojunction.utility.exception_classes.incorrectdimensionerror attribute)": [[15, "phylojunction.utility.exception_classes.IncorrectDimensionError.message"]], "message (phylojunction.utility.exception_classes.inexistentvariableerror attribute)": [[15, "phylojunction.utility.exception_classes.InexistentVariableError.message"]], "message (phylojunction.utility.exception_classes.invalidmcmcchainlength attribute)": [[15, "phylojunction.utility.exception_classes.InvalidMCMCChainLength.message"]], "message (phylojunction.utility.exception_classes.missingcolumnname attribute)": [[15, "phylojunction.utility.exception_classes.MissingColumnName.message"]], "message (phylojunction.utility.exception_classes.noplatingallowederror attribute)": [[15, "phylojunction.utility.exception_classes.NoPlatingAllowedError.message"]], "message (phylojunction.utility.exception_classes.nodedagstatcantfloaterror attribute)": [[15, "phylojunction.utility.exception_classes.NodeDAGStatCantFloatError.message"]], "message (phylojunction.utility.exception_classes.nodeinferencedimensionalityerror attribute)": [[15, "phylojunction.utility.exception_classes.NodeInferenceDimensionalityError.message"]], "message (phylojunction.utility.exception_classes.notbetweenzeroandoneerror attribute)": [[15, "phylojunction.utility.exception_classes.NotBetweenZeroAndOneError.message"]], "message (phylojunction.utility.exception_classes.objinitincorrectdimensionerror attribute)": [[15, "phylojunction.utility.exception_classes.ObjInitIncorrectDimensionError.message"]], "message (phylojunction.utility.exception_classes.objinitinvalidargerror attribute)": [[15, "phylojunction.utility.exception_classes.ObjInitInvalidArgError.message"]], "message (phylojunction.utility.exception_classes.objinitmissingparametererror attribute)": [[15, "phylojunction.utility.exception_classes.ObjInitMissingParameterError.message"]], "message (phylojunction.utility.exception_classes.objinitmissingstatedependentparametererror attribute)": [[15, "phylojunction.utility.exception_classes.ObjInitMissingStateDependentParameterError.message"]], "message (phylojunction.utility.exception_classes.objinitrepeatedstatedependentparametererror attribute)": [[15, "phylojunction.utility.exception_classes.ObjInitRepeatedStateDependentParameterError.message"]], "message (phylojunction.utility.exception_classes.objinitrequirenonzerostatedependentparametererror attribute)": [[15, "phylojunction.utility.exception_classes.ObjInitRequireNonZeroStateDependentParameterError.message"]], "message (phylojunction.utility.exception_classes.objinitrequiresameparametertypeerror attribute)": [[15, "phylojunction.utility.exception_classes.ObjInitRequireSameParameterTypeError.message"]], "message (phylojunction.utility.exception_classes.pjcliinvalidinputerror attribute)": [[15, "phylojunction.utility.exception_classes.PJCLIInvalidInputError.message"]], "message (phylojunction.utility.exception_classes.parsectfninitfailerror attribute)": [[15, "phylojunction.utility.exception_classes.ParseCtFnInitFailError.message"]], "message (phylojunction.utility.exception_classes.parsedetfninitfailerror attribute)": [[15, "phylojunction.utility.exception_classes.ParseDetFnInitFailError.message"]], "message (phylojunction.utility.exception_classes.parsedninitfailerror attribute)": [[15, "phylojunction.utility.exception_classes.ParseDnInitFailError.message"]], "message (phylojunction.utility.exception_classes.parsefunctionargerror attribute)": [[15, "phylojunction.utility.exception_classes.ParseFunctionArgError.message"]], "message (phylojunction.utility.exception_classes.parseinvalidargumenterror attribute)": [[15, "phylojunction.utility.exception_classes.ParseInvalidArgumentError.message"]], "message (phylojunction.utility.exception_classes.parseinvalidnewickstringerror attribute)": [[15, "phylojunction.utility.exception_classes.ParseInvalidNewickStringError.message"]], "message (phylojunction.utility.exception_classes.parsemissingargumenterror attribute)": [[15, "phylojunction.utility.exception_classes.ParseMissingArgumentError.message"]], "message (phylojunction.utility.exception_classes.parsemissingparametererror attribute)": [[15, "phylojunction.utility.exception_classes.ParseMissingParameterError.message"]], "message (phylojunction.utility.exception_classes.parsemissingspecificationerror attribute)": [[15, "phylojunction.utility.exception_classes.ParseMissingSpecificationError.message"]], "message (phylojunction.utility.exception_classes.parsemutuallyexclusiveparameterserror attribute)": [[15, "phylojunction.utility.exception_classes.ParseMutuallyExclusiveParametersError.message"]], "message (phylojunction.utility.exception_classes.parsenotaparametererror attribute)": [[15, "phylojunction.utility.exception_classes.ParseNotAParameterError.message"]], "message (phylojunction.utility.exception_classes.parsepathdoesnotexisterror attribute)": [[15, "phylojunction.utility.exception_classes.ParsePathDoesNotExistError.message"]], "message (phylojunction.utility.exception_classes.parserequireintegererror attribute)": [[15, "phylojunction.utility.exception_classes.ParseRequireIntegerError.message"]], "message (phylojunction.utility.exception_classes.parserequirenumericerror attribute)": [[15, "phylojunction.utility.exception_classes.ParseRequireNumericError.message"]], "message (phylojunction.utility.exception_classes.parserequirepositiveintegererror attribute)": [[15, "phylojunction.utility.exception_classes.ParseRequirePositiveIntegerError.message"]], "message (phylojunction.utility.exception_classes.parserequiresinglevalueerror attribute)": [[15, "phylojunction.utility.exception_classes.ParseRequireSingleValueError.message"]], "message (phylojunction.utility.exception_classes.replicatenumbererror attribute)": [[15, "phylojunction.utility.exception_classes.ReplicateNumberError.message"]], "message (phylojunction.utility.exception_classes.ssestashmisspec attribute)": [[15, "phylojunction.utility.exception_classes.SSEStashMisspec.message"]], "message (phylojunction.utility.exception_classes.scriptsyntaxerror attribute)": [[15, "phylojunction.utility.exception_classes.ScriptSyntaxError.message"]], "message (phylojunction.utility.exception_classes.statedependentparametermisspec attribute)": [[15, "phylojunction.utility.exception_classes.StateDependentParameterMisspec.message"]], "message (phylojunction.utility.exception_classes.variableassignmenterror attribute)": [[15, "phylojunction.utility.exception_classes.VariableAssignmentError.message"]], "message (phylojunction.utility.exception_classes.variablemisspec attribute)": [[15, "phylojunction.utility.exception_classes.VariableMisspec.message"]], "mutually_exclusive_par_name (phylojunction.utility.exception_classes.parsemutuallyexclusiveparameterserror attribute)": [[15, "phylojunction.utility.exception_classes.ParseMutuallyExclusiveParametersError.mutually_exclusive_par_name"]], "n_diff_par (phylojunction.utility.exception_classes.objinitrequiresameparametertypeerror attribute)": [[15, "phylojunction.utility.exception_classes.ObjInitRequireSameParameterTypeError.n_diff_par"]], "node_dag_name (phylojunction.utility.exception_classes.noplatingallowederror attribute)": [[15, "phylojunction.utility.exception_classes.NoPlatingAllowedError.node_dag_name"]], "node_name (phylojunction.utility.exception_classes.nodeinferencedimensionalityerror attribute)": [[15, "phylojunction.utility.exception_classes.NodeInferenceDimensionalityError.node_name"]], "node_name (phylojunction.utility.exception_classes.replicatenumbererror attribute)": [[15, "phylojunction.utility.exception_classes.ReplicateNumberError.node_name"]], "obj_name (phylojunction.utility.exception_classes.objinitincorrectdimensionerror attribute)": [[15, "phylojunction.utility.exception_classes.ObjInitIncorrectDimensionError.obj_name"]], "obj_name (phylojunction.utility.exception_classes.objinitinvalidargerror attribute)": [[15, "phylojunction.utility.exception_classes.ObjInitInvalidArgError.obj_name"]], "obj_name (phylojunction.utility.exception_classes.objinitmissingparametererror attribute)": [[15, "phylojunction.utility.exception_classes.ObjInitMissingParameterError.obj_name"]], "obj_name (phylojunction.utility.exception_classes.objinitrequirenonzerostatedependentparametererror attribute)": [[15, "phylojunction.utility.exception_classes.ObjInitRequireNonZeroStateDependentParameterError.obj_name"]], "obj_name (phylojunction.utility.exception_classes.objinitrequiresameparametertypeerror attribute)": [[15, "phylojunction.utility.exception_classes.ObjInitRequireSameParameterTypeError.obj_name"]], "obj_name (phylojunction.utility.exception_classes.parserequireintegererror attribute)": [[15, "phylojunction.utility.exception_classes.ParseRequireIntegerError.obj_name"]], "obj_name (phylojunction.utility.exception_classes.parserequirenumericerror attribute)": [[15, "phylojunction.utility.exception_classes.ParseRequireNumericError.obj_name"]], "obj_name (phylojunction.utility.exception_classes.parserequirepositiveintegererror attribute)": [[15, "phylojunction.utility.exception_classes.ParseRequirePositiveIntegerError.obj_name"]], "obj_name (phylojunction.utility.exception_classes.parserequiresinglevalueerror attribute)": [[15, "phylojunction.utility.exception_classes.ParseRequireSingleValueError.obj_name"]], "obs_len (phylojunction.utility.exception_classes.incorrectdimensionerror attribute)": [[15, "phylojunction.utility.exception_classes.IncorrectDimensionError.obs_len"]], "obs_len (phylojunction.utility.exception_classes.objinitincorrectdimensionerror attribute)": [[15, "phylojunction.utility.exception_classes.ObjInitIncorrectDimensionError.obs_len"]], "par_name (phylojunction.utility.exception_classes.dimensionalityerror attribute)": [[15, "phylojunction.utility.exception_classes.DimensionalityError.par_name"]], "par_name (phylojunction.utility.exception_classes.notbetweenzeroandoneerror attribute)": [[15, "phylojunction.utility.exception_classes.NotBetweenZeroAndOneError.par_name"]], "par_name (phylojunction.utility.exception_classes.pjcliinvalidinputerror attribute)": [[15, "phylojunction.utility.exception_classes.PJCLIInvalidInputError.par_name"]], "par_name (phylojunction.utility.exception_classes.parsefunctionargerror attribute)": [[15, "phylojunction.utility.exception_classes.ParseFunctionArgError.par_name"]], "par_name (phylojunction.utility.exception_classes.parseinvalidargumenterror attribute)": [[15, "phylojunction.utility.exception_classes.ParseInvalidArgumentError.par_name"]], "par_name (phylojunction.utility.exception_classes.parseinvalidnewickstringerror attribute)": [[15, "phylojunction.utility.exception_classes.ParseInvalidNewickStringError.par_name"]], "par_name (phylojunction.utility.exception_classes.parsemissingargumenterror attribute)": [[15, "phylojunction.utility.exception_classes.ParseMissingArgumentError.par_name"]], "par_name (phylojunction.utility.exception_classes.parsemissingparametererror attribute)": [[15, "phylojunction.utility.exception_classes.ParseMissingParameterError.par_name"]], "par_name (phylojunction.utility.exception_classes.parsemutuallyexclusiveparameterserror attribute)": [[15, "phylojunction.utility.exception_classes.ParseMutuallyExclusiveParametersError.par_name"]], "par_name (phylojunction.utility.exception_classes.parsenotaparametererror attribute)": [[15, "phylojunction.utility.exception_classes.ParseNotAParameterError.par_name"]], "par_name (phylojunction.utility.exception_classes.parsepathdoesnotexisterror attribute)": [[15, "phylojunction.utility.exception_classes.ParsePathDoesNotExistError.par_name"]], "path_str (phylojunction.utility.exception_classes.parsepathdoesnotexisterror attribute)": [[15, "phylojunction.utility.exception_classes.ParsePathDoesNotExistError.path_str"]], "phylojunction.utility": [[15, "module-phylojunction.utility"]], "phylojunction.utility.exception_classes": [[15, "module-phylojunction.utility.exception_classes"]], "phylojunction.utility.helper_functions": [[15, "module-phylojunction.utility.helper_functions"]], "print_progress() (in module phylojunction.utility.helper_functions)": [[15, "phylojunction.utility.helper_functions.print_progress"]], "rv_name (phylojunction.utility.exception_classes.dimensionalitywarning attribute)": [[15, "phylojunction.utility.exception_classes.DimensionalityWarning.rv_name"]], "rv_name (phylojunction.utility.exception_classes.inexistentvariableerror attribute)": [[15, "phylojunction.utility.exception_classes.InexistentVariableError.rv_name"]], "rv_name (phylojunction.utility.exception_classes.variableassignmenterror attribute)": [[15, "phylojunction.utility.exception_classes.VariableAssignmentError.rv_name"]], "rv_name (phylojunction.utility.exception_classes.variablemisspec attribute)": [[15, "phylojunction.utility.exception_classes.VariableMisspec.rv_name"]], "symmetric_diff_str (phylojunction.utility.exception_classes.objinitmissingstatedependentparametererror attribute)": [[15, "phylojunction.utility.exception_classes.ObjInitMissingStateDependentParameterError.symmetric_diff_str"]], "symmetric_difference() (in module phylojunction.utility.helper_functions)": [[15, "phylojunction.utility.helper_functions.symmetric_difference"]]}})
\ No newline at end of file
diff --git a/examples/birthdeath_incomplete_sampling.pj b/examples/birthdeath_incomplete_sampling.pj
new file mode 100644
index 0000000..06fbfaa
--- /dev/null
+++ b/examples/birthdeath_incomplete_sampling.pj
@@ -0,0 +1,20 @@
+# constant-node variable ('birth_rate', etc.) assignment
+birth_rate <- 1.0
+death_rate <- 0.2
+
+# deterministic-node variable ('det_birth_rate', etc.) assignment
+det_birth_rate := sse_rate(name="birth_rate", value=birth_rate, event="speciation")
+det_death_rate := sse_rate(name="death_rate", value=death_rate, event="extinction")
+
+# constant-node variable ('sampling_rate') assignment
+sampling_prob <- 0.5
+
+# deterministic-node variable ('det_sampling_rate') assignment
+det_sampling_prob := sse_prob(name="rho", value=sampling_prob, state=0)
+
+# deterministic-node variable ('meh') assignment
+stash := sse_stash(flat_rate_mat=[det_birth_rate, det_death_rate], flat_prob_mat=[det_sampling_prob], n_states=1, n_epochs=1)
+
+# stochastic-node variable ('trs') assignment
+ori <- 1.0
+trs ~ discrete_sse(n=2, nr=2, stash=stash, start_state=[0,0], stop="age", stop_value=ori, origin="true")
\ No newline at end of file
diff --git a/examples/birthdeath_timehet.pj b/examples/birthdeath_timehet.pj
index 566cc39..70baa52 100644
--- a/examples/birthdeath_timehet.pj
+++ b/examples/birthdeath_timehet.pj
@@ -20,4 +20,5 @@ det_death_rate_t1 := sse_rate(name="mu_t1", value=death_rate_t1, states=[0], eve
 stash := sse_stash(flat_rate_mat=[det_birth_rate_t0,det_death_rate_t0,det_birth_rate_t1,det_death_rate_t1], n_states=1, n_epochs=2, epoch_age_ends=[1.5], seed_age=3.0)
 
 # stochastic-node variable ('trs') assignment
-trs ~ discrete_sse(n=100, stash=stash, start_state=[0], stop="age", stop_value=3.0, origin="true")
\ No newline at end of file
+ori <- 3.0
+trs ~ discrete_sse(n=2, nr=2, stash=stash, start_state=[0], stop="age", stop_value=ori, origin="true")
\ No newline at end of file
diff --git a/examples/bisse.pj b/examples/bisse.pj
index d3a82cb..73b7292 100644
--- a/examples/bisse.pj
+++ b/examples/bisse.pj
@@ -16,7 +16,8 @@ det_death_rate1 := sse_rate(name="mu1", value=death_rate1, states=[1], event="ex
 det_trans_rate_10 := sse_rate(name="q10", value=trans_rate_10, states=[1,0], event="transition")
 
 # deterministic-node variable ('sse_stash') assignment
-stash := sse_stash(flat_rate_mat=[det_birth_rate0, det_death_rate0, det_trans_rate_01, det_birth_rate1, det_death_rate1, det_trans_rate_10], n_states=2, n_epochs=1) 
+stash := sse_stash(flat_rate_mat=[det_birth_rate0, det_death_rate0, det_trans_rate_01, det_birth_rate1, det_death_rate1, det_trans_rate_10], n_states=2) 
 
 # stochastic-node variable ('trs') assignment
-trs ~ discrete_sse(n=3, stash=stash, start_state=[0,0], stop="age", stop_value=3.0, origin="true", cond_spn="true", cond_surv="true")
\ No newline at end of file
+ori <- 3.0
+trs ~ discrete_sse(n=2, nr=2, stash=stash, start_state=[0], stop="age", stop_value=3.0, origin="true", cond_spn="true", cond_surv="true")
\ No newline at end of file
diff --git a/examples/bisse_timehet.pj b/examples/bisse_timehet.pj
index 6fbd989..ecb9d9e 100644
--- a/examples/bisse_timehet.pj
+++ b/examples/bisse_timehet.pj
@@ -33,8 +33,8 @@ det_trans_rate01_t1 := sse_rate(name="q01_t1", value=trans_rate01_t1, states=[0,
 det_trans_rate10_t1 := sse_rate(name="q10_t1", value=trans_rate10_t1, states=[1,0], event="transition", epoch=2)
 
 # deterministic-node variable ('sse_stash') assignment
-# all first-epoch rates first, then all second-epoch rates!
 stash := sse_stash(flat_rate_mat=[det_birth_rate0_t0, det_death_rate0_t0, det_birth_rate1_t0, det_death_rate1_t0, det_trans_rate01_t0, det_trans_rate10_t0, det_birth_rate0_t1, det_death_rate0_t1, det_birth_rate1_t1, det_death_rate1_t1, det_trans_rate01_t1, det_trans_rate10_t1], n_states=2, n_epochs=2, epoch_age_ends=[1.5], seed_age=3.0)
 
 # stochastic-node variable ('trs') assignment
-trs ~ discrete_sse(n=100, stash=stash, start_state=[0], stop="age", stop_value=3.0, origin="true")
\ No newline at end of file
+ori <- 3.0
+trs ~ discrete_sse(n=2, nr=2, stash=stash, start_state=[0,0], stop="age", stop_value=ori, origin="true")
\ No newline at end of file
diff --git a/examples/fbd.pj b/examples/fbd.pj
index bf23f80..326241b 100644
--- a/examples/fbd.pj
+++ b/examples/fbd.pj
@@ -9,7 +9,8 @@ det_death_rate := sse_rate(name="mu", value=death_rate, states=[0], event="extin
 det_fossil_rate := sse_rate(name="psi", value=fossil_rate, states=[0], event="anc_sampling")
 
 # deterministic-node variable ('sse_stash') assignment
-stash := sse_stash(flat_rate_mat=[det_birth_rate, det_death_rate, det_fossil_rate], n_states=1, n_epochs=1) 
+stash := sse_stash(flat_rate_mat=[det_birth_rate, det_death_rate, det_fossil_rate], n_states=1) 
 
 # stochastic-node variable ('trs') assignment
-trs ~ discrete_sse(n=100, stash=stash, start_state=[0], stop="age", stop_value=3.0, origin="true", cond_spn="true", cond_surv="true")
\ No newline at end of file
+ori <- 3.0
+trs ~ discrete_sse(n=2, nr=2, stash=stash, start_state=[0,0], stop="age", stop_value=ori, origin="true", cond_spn="true", cond_surv="true")
\ No newline at end of file
diff --git a/examples/geosse.pj b/examples/geosse.pj
index bdc0ec2..203d279 100644
--- a/examples/geosse.pj
+++ b/examples/geosse.pj
@@ -29,7 +29,8 @@ det_trans_rate_20 := sse_rate(name="q20", value=trans_rate_20, states=[2,0], eve
 det_trans_rate_21 := sse_rate(name="q21", value=trans_rate_21, states=[2,1], event="transition")
 
 # deterministic-node variable ('sse_stash') assignment
-stash := sse_stash(flat_rate_mat=[det_w_birth_rate0, det_death_rate0, det_trans_rate_02, det_w_birth_rate1, det_death_rate1, det_trans_rate_12, det_b_birth_rate201, det_b_birth_rate202, det_b_birth_rate212, det_trans_rate_20, det_trans_rate_21], n_states=3, n_epochs=1) 
+stash := sse_stash(flat_rate_mat=[det_w_birth_rate0, det_death_rate0, det_trans_rate_02, det_w_birth_rate1, det_death_rate1, det_trans_rate_12, det_b_birth_rate201, det_b_birth_rate202, det_b_birth_rate212, det_trans_rate_20, det_trans_rate_21], n_states=3) 
 
 # stochastic-node variable ('trs') assignment
-trs ~ discrete_sse(n=1, stash=stash, start_state=[0], stop="age", stop_value=3.0, origin="true", cond_spn="true", cond_surv="true")
\ No newline at end of file
+ori <- 3.0
+trs ~ discrete_sse(n=2, nr=2, stash=stash, start_state=[2,2], stop="age", stop_value=ori, origin="true", cond_spn="true", cond_surv="true")
\ No newline at end of file
diff --git a/examples/geosse_timehet.pj b/examples/geosse_timehet.pj
index be14c33..00ac638 100644
--- a/examples/geosse_timehet.pj
+++ b/examples/geosse_timehet.pj
@@ -1,4 +1,4 @@
-# constant-node variable ('birth_rate0_t0') assignment
+# constant-node variable ('w_birth_rate0_t0') assignment
 # first epoch (old)
 # state 0
 w_birth_rate0_t0 <- 1.5
@@ -35,7 +35,7 @@ b_birth_rate2_1_2_t1 <- 1.25
 trans_rate2_0_t1 <- 0.75
 trans_rate2_1_t1 <- 0.75
 
-# deterministic-node variable ('det_birth_rate0_t0') assignment
+# deterministic-node variable ('det_w_birth_rate0_t0') assignment
 # first epoch (old)
 # state 0
 det_w_birth_rate0_t0 := sse_rate(name="lambda0_t0", value=w_birth_rate0_t0, states=[0,0,0], event="w_speciation", epoch=1)
@@ -74,5 +74,7 @@ det_trans_rate2_1_t1 := sse_rate(name="q2_1_t1", value=trans_rate2_1_t1, states=
 
 # wrapping up all rates
 stash := sse_stash(flat_rate_mat=[det_w_birth_rate0_t0, det_death_rate0_t0, det_trans_rate0_2_t0, det_w_birth_rate1_t0, det_death_rate1_t0, det_trans_rate1_2_t0, det_b_birth_rate2_0_1_t0, det_b_birth_rate2_0_2_t0, det_b_birth_rate2_1_2_t0, det_trans_rate2_0_t0, det_trans_rate2_1_t0, det_w_birth_rate0_t1, det_death_rate0_t1, det_trans_rate0_2_t1, det_w_birth_rate1_t1, det_death_rate1_t1, det_trans_rate1_2_t1, det_b_birth_rate2_0_1_t1, det_b_birth_rate2_0_2_t1, det_b_birth_rate2_1_2_t1, det_trans_rate2_0_t1, det_trans_rate2_1_t1], n_states=3, n_epochs=2, seed_age=2.0, epoch_age_ends=[1.0])
+
 # stochastic-node variable ('trs') assignment
-trs ~ discrete_sse(n=2, nr=50, stash=stash, start_state=[0], stop="age", stop_value=2.0, origin="true")
\ No newline at end of file
+ori <- 2.0
+trs ~ discrete_sse(n=2, nr=2, stash=stash, start_state=[0,0], stop="age", stop_value=2.0, origin="true")
\ No newline at end of file
diff --git a/examples/yule.pj b/examples/yule.pj
index 040c3db..085cc59 100644
--- a/examples/yule.pj
+++ b/examples/yule.pj
@@ -22,4 +22,5 @@ det_birth_rate := sse_rate(name="lambda", value=birth_rate, event="speciation")
 stash := sse_stash(flat_rate_mat=[det_birth_rate])
 
 # stochastic-node variable ('trs') assignment
-trs ~ discrete_sse(n=n_sim, nr=n_rep, stash=stash, start_state=[0,0], stop="age", stop_value=2.0, origin="true")
\ No newline at end of file
+ori <- 2.0
+trs ~ discrete_sse(n=n_sim, nr=n_rep, stash=stash, start_state=[0,0], stop="age", stop_value=ori, origin="true")
\ No newline at end of file
diff --git a/examples/yule_incomplete_sampling.pj b/examples/yule_incomplete_sampling.pj
deleted file mode 100644
index aade822..0000000
--- a/examples/yule_incomplete_sampling.pj
+++ /dev/null
@@ -1,27 +0,0 @@
-# number of simulations
-n_sim <- 2
-
-# number of replicate trees per simulation
-n_rep <- 2
-
-# constant-node variable ('birth_rate') assignment
-birth_rate <- [0.8, 0.9]
-
-# alternatively, stochastic-node variable ('birth_rate') assignment
-# (comment out previous command)
-# birth_rate ~ exponential(n=n_sim, rate=1.0)
-
-# deterministic-node variable ('det_birth_rate') assignment
-det_birth_rate := sse_rate(name="lambda", value=birth_rate, states=[0,0,0], event="w_speciation")
-
-# constant-node variable ('sampling_rate') assignment
-sampling_rate <- [0.5, 0.5]
-
-# deterministic-node variable ('det_sampling_rate') assignment
-det_sampling_rate := sse_prob(name="rho", value=sampling_rate, state=0)
-
-# deterministic-node variable ('meh') assignment
-stash := sse_stash(flat_rate_mat=[det_birth_rate], flat_prob_mat=[det_sampling_rate], n_states=1, n_epochs=1)
-
-# stochastic-node variable ('trs') assignment
-trs ~ discrete_sse(n=n_sim, nr=n_rep, stash=stash, start_state=[0,0], stop="age", stop_value=1.0, origin="true")
\ No newline at end of file