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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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<title>CAFE: /mnt/c/Users/befulton/Documents/GIT/CAFE/libtree/birthdeath.h File Reference</title>
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<div class="header">
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<a href="#nested-classes">Data Structures</a> |
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<div class="title">birthdeath.h File Reference</div> </div>
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<div class="textblock"><code>#include <assert.h></code><br />
<code>#include "<a class="el" href="hashtable_8h_source.html">hashtable.h</a>"</code><br />
<code>#include "<a class="el" href="chooseln__cache_8h_source.html">chooseln_cache.h</a>"</code><br />
</div>
<p><a href="birthdeath_8h_source.html">Go to the source code of this file.</a></p>
<table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="nested-classes"></a>
Data Structures</h2></td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">struct  </td><td class="memItemRight" valign="bottom"><a class="el" href="structsquare__matrix.html">square_matrix</a></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">struct  </td><td class="memItemRight" valign="bottom"><a class="el" href="structBirthDeathCacheKey.html">BirthDeathCacheKey</a></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">struct  </td><td class="memItemRight" valign="bottom"><a class="el" href="structBirthDeathCacheArray.html">BirthDeathCacheArray</a></td></tr>
<tr class="memdesc:"><td class="mdescLeft"> </td><td class="mdescRight">A cache of values of family size transition probabilities. <a href="structBirthDeathCacheArray.html#details">More...</a><br /></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="typedef-members"></a>
Typedefs</h2></td></tr>
<tr class="memitem:a90a95c13f76b838d9b5174e5ccd41207"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="structBirthDeathCacheArray.html">BirthDeathCacheArray</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="birthdeath_8h.html#a90a95c13f76b838d9b5174e5ccd41207">pBirthDeathCacheArray</a></td></tr>
<tr class="separator:a90a95c13f76b838d9b5174e5ccd41207"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="func-members"></a>
Functions</h2></td></tr>
<tr class="memitem:a0591437ef7fd11db5e93fa5fabb816b1"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="birthdeath_8h.html#a0591437ef7fd11db5e93fa5fabb816b1">square_matrix_init</a> (struct <a class="el" href="structsquare__matrix.html">square_matrix</a> *matrix, int sz)</td></tr>
<tr class="separator:a0591437ef7fd11db5e93fa5fabb816b1"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a55210fef902b15de5b68eb0fa8b2991d"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="birthdeath_8h.html#a55210fef902b15de5b68eb0fa8b2991d">square_matrix_set</a> (struct <a class="el" href="structsquare__matrix.html">square_matrix</a> *matrix, int x, int y, double val)</td></tr>
<tr class="separator:a55210fef902b15de5b68eb0fa8b2991d"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a54db5bf74e4c2d015f22cc13a8f3c7ec"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="birthdeath_8h.html#a54db5bf74e4c2d015f22cc13a8f3c7ec">square_matrix_resize</a> (struct <a class="el" href="structsquare__matrix.html">square_matrix</a> *matrix, int new_size)</td></tr>
<tr class="separator:a54db5bf74e4c2d015f22cc13a8f3c7ec"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a2e4ee2c0a2fb7a45e4ebbe56c0891874"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="birthdeath_8h.html#a2e4ee2c0a2fb7a45e4ebbe56c0891874">birthdeath_cache_array_free</a> (<a class="el" href="birthdeath_8h.html#a90a95c13f76b838d9b5174e5ccd41207">pBirthDeathCacheArray</a> pbdc_array)</td></tr>
<tr class="separator:a2e4ee2c0a2fb7a45e4ebbe56c0891874"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a9f7b48d071f48f0e644d38c1b7f79e06"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="birthdeath_8h.html#a9f7b48d071f48f0e644d38c1b7f79e06">birthdeath_likelihood_with_s_c</a> (int s, int c, double branchlength, double lambda, double mu, struct <a class="el" href="structchooseln__cache.html">chooseln_cache</a> *<a class="el" href="birthdeath_8c.html#a018ffb515cded9e77be4179f12b3aca6">cache</a>)</td></tr>
<tr class="memdesc:a9f7b48d071f48f0e644d38c1b7f79e06"><td class="mdescLeft"> </td><td class="mdescRight">Calculates the probability of transitioning from root_family_size to family_size. <a href="#a9f7b48d071f48f0e644d38c1b7f79e06">More...</a><br /></td></tr>
<tr class="separator:a9f7b48d071f48f0e644d38c1b7f79e06"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ab81fd61e47717a7a47f7b6e0855ff7ea"><td class="memItemLeft" align="right" valign="top">struct <a class="el" href="structsquare__matrix.html">square_matrix</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="birthdeath_8h.html#ab81fd61e47717a7a47f7b6e0855ff7ea">compute_birthdeath_rates</a> (double branchlength, double lambda, double mu, int maxFamilysize)</td></tr>
<tr class="separator:ab81fd61e47717a7a47f7b6e0855ff7ea"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aa982e6083894fa476afdb492d761d750"><td class="memItemLeft" align="right" valign="top">struct <a class="el" href="structsquare__matrix.html">square_matrix</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="birthdeath_8h.html#aa982e6083894fa476afdb492d761d750">birthdeath_cache_get_matrix</a> (<a class="el" href="birthdeath_8h.html#a90a95c13f76b838d9b5174e5ccd41207">pBirthDeathCacheArray</a> pbdc_array, double branchlength, double lambda, double mu)</td></tr>
<tr class="separator:aa982e6083894fa476afdb492d761d750"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a1b8ab0e80d86531a457af9375f6bc7f3"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="birthdeath_8h.html#a1b8ab0e80d86531a457af9375f6bc7f3">thread_run</a> (int numthreads, void *(*run)(void *), void *param, int size)</td></tr>
<tr class="separator:a1b8ab0e80d86531a457af9375f6bc7f3"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aa5c47a4f72dd7cf153dd936445658803"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="birthdeath_8h.html#aa5c47a4f72dd7cf153dd936445658803">birthdeath_rate_with_log_alpha</a> (int s, int c, double log_alpha, double coeff, struct <a class="el" href="structchooseln__cache.html">chooseln_cache</a> *<a class="el" href="birthdeath_8c.html#a018ffb515cded9e77be4179f12b3aca6">cache</a>)</td></tr>
<tr class="separator:aa5c47a4f72dd7cf153dd936445658803"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ab7e1183541f7f4df889de49ba641ef6e"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="birthdeath_8h.html#ab7e1183541f7f4df889de49ba641ef6e">birthdeath_cache_resize</a> (<a class="el" href="birthdeath_8h.html#a90a95c13f76b838d9b5174e5ccd41207">pBirthDeathCacheArray</a> pbdc_array, int remaxFamilysize)</td></tr>
<tr class="separator:ab7e1183541f7f4df889de49ba641ef6e"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:acb434d43589b596ee743b5543427b557"><td class="memItemLeft" align="right" valign="top"><a class="el" href="birthdeath_8h.html#a90a95c13f76b838d9b5174e5ccd41207">pBirthDeathCacheArray</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="birthdeath_8h.html#acb434d43589b596ee743b5543427b557">birthdeath_cache_init</a> (int size)</td></tr>
<tr class="separator:acb434d43589b596ee743b5543427b557"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a7d8009f8674aba748af4967df333eb19"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="birthdeath_8h.html#a7d8009f8674aba748af4967df333eb19">chooseln_is_init</a> ()</td></tr>
<tr class="memdesc:a7d8009f8674aba748af4967df333eb19"><td class="mdescLeft"> </td><td class="mdescRight">A cache of values of chooseln. <a href="#a7d8009f8674aba748af4967df333eb19">More...</a><br /></td></tr>
<tr class="separator:a7d8009f8674aba748af4967df333eb19"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ab3789b16221fb4d85c7282d967d91762"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="birthdeath_8h.html#ab3789b16221fb4d85c7282d967d91762">get_chooseln_cache_size</a> ()</td></tr>
<tr class="separator:ab3789b16221fb4d85c7282d967d91762"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a4e2bebf13208d2df0bba306e360c53b2"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="birthdeath_8h.html#a4e2bebf13208d2df0bba306e360c53b2">chooseln_cache_init</a> (int size)</td></tr>
<tr class="separator:a4e2bebf13208d2df0bba306e360c53b2"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ab2c5d1b9de4e210bd5c7a01f0ea134db"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="birthdeath_8h.html#ab2c5d1b9de4e210bd5c7a01f0ea134db">chooseln_cache_resize</a> (int resize)</td></tr>
<tr class="separator:ab2c5d1b9de4e210bd5c7a01f0ea134db"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:accc6679ce0e73edbf1b3065eacb2bd61"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="birthdeath_8h.html#accc6679ce0e73edbf1b3065eacb2bd61">chooseln_cache_free</a> ()</td></tr>
<tr class="separator:accc6679ce0e73edbf1b3065eacb2bd61"><td class="memSeparator" colspan="2"> </td></tr>
</table>
<h2 class="groupheader">Typedef Documentation</h2>
<a id="a90a95c13f76b838d9b5174e5ccd41207"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a90a95c13f76b838d9b5174e5ccd41207">§ </a></span>pBirthDeathCacheArray</h2>
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<td class="memname">typedef <a class="el" href="structBirthDeathCacheArray.html">BirthDeathCacheArray</a>* <a class="el" href="birthdeath_8h.html#a90a95c13f76b838d9b5174e5ccd41207">pBirthDeathCacheArray</a></td>
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</div><div class="memdoc">
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<h2 class="groupheader">Function Documentation</h2>
<a id="a2e4ee2c0a2fb7a45e4ebbe56c0891874"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a2e4ee2c0a2fb7a45e4ebbe56c0891874">§ </a></span>birthdeath_cache_array_free()</h2>
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<td class="memname">void birthdeath_cache_array_free </td>
<td>(</td>
<td class="paramtype"><a class="el" href="birthdeath_8h.html#a90a95c13f76b838d9b5174e5ccd41207">pBirthDeathCacheArray</a> </td>
<td class="paramname"><em>pbdc_array</em></td><td>)</td>
<td></td>
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<a id="aa982e6083894fa476afdb492d761d750"></a>
<h2 class="memtitle"><span class="permalink"><a href="#aa982e6083894fa476afdb492d761d750">§ </a></span>birthdeath_cache_get_matrix()</h2>
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<td class="memname">struct <a class="el" href="structsquare__matrix.html">square_matrix</a>* birthdeath_cache_get_matrix </td>
<td>(</td>
<td class="paramtype"><a class="el" href="birthdeath_8h.html#a90a95c13f76b838d9b5174e5ccd41207">pBirthDeathCacheArray</a> </td>
<td class="paramname"><em>pbdc_array</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"><em>branchlength</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"><em>lambda</em>, </td>
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<td></td>
<td class="paramtype">double </td>
<td class="paramname"><em>mu</em> </td>
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<td>)</td>
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<p>Returns square matrix of doubles, rows and columns representing the transition probability in birthdeath rate in a change of one family size to another, with the given values of branch length, lambda, and mu </p>
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<h2 class="memtitle"><span class="permalink"><a href="#acb434d43589b596ee743b5543427b557">§ </a></span>birthdeath_cache_init()</h2>
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<td class="memname"><a class="el" href="birthdeath_8h.html#a90a95c13f76b838d9b5174e5ccd41207">pBirthDeathCacheArray</a> birthdeath_cache_init </td>
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<td class="paramtype">int </td>
<td class="paramname"><em>size</em></td><td>)</td>
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<h2 class="memtitle"><span class="permalink"><a href="#ab7e1183541f7f4df889de49ba641ef6e">§ </a></span>birthdeath_cache_resize()</h2>
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<td class="memname">void birthdeath_cache_resize </td>
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<td class="paramtype"><a class="el" href="birthdeath_8h.html#a90a95c13f76b838d9b5174e5ccd41207">pBirthDeathCacheArray</a> </td>
<td class="paramname"><em>pbdc_array</em>, </td>
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<td class="paramtype">int </td>
<td class="paramname"><em>remaxFamilysize</em> </td>
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<h2 class="memtitle"><span class="permalink"><a href="#a9f7b48d071f48f0e644d38c1b7f79e06">§ </a></span>birthdeath_likelihood_with_s_c()</h2>
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<td class="memname">double birthdeath_likelihood_with_s_c </td>
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<td class="paramname"><em>root_family_size</em>, </td>
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<td class="paramtype">int </td>
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<td class="paramtype">double </td>
<td class="paramname"><em>branchlength</em>, </td>
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<td class="paramtype">double </td>
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<td class="paramtype">double </td>
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<td class="paramtype">struct <a class="el" href="structchooseln__cache.html">chooseln_cache</a> * </td>
<td class="paramname"><em>cache</em> </td>
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<p>Calculates the probability of transitioning from root_family_size to family_size. </p>
<p>Given the branch length and the expected change rate lammbda </p>
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<h2 class="memtitle"><span class="permalink"><a href="#aa5c47a4f72dd7cf153dd936445658803">§ </a></span>birthdeath_rate_with_log_alpha()</h2>
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<td class="memname">double birthdeath_rate_with_log_alpha </td>
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<td class="paramtype">double </td>
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<td class="paramtype">struct <a class="el" href="structchooseln__cache.html">chooseln_cache</a> * </td>
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<h2 class="memtitle"><span class="permalink"><a href="#accc6679ce0e73edbf1b3065eacb2bd61">§ </a></span>chooseln_cache_free()</h2>
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<td class="memname">void chooseln_cache_free </td>
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<h2 class="memtitle"><span class="permalink"><a href="#a4e2bebf13208d2df0bba306e360c53b2">§ </a></span>chooseln_cache_init()</h2>
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<td class="memname">void chooseln_cache_init </td>
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<h2 class="memtitle"><span class="permalink"><a href="#ab2c5d1b9de4e210bd5c7a01f0ea134db">§ </a></span>chooseln_cache_resize()</h2>
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<td class="memname">void chooseln_cache_resize </td>
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<td class="paramname"><em>resize</em></td><td>)</td>
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<h2 class="memtitle"><span class="permalink"><a href="#a7d8009f8674aba748af4967df333eb19">§ </a></span>chooseln_is_init()</h2>
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<td class="memname">int chooseln_is_init </td>
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<p>A cache of values of chooseln. </p>
<p>Chooseln evaluates the natural logarithm of Gamma(n+1)/(Gamma(k+1)*Gamma(n-k+1)) The cache holds values for integer values of n and k. It does not appear to be threadsafe. </p>
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<h2 class="memtitle"><span class="permalink"><a href="#ab81fd61e47717a7a47f7b6e0855ff7ea">§ </a></span>compute_birthdeath_rates()</h2>
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<td class="memname">struct <a class="el" href="structsquare__matrix.html">square_matrix</a>* compute_birthdeath_rates </td>
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<p>returns a structure representing a matrix of precalculated transition probabilites from one family size to another, given the specified values of branch length, lambda, and mu. Values are calculated from 0 to the given maxFamilySize. All relevant values are stored in the structure.</p>
<p>lambda is the probability of both gene gain and loss per gene per unit time in the phylogeny [CAFE assumes that gene birth and death are equally probable, see Hahn et al. (2005)]. If mu is provided, lambda and mu represent the probability of gene birth and gene death, respectively. </p>
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<h2 class="memtitle"><span class="permalink"><a href="#ab3789b16221fb4d85c7282d967d91762">§ </a></span>get_chooseln_cache_size()</h2>
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<td class="memname">int get_chooseln_cache_size </td>
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<h2 class="memtitle"><span class="permalink"><a href="#a0591437ef7fd11db5e93fa5fabb816b1">§ </a></span>square_matrix_init()</h2>
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<td class="memname">void square_matrix_init </td>
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<td class="paramtype">struct <a class="el" href="structsquare__matrix.html">square_matrix</a> * </td>
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<h2 class="memtitle"><span class="permalink"><a href="#a54db5bf74e4c2d015f22cc13a8f3c7ec">§ </a></span>square_matrix_resize()</h2>
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<td class="memname">void square_matrix_resize </td>
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<td class="memname">void square_matrix_set </td>
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<h2 class="memtitle"><span class="permalink"><a href="#a1b8ab0e80d86531a457af9375f6bc7f3">§ </a></span>thread_run()</h2>
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<td class="memname">void thread_run </td>
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