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PopSim-bot committed Dec 20, 2024
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11 changes: 10 additions & 1 deletion main/_sources/tutorial.rst.txt
Original file line number Diff line number Diff line change
Expand Up @@ -683,7 +683,16 @@ defined above. The simulation results are recorded in a tree sequence object

.. code-block:: python
ts = engine.simulate(model, contig, samples)
ts = engine.simulate(
model, contig, samples, msprime_model="dtwf", msprime_change_model=[(20, "hudson")]
)
The `msprime_model` argument is optional; it specifies that the most recent 20
generations be simulated with the discrete time Wright-Fisher ("dtwf") model
(followed by a switch to the more efficient "hudson" coalescent model). This is
good practice for large samples, for which the Hudson model can be an
`inaccurate approximation <https://doi.org/10.1371/journal.pgen.1008619>`__
for the most recent few generations.

Sanity check the tree sequence output
-------------------------------------
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2 changes: 1 addition & 1 deletion main/searchindex.js

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10 changes: 9 additions & 1 deletion main/tutorial.html
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Expand Up @@ -828,9 +828,17 @@ <h4>Choose a sampling scheme, and simulate<a class="headerlink" href="#id1" titl
<p>Finally, we simulate the model with the contig length and number of samples we
defined above. The simulation results are recorded in a tree sequence object
(<a class="reference external" href="https://tskit.dev/tskit/docs/stable/python-api.html#tskit.TreeSequence" title="(in Project name not set)"><code class="xref py py-class docutils literal notranslate"><span class="pre">tskit.TreeSequence</span></code></a>).</p>
<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">ts</span> <span class="o">=</span> <span class="n">engine</span><span class="o">.</span><span class="n">simulate</span><span class="p">(</span><span class="n">model</span><span class="p">,</span> <span class="n">contig</span><span class="p">,</span> <span class="n">samples</span><span class="p">)</span>
<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">ts</span> <span class="o">=</span> <span class="n">engine</span><span class="o">.</span><span class="n">simulate</span><span class="p">(</span>
<span class="n">model</span><span class="p">,</span> <span class="n">contig</span><span class="p">,</span> <span class="n">samples</span><span class="p">,</span> <span class="n">msprime_model</span><span class="o">=</span><span class="s2">&quot;dtwf&quot;</span><span class="p">,</span> <span class="n">msprime_change_model</span><span class="o">=</span><span class="p">[(</span><span class="mi">20</span><span class="p">,</span> <span class="s2">&quot;hudson&quot;</span><span class="p">)]</span>
<span class="p">)</span>
</pre></div>
</div>
<p>The <cite>msprime_model</cite> argument is optional; it specifies that the most recent 20
generations be simulated with the discrete time Wright-Fisher (“dtwf”) model
(followed by a switch to the more efficient “hudson” coalescent model). This is
good practice for large samples, for which the Hudson model can be an
<a class="reference external" href="https://doi.org/10.1371/journal.pgen.1008619">inaccurate approximation</a>
for the most recent few generations.</p>
</section>
<section id="sanity-check-the-tree-sequence-output">
<h4>Sanity check the tree sequence output<a class="headerlink" href="#sanity-check-the-tree-sequence-output" title="Permalink to this heading"></a></h4>
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