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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/cafe/cafe_main.c File Reference</title>
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<li class="navelem"><a class="el" href="dir_815ec9b478b15e8b47eb45d0c766f1f4.html">cafe</a></li> </ul>
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<div class="header">
<div class="summary">
<a href="#nested-classes">Data Structures</a> |
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<div class="title">cafe_main.c File Reference</div> </div>
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<div class="textblock"><code>#include "<a class="el" href="cafe_8h_source.html">cafe.h</a>"</code><br />
<code>#include <stdlib.h></code><br />
<code>#include <math.h></code><br />
<code>#include <stdio.h></code><br />
<code>#include <pthread.h></code><br />
<code>#include <<a class="el" href="mathfunc_8h_source.html">mathfunc.h</a>></code><br />
<code>#include <<a class="el" href="memalloc_8h_source.html">memalloc.h</a>></code><br />
<code>#include <<a class="el" href="utils_8h_source.html">utils.h</a>></code><br />
<code>#include "<a class="el" href="viterbi_8h_source.html">viterbi.h</a>"</code><br />
</div><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="structCDParam.html">CDParam</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="structViterbiParam.html">ViterbiParam</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="structBranchCuttingParam.html">BranchCuttingParam</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="structLRTParam.html">LRTParam</a></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:abb7a0930eda7c3441dcf29ba2b890ac9"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="structCDParam.html">CDParam</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__main_8c.html#abb7a0930eda7c3441dcf29ba2b890ac9">pCDParam</a></td></tr>
<tr class="separator:abb7a0930eda7c3441dcf29ba2b890ac9"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ae60e280e6e9d0dc3077aeed7f0e7ab20"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="structViterbiParam.html">ViterbiParam</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__main_8c.html#ae60e280e6e9d0dc3077aeed7f0e7ab20">pViterbiParam</a></td></tr>
<tr class="separator:ae60e280e6e9d0dc3077aeed7f0e7ab20"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aec95b271b5882d519d3228f8d493546f"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="structBranchCuttingParam.html">BranchCuttingParam</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__main_8c.html#aec95b271b5882d519d3228f8d493546f">pBranchCuttingParam</a></td></tr>
<tr class="separator:aec95b271b5882d519d3228f8d493546f"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:abbda5357d81200c860d394ddea14652e"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="structLRTParam.html">LRTParam</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__main_8c.html#abbda5357d81200c860d394ddea14652e">pLRTParam</a></td></tr>
<tr class="separator:abbda5357d81200c860d394ddea14652e"><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:a41fd4a22d96314d20f0c9192c6f02339"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__main_8c.html#a41fd4a22d96314d20f0c9192c6f02339">cafe_log</a> (<a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> param, const char *msg,...)</td></tr>
<tr class="separator:a41fd4a22d96314d20f0c9192c6f02339"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:af2ed23d5716b6075fa222a6b6cf326a8"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__main_8c.html#af2ed23d5716b6075fa222a6b6cf326a8">cafe_free_birthdeath_cache</a> (<a class="el" href="family_8h.html#a6a4ec1f259847cbd066832bc18512d2f">pCafeTree</a> pcafe)</td></tr>
<tr class="separator:af2ed23d5716b6075fa222a6b6cf326a8"><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="cafe__main_8c.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:a1ade416c3d64823d5324efc631239afb"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__main_8c.html#a1ade416c3d64823d5324efc631239afb">thread_run_with_arraylist</a> (int numthreads, void *(*run)(void *), <a class="el" href="utils_8h.html#ad73ff6d7497dcfb930530cd89ce5a8c7">pArrayList</a> pal)</td></tr>
<tr class="separator:a1ade416c3d64823d5324efc631239afb"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a4a269c2694070c23c8dd643d7bf219e1"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__main_8c.html#a4a269c2694070c23c8dd643d7bf219e1">cafe_lambda_set_default</a> (<a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> param, double *lambda)</td></tr>
<tr class="separator:a4a269c2694070c23c8dd643d7bf219e1"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a782da751318188b58268567d0ef70e2a"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__main_8c.html#a782da751318188b58268567d0ef70e2a">__cafe_best_lambda_search</a> (double *plambda, void *args)</td></tr>
<tr class="separator:a782da751318188b58268567d0ef70e2a"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a40e1fa38255505c9a57ad590afed6ddb"><td class="memItemLeft" align="right" valign="top"><a class="el" href="gmatrix_8h.html#aba3fd0ac2746bc814d237f210086a0ff">pGMatrix</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__main_8c.html#a40e1fa38255505c9a57ad590afed6ddb">cafe_lambda_distribution</a> (<a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> param, int numrange, double **range)</td></tr>
<tr class="separator:a40e1fa38255505c9a57ad590afed6ddb"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a9bbb34d47645038d197f02a60c61379b"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__main_8c.html#a9bbb34d47645038d197f02a60c61379b">show_sizes</a> (FILE *f, <a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> param, <a class="el" href="cafe_8h.html#a7df7eea55178141f0d7cef33a0712b93">pCafeFamilyItem</a> pitem, int i)</td></tr>
<tr class="separator:a9bbb34d47645038d197f02a60c61379b"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:af1e282522a8c75ed3ea3a186ccbba962"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__main_8c.html#af1e282522a8c75ed3ea3a186ccbba962">cafe_get_posterior</a> (<a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> param)</td></tr>
<tr class="separator:af1e282522a8c75ed3ea3a186ccbba962"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aa093a3fdf45fba2498a881f41d1080fa"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__main_8c.html#aa093a3fdf45fba2498a881f41d1080fa">__cafe_randomize_cluster_parameters</a> (<a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> param, int lambda_len, int mu_len, int k)</td></tr>
<tr class="separator:aa093a3fdf45fba2498a881f41d1080fa"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a02cf862d2c1a49bfdd1f9443795e977e"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__main_8c.html#a02cf862d2c1a49bfdd1f9443795e977e">__cafe_scaleup_cluster_parameters</a> (<a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> param, int lambda_len, int mu_len, int k)</td></tr>
<tr class="separator:a02cf862d2c1a49bfdd1f9443795e977e"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a03af8665323a085492e028328027d60c"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__main_8c.html#a03af8665323a085492e028328027d60c">__cafe_scaledown_cluster_parameters</a> (<a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> param, int lambda_len, int mu_len, int k)</td></tr>
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<tr class="memitem:a68b1cb11f1e2231ed8e6f02864982471"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__main_8c.html#a68b1cb11f1e2231ed8e6f02864982471">cafe_get_clustered_posterior</a> (<a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> param)</td></tr>
<tr class="separator:a68b1cb11f1e2231ed8e6f02864982471"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a093deecb6e9b99de0df5480851d9f1bc"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__main_8c.html#a093deecb6e9b99de0df5480851d9f1bc">__lnLPoisson</a> (double *plambda, void *data)</td></tr>
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<tr class="memitem:a9dd81b940123877689e58892e9c08abf"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__main_8c.html#a9dd81b940123877689e58892e9c08abf">__lnLGamma</a> (double *palphabeta, void *data)</td></tr>
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<tr class="memitem:ac7cc56df589132d2e2d9306da6413497"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__main_8c.html#ac7cc56df589132d2e2d9306da6413497">cafe_set_prior_rfsize_poisson_lambda</a> (<a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> param, double *lambda)</td></tr>
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<tr class="memitem:af9ae3976765e29062e2d678af52322da"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__main_8c.html#af9ae3976765e29062e2d678af52322da">cafe_set_prior_rfsize_empirical</a> (<a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> param)</td></tr>
<tr class="memdesc:af9ae3976765e29062e2d678af52322da"><td class="mdescLeft"> </td><td class="mdescRight">set empirical prior on rootsize based on the assumption that rootsize follows leaf size distribution <a href="#af9ae3976765e29062e2d678af52322da">More...</a><br /></td></tr>
<tr class="separator:af9ae3976765e29062e2d678af52322da"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a0bf9fdfa9a334cb7a3b6471acece6153"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__main_8c.html#a0bf9fdfa9a334cb7a3b6471acece6153">__cafe_cluster_lambda_search</a> (double *parameters, void *args)</td></tr>
<tr class="separator:a0bf9fdfa9a334cb7a3b6471acece6153"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a2b635c7c05782edf03bce4eb94ed13aa"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__main_8c.html#a2b635c7c05782edf03bce4eb94ed13aa">__cafe_cluster_lambda_mu_search</a> (double *parameters, void *args)</td></tr>
<tr class="separator:a2b635c7c05782edf03bce4eb94ed13aa"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aea87f1357c04c684806e6724be2edb9e"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__main_8c.html#aea87f1357c04c684806e6724be2edb9e">__cafe_best_lambda_mu_search</a> (double *parameters, void *args)</td></tr>
<tr class="separator:aea87f1357c04c684806e6724be2edb9e"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a6276b68a56c6403d815d512080dc46a4"><td class="memItemLeft" align="right" valign="top">double * </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__main_8c.html#a6276b68a56c6403d815d512080dc46a4">cafe_best_lambda_by_fminsearch</a> (<a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> param, int lambda_len, int k)</td></tr>
<tr class="separator:a6276b68a56c6403d815d512080dc46a4"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ac44e4ab06944b45e4a1cfd923c8eb9cb"><td class="memItemLeft" align="right" valign="top">double * </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__main_8c.html#ac44e4ab06944b45e4a1cfd923c8eb9cb">cafe_best_lambda_mu_by_fminsearch</a> (<a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> param, int lambda_len, int mu_len, int k)</td></tr>
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<tr class="memitem:a41e16620ee39f8c3fcfcdfce15f8f874"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__main_8c.html#a41e16620ee39f8c3fcfcdfce15f8f874">cafe_set_birthdeath_cache_thread</a> (<a class="el" href="family_8h.html#a6a4ec1f259847cbd066832bc18512d2f">pCafeTree</a> tree, int k_value, int *family_sizes, int *rootfamily_sizes)</td></tr>
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<tr class="memitem:aeb4ab292a60df57301d00e11cfd01822"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__main_8c.html#aeb4ab292a60df57301d00e11cfd01822">cafe_set_birthdeath_cache</a> (<a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> param)</td></tr>
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<tr class="memitem:af0e8ea7cc10bd5fccdf3fe2d5b76eb78"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__main_8c.html#af0e8ea7cc10bd5fccdf3fe2d5b76eb78">__cafe_each_best_lambda_search</a> (double *plambda, void *args)</td></tr>
<tr class="separator:af0e8ea7cc10bd5fccdf3fe2d5b76eb78"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:abc6a1f95000e9407117ed11904be6864"><td class="memItemLeft" align="right" valign="top">double * </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__main_8c.html#abc6a1f95000e9407117ed11904be6864">cafe_each_best_lambda_by_fminsearch</a> (<a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> param, int lambda_len)</td></tr>
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<tr class="memitem:aeab7fe3e33c015780b8881ebd0da4461"><td class="memItemLeft" align="right" valign="top">void * </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__main_8c.html#aeab7fe3e33c015780b8881ebd0da4461">__cafe_conditional_distribution_thread_func</a> (void *ptr)</td></tr>
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<tr class="memitem:a28b01083e12d908b4a3d54a7d1d02726"><td class="memItemLeft" align="right" valign="top"><a class="el" href="utils_8h.html#ad73ff6d7497dcfb930530cd89ce5a8c7">pArrayList</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__main_8c.html#a28b01083e12d908b4a3d54a7d1d02726">cafe_conditional_distribution</a> (<a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> param)</td></tr>
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<tr class="memitem:a5a27b38fc9f9bb4e2805968ebb1efc3a"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__main_8c.html#a5a27b38fc9f9bb4e2805968ebb1efc3a">viterbi_section</a> (<a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> param, int i, <a class="el" href="family_8h.html#a6a4ec1f259847cbd066832bc18512d2f">pCafeTree</a> pcafe, double *cP, <a class="el" href="utils_8h.html#ad73ff6d7497dcfb930530cd89ce5a8c7">pArrayList</a> pCD)</td></tr>
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<tr class="memitem:a6e702b0570b1d887cf2f49ef27df2c56"><td class="memItemLeft" align="right" valign="top">void * </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__main_8c.html#a6e702b0570b1d887cf2f49ef27df2c56">__cafe_viterbi_thread_func</a> (void *ptr)</td></tr>
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<tr class="memitem:a50a8afe408546920e6a0920cec164ed2"><td class="memItemLeft" align="right" valign="top"><a class="el" href="utils_8h.html#ad73ff6d7497dcfb930530cd89ce5a8c7">pArrayList</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__main_8c.html#a50a8afe408546920e6a0920cec164ed2">cafe_viterbi</a> (<a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> param, <a class="el" href="utils_8h.html#ad73ff6d7497dcfb930530cd89ce5a8c7">pArrayList</a> pCD)</td></tr>
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<tr class="memitem:a2a37b9a22b8a43e5331507752fae96b2"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__main_8c.html#a2a37b9a22b8a43e5331507752fae96b2">cafe_viterbi_print</a> (<a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> param)</td></tr>
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<tr class="memitem:af9f3920b1054f4b3d489d7097c5b0780"><td class="memItemLeft" align="right" valign="top">void * </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__main_8c.html#af9f3920b1054f4b3d489d7097c5b0780">__cafe_branch_cutting_thread_func</a> (void *ptr)</td></tr>
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<tr class="memitem:adf53bc2a22b3f10d28b5bf5c226b371d"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__main_8c.html#adf53bc2a22b3f10d28b5bf5c226b371d">cafe_branch_cutting</a> (<a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> param)</td></tr>
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<tr class="memitem:afdfb3c11afe02a9edcf47716d10e539b"><td class="memItemLeft" align="right" valign="top">void * </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__main_8c.html#afdfb3c11afe02a9edcf47716d10e539b">__cafe_likelihood_ratio_test_thread_func</a> (void *ptr)</td></tr>
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<tr class="memitem:abc9d347c972a12d7a86277efdd4c6b9d"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__main_8c.html#abc9d347c972a12d7a86277efdd4c6b9d">cafe_likelihood_ratio_test</a> (<a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> param)</td></tr>
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<tr class="memitem:a0a54e602c59702bd6cc844332b6c2a7a"><td class="memItemLeft" align="right" valign="top"><a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__main_8c.html#a0a54e602c59702bd6cc844332b6c2a7a">cafe_copy_parameters</a> (<a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> psrc)</td></tr>
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<tr class="memitem:a72db0fc19498016c5023420f510bad9c"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__main_8c.html#a72db0fc19498016c5023420f510bad9c">cafe_free_copy_parameters</a> (<a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> param)</td></tr>
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<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="var-members"></a>
Variables</h2></td></tr>
<tr class="memitem:ab022c096f87385cf60838c6d14634b61"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__main_8c.html#ab022c096f87385cf60838c6d14634b61">chooseln_cache_size</a></td></tr>
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<tr class="memitem:a9658b6be1ee7f42eda042faed308c41a"><td class="memItemLeft" align="right" valign="top">pthread_mutex_t </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__main_8c.html#a9658b6be1ee7f42eda042faed308c41a">mutex_cafe_viterbi</a> = PTHREAD_MUTEX_INITIALIZER</td></tr>
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<tr class="memitem:a42828a8f84597cc6e8a1a8a9bca1ca3e"><td class="memItemLeft" align="right" valign="top">pthread_mutex_t </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__main_8c.html#a42828a8f84597cc6e8a1a8a9bca1ca3e">mutex_cafe_likelihood</a> = PTHREAD_MUTEX_INITIALIZER</td></tr>
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<h2 class="groupheader">Typedef Documentation</h2>
<a id="aec95b271b5882d519d3228f8d493546f"></a>
<h2 class="memtitle"><span class="permalink"><a href="#aec95b271b5882d519d3228f8d493546f">§ </a></span>pBranchCuttingParam</h2>
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<td class="memname">typedef <a class="el" href="structBranchCuttingParam.html">BranchCuttingParam</a>* <a class="el" href="cafe__main_8c.html#aec95b271b5882d519d3228f8d493546f">pBranchCuttingParam</a></td>
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<a id="abb7a0930eda7c3441dcf29ba2b890ac9"></a>
<h2 class="memtitle"><span class="permalink"><a href="#abb7a0930eda7c3441dcf29ba2b890ac9">§ </a></span>pCDParam</h2>
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<td class="memname">typedef <a class="el" href="structCDParam.html">CDParam</a>* <a class="el" href="cafe__main_8c.html#abb7a0930eda7c3441dcf29ba2b890ac9">pCDParam</a></td>
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<a id="abbda5357d81200c860d394ddea14652e"></a>
<h2 class="memtitle"><span class="permalink"><a href="#abbda5357d81200c860d394ddea14652e">§ </a></span>pLRTParam</h2>
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<td class="memname">typedef <a class="el" href="structLRTParam.html">LRTParam</a>* <a class="el" href="cafe__main_8c.html#abbda5357d81200c860d394ddea14652e">pLRTParam</a></td>
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<h2 class="memtitle"><span class="permalink"><a href="#ae60e280e6e9d0dc3077aeed7f0e7ab20">§ </a></span>pViterbiParam</h2>
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<td class="memname">typedef <a class="el" href="structViterbiParam.html">ViterbiParam</a>* <a class="el" href="cafe__main_8c.html#ae60e280e6e9d0dc3077aeed7f0e7ab20">pViterbiParam</a></td>
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<h2 class="groupheader">Function Documentation</h2>
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<h2 class="memtitle"><span class="permalink"><a href="#aea87f1357c04c684806e6724be2edb9e">§ </a></span>__cafe_best_lambda_mu_search()</h2>
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<td class="memname">double __cafe_best_lambda_mu_search </td>
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<td class="paramtype">double * </td>
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<h2 class="memtitle"><span class="permalink"><a href="#a782da751318188b58268567d0ef70e2a">§ </a></span>__cafe_best_lambda_search()</h2>
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<td class="memname">double __cafe_best_lambda_search </td>
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<td class="paramtype">double * </td>
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<td class="memname">void* __cafe_branch_cutting_thread_func </td>
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<h2 class="memtitle"><span class="permalink"><a href="#a2b635c7c05782edf03bce4eb94ed13aa">§ </a></span>__cafe_cluster_lambda_mu_search()</h2>
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<td class="memname">double __cafe_cluster_lambda_mu_search </td>
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<td class="paramname"><em>parameters</em>, </td>
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<h2 class="memtitle"><span class="permalink"><a href="#a0bf9fdfa9a334cb7a3b6471acece6153">§ </a></span>__cafe_cluster_lambda_search()</h2>
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<td class="memname">double __cafe_cluster_lambda_search </td>
<td>(</td>
<td class="paramtype">double * </td>
<td class="paramname"><em>parameters</em>, </td>
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<td class="paramtype">void * </td>
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<h2 class="memtitle"><span class="permalink"><a href="#aeab7fe3e33c015780b8881ebd0da4461">§ </a></span>__cafe_conditional_distribution_thread_func()</h2>
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<td class="memname">void* __cafe_conditional_distribution_thread_func </td>
<td>(</td>
<td class="paramtype">void * </td>
<td class="paramname"><em>ptr</em></td><td>)</td>
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<h2 class="memtitle"><span class="permalink"><a href="#af0e8ea7cc10bd5fccdf3fe2d5b76eb78">§ </a></span>__cafe_each_best_lambda_search()</h2>
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<td class="memname">double __cafe_each_best_lambda_search </td>
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<td class="paramname"><em>plambda</em>, </td>
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<td class="paramtype">void * </td>
<td class="paramname"><em>args</em> </td>
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<h2 class="memtitle"><span class="permalink"><a href="#afdfb3c11afe02a9edcf47716d10e539b">§ </a></span>__cafe_likelihood_ratio_test_thread_func()</h2>
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<td class="memname">void* __cafe_likelihood_ratio_test_thread_func </td>
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<td class="paramname"><em>ptr</em></td><td>)</td>
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<h2 class="memtitle"><span class="permalink"><a href="#aa093a3fdf45fba2498a881f41d1080fa">§ </a></span>__cafe_randomize_cluster_parameters()</h2>
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<td class="memname">void __cafe_randomize_cluster_parameters </td>
<td>(</td>
<td class="paramtype"><a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> </td>
<td class="paramname"><em>param</em>, </td>
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<td class="paramtype">int </td>
<td class="paramname"><em>lambda_len</em>, </td>
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<td class="paramtype">int </td>
<td class="paramname"><em>mu_len</em>, </td>
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<td class="paramtype">int </td>
<td class="paramname"><em>k</em> </td>
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<h2 class="memtitle"><span class="permalink"><a href="#a03af8665323a085492e028328027d60c">§ </a></span>__cafe_scaledown_cluster_parameters()</h2>
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<td class="memname">void __cafe_scaledown_cluster_parameters </td>
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<td class="paramtype"><a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> </td>
<td class="paramname"><em>param</em>, </td>
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<td class="paramtype">int </td>
<td class="paramname"><em>lambda_len</em>, </td>
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<td class="paramtype">int </td>
<td class="paramname"><em>mu_len</em>, </td>
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<td class="paramtype">int </td>
<td class="paramname"><em>k</em> </td>
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<h2 class="memtitle"><span class="permalink"><a href="#a02cf862d2c1a49bfdd1f9443795e977e">§ </a></span>__cafe_scaleup_cluster_parameters()</h2>
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<td class="memname">void __cafe_scaleup_cluster_parameters </td>
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<td class="paramtype"><a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> </td>
<td class="paramname"><em>param</em>, </td>
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<td class="paramname"><em>lambda_len</em>, </td>
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<td class="paramname"><em>mu_len</em>, </td>
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<td class="paramname"><em>k</em> </td>
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<h2 class="memtitle"><span class="permalink"><a href="#a6e702b0570b1d887cf2f49ef27df2c56">§ </a></span>__cafe_viterbi_thread_func()</h2>
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<td class="memname">void* __cafe_viterbi_thread_func </td>
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<h2 class="memtitle"><span class="permalink"><a href="#a9dd81b940123877689e58892e9c08abf">§ </a></span>__lnLGamma()</h2>
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<td class="memname">double __lnLGamma </td>
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<td class="paramtype">double * </td>
<td class="paramname"><em>palphabeta</em>, </td>
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<td class="paramname"><em>data</em> </td>
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<h2 class="memtitle"><span class="permalink"><a href="#a093deecb6e9b99de0df5480851d9f1bc">§ </a></span>__lnLPoisson()</h2>
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<td class="memname">double __lnLPoisson </td>
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<td class="paramtype">double * </td>
<td class="paramname"><em>plambda</em>, </td>
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<h2 class="memtitle"><span class="permalink"><a href="#a6276b68a56c6403d815d512080dc46a4">§ </a></span>cafe_best_lambda_by_fminsearch()</h2>
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<td class="memname">double* cafe_best_lambda_by_fminsearch </td>
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<td class="paramtype"><a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> </td>
<td class="paramname"><em>param</em>, </td>
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<td class="paramtype">int </td>
<td class="paramname"><em>lambda_len</em>, </td>
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<td class="paramname"><em>k</em> </td>
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<h2 class="memtitle"><span class="permalink"><a href="#ac44e4ab06944b45e4a1cfd923c8eb9cb">§ </a></span>cafe_best_lambda_mu_by_fminsearch()</h2>
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<td class="memname">double* cafe_best_lambda_mu_by_fminsearch </td>
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<td class="paramtype"><a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> </td>
<td class="paramname"><em>param</em>, </td>
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<td class="paramtype">int </td>
<td class="paramname"><em>lambda_len</em>, </td>
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<td class="paramtype">int </td>
<td class="paramname"><em>mu_len</em>, </td>
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<td class="paramname"><em>k</em> </td>
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<h2 class="memtitle"><span class="permalink"><a href="#adf53bc2a22b3f10d28b5bf5c226b371d">§ </a></span>cafe_branch_cutting()</h2>
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<td class="memname">void cafe_branch_cutting </td>
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<td class="paramtype"><a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> </td>
<td class="paramname"><em>param</em></td><td>)</td>
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<h2 class="memtitle"><span class="permalink"><a href="#a28b01083e12d908b4a3d54a7d1d02726">§ </a></span>cafe_conditional_distribution()</h2>
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<td class="memname"><a class="el" href="utils_8h.html#ad73ff6d7497dcfb930530cd89ce5a8c7">pArrayList</a> cafe_conditional_distribution </td>
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<td class="paramtype"><a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> </td>
<td class="paramname"><em>param</em></td><td>)</td>
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<h2 class="memtitle"><span class="permalink"><a href="#a0a54e602c59702bd6cc844332b6c2a7a">§ </a></span>cafe_copy_parameters()</h2>
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<td class="memname"><a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> cafe_copy_parameters </td>
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<td class="paramtype"><a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> </td>
<td class="paramname"><em>psrc</em></td><td>)</td>
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<h2 class="memtitle"><span class="permalink"><a href="#abc6a1f95000e9407117ed11904be6864">§ </a></span>cafe_each_best_lambda_by_fminsearch()</h2>
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<td class="memname">double* cafe_each_best_lambda_by_fminsearch </td>
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<td class="paramtype"><a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> </td>
<td class="paramname"><em>param</em>, </td>
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<td></td>
<td class="paramtype">int </td>
<td class="paramname"><em>lambda_len</em> </td>
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<h2 class="memtitle"><span class="permalink"><a href="#af2ed23d5716b6075fa222a6b6cf326a8">§ </a></span>cafe_free_birthdeath_cache()</h2>
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<td class="memname">void cafe_free_birthdeath_cache </td>
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<td class="paramtype"><a class="el" href="family_8h.html#a6a4ec1f259847cbd066832bc18512d2f">pCafeTree</a> </td>
<td class="paramname"><em>pcafe</em></td><td>)</td>
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<h2 class="memtitle"><span class="permalink"><a href="#a72db0fc19498016c5023420f510bad9c">§ </a></span>cafe_free_copy_parameters()</h2>
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<td class="memname">void cafe_free_copy_parameters </td>
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<td class="paramtype"><a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> </td>
<td class="paramname"><em>param</em></td><td>)</td>
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<h2 class="memtitle"><span class="permalink"><a href="#a68b1cb11f1e2231ed8e6f02864982471">§ </a></span>cafe_get_clustered_posterior()</h2>
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<td class="memname">double cafe_get_clustered_posterior </td>
<td>(</td>
<td class="paramtype"><a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> </td>
<td class="paramname"><em>param</em></td><td>)</td>
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<h2 class="memtitle"><span class="permalink"><a href="#af1e282522a8c75ed3ea3a186ccbba962">§ </a></span>cafe_get_posterior()</h2>
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<td class="memname">double cafe_get_posterior </td>
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<td class="paramtype"><a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> </td>
<td class="paramname"><em>param</em></td><td>)</td>
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<h2 class="memtitle"><span class="permalink"><a href="#a40e1fa38255505c9a57ad590afed6ddb">§ </a></span>cafe_lambda_distribution()</h2>
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<td class="memname"><a class="el" href="gmatrix_8h.html#aba3fd0ac2746bc814d237f210086a0ff">pGMatrix</a> cafe_lambda_distribution </td>
<td>(</td>
<td class="paramtype"><a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> </td>
<td class="paramname"><em>param</em>, </td>
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<td class="paramtype">int </td>
<td class="paramname"><em>numrange</em>, </td>
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<td class="paramtype">double ** </td>
<td class="paramname"><em>range</em> </td>
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<h2 class="memtitle"><span class="permalink"><a href="#a4a269c2694070c23c8dd643d7bf219e1">§ </a></span>cafe_lambda_set_default()</h2>
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<td class="memname">void cafe_lambda_set_default </td>
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<td class="paramtype"><a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> </td>
<td class="paramname"><em>param</em>, </td>
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<td class="paramtype">double * </td>
<td class="paramname"><em>lambda</em> </td>
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<h2 class="memtitle"><span class="permalink"><a href="#abc9d347c972a12d7a86277efdd4c6b9d">§ </a></span>cafe_likelihood_ratio_test()</h2>
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<td class="memname">void cafe_likelihood_ratio_test </td>
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<td class="paramtype"><a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> </td>
<td class="paramname"><em>param</em></td><td>)</td>
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<h2 class="memtitle"><span class="permalink"><a href="#a41fd4a22d96314d20f0c9192c6f02339">§ </a></span>cafe_log()</h2>
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<td class="memname">void cafe_log </td>
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<td class="paramtype"><a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> </td>
<td class="paramname"><em>param</em>, </td>
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<td class="paramtype">const char * </td>
<td class="paramname"><em>msg</em>, </td>
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<td class="paramtype"> </td>
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<h2 class="memtitle"><span class="permalink"><a href="#aeb4ab292a60df57301d00e11cfd01822">§ </a></span>cafe_set_birthdeath_cache()</h2>
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<td class="memname">void cafe_set_birthdeath_cache </td>
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