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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_shell.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="#define-members">Macros</a> |
<a href="#func-members">Functions</a> |
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<div class="title">cafe_shell.c File Reference</div> </div>
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<p>Functions corresponding to the commands available in Cafe.
<a href="#details">More...</a></p>
<div class="textblock"><code>#include <<a class="el" href="mathfunc_8h_source.html">mathfunc.h</a>></code><br />
<code>#include <ctype.h></code><br />
<code>#include <assert.h></code><br />
<code>#include <float.h></code><br />
<code>#include <stdarg.h></code><br />
<code>#include <stdio.h></code><br />
<code>#include <<a class="el" href="io_8h_source.html">io.h</a>></code><br />
<code>#include "<a class="el" href="cafe_8h_source.html">cafe.h</a>"</code><br />
<code>#include "<a class="el" href="cafe__shell_8h_source.html">cafe_shell.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="define-members"></a>
Macros</h2></td></tr>
<tr class="memitem:a993ec84369cb5e52517ee96843e4aeeb"><td class="memItemLeft" align="right" valign="top">#define </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#a993ec84369cb5e52517ee96843e4aeeb">STDERR_IF</a>(a, b)   if ( a ) { fprintf(stderr,b); return -1; }</td></tr>
<tr class="separator:a993ec84369cb5e52517ee96843e4aeeb"><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:a41a58278ae144c504961cd76cc907ccd"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#a41a58278ae144c504961cd76cc907ccd">cafe_shell_dispatch_commandf</a> (char *format,...)</td></tr>
<tr class="separator:a41a58278ae144c504961cd76cc907ccd"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:af9debf3a25638315c5449502247170e8"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#af9debf3a25638315c5449502247170e8">__cafe_cmd_log</a> (int argc, char *argv[])</td></tr>
<tr class="separator:af9debf3a25638315c5449502247170e8"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a3adf5f4770c6c89b152417ee4b03e360"><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__shell_8c.html#a3adf5f4770c6c89b152417ee4b03e360">cafe_shell_build_argument</a> (int argc, char *argv[])</td></tr>
<tr class="separator:a3adf5f4770c6c89b152417ee4b03e360"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a288f5f2ddc4acf86d785deff10ed8e21"><td class="memItemLeft" align="right" valign="top"><a class="el" href="cafe__shell_8h.html#ac5a9bebec6d47b2a769221139a167876">pArgument</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#a288f5f2ddc4acf86d785deff10ed8e21">cafe_shell_get_argument</a> (char *opt, <a class="el" href="utils_8h.html#ad73ff6d7497dcfb930530cd89ce5a8c7">pArrayList</a> pal)</td></tr>
<tr class="separator:a288f5f2ddc4acf86d785deff10ed8e21"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aa4d4e91f878146701ebbb2a9bdec0e58"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#aa4d4e91f878146701ebbb2a9bdec0e58">cafe_shell_set_lambda</a> (<a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> param, double *lambda)</td></tr>
<tr class="separator:aa4d4e91f878146701ebbb2a9bdec0e58"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a69136530face607391c301737ac59a50"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#a69136530face607391c301737ac59a50">cafe_shell_set_lambda_mu</a> (<a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> param, double *parameters)</td></tr>
<tr class="separator:a69136530face607391c301737ac59a50"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a6cf77b13baac8ca00b269eaf45c031cd"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#a6cf77b13baac8ca00b269eaf45c031cd">viterbi_parameters_init</a> (<a class="el" href="structviterbi__parameters.html">viterbi_parameters</a> *viterbi, int nnodes, int nrows)</td></tr>
<tr class="separator:a6cf77b13baac8ca00b269eaf45c031cd"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ac7377c0d5f6156ab08fc22433aa8bf8b"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#ac7377c0d5f6156ab08fc22433aa8bf8b">viterbi_parameters_clear</a> (<a class="el" href="structviterbi__parameters.html">viterbi_parameters</a> *viterbi, int nnodes)</td></tr>
<tr class="separator:ac7377c0d5f6156ab08fc22433aa8bf8b"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a99843f463c76110955e409c3dab5a216"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#a99843f463c76110955e409c3dab5a216">viterbi_set_max_pvalue</a> (<a class="el" href="structviterbi__parameters.html">viterbi_parameters</a> *viterbi, int index, double val)</td></tr>
<tr class="separator:a99843f463c76110955e409c3dab5a216"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a3a0b1c333839b083bf301f9418d44a40"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#a3a0b1c333839b083bf301f9418d44a40">cafe_shell_clear_param</a> (<a class="el" href="family_8h.html#a74aeadd6aca74b33994949cd3b7017ea">pCafeParam</a> param, int btree_skip)</td></tr>
<tr class="separator:a3a0b1c333839b083bf301f9418d44a40"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a82e7144c7b62a989a5fd3d855a1500a8"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#a82e7144c7b62a989a5fd3d855a1500a8">cafe_shell_set_sizes</a> ()</td></tr>
<tr class="separator:a82e7144c7b62a989a5fd3d855a1500a8"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:adbb978cbbd721d21fcecfd372604af76"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#adbb978cbbd721d21fcecfd372604af76">cafe_shell_prompt</a> (char *prompt, char *format,...)</td></tr>
<tr class="separator:adbb978cbbd721d21fcecfd372604af76"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a20306fdf5805e9059e240dab93b51e7f"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#a20306fdf5805e9059e240dab93b51e7f">reset_k_likelihoods</a> (<a class="el" href="family_8h.html#a44c8e7c896165b78ce90c053b0352639">pCafeNode</a> pcnode, int k, int num_factors)</td></tr>
<tr class="separator:a20306fdf5805e9059e240dab93b51e7f"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:af4aaab71abb20ea8e727b6a92361db89"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#af4aaab71abb20ea8e727b6a92361db89">cafe_shell_parse_familysize</a> (int argc, char *argv[])</td></tr>
<tr class="separator:af4aaab71abb20ea8e727b6a92361db89"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:afe9a3e66ef89dac3abaa6a96b694774c"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#afe9a3e66ef89dac3abaa6a96b694774c">cafe_shell_set_familysize</a> ()</td></tr>
<tr class="separator:afe9a3e66ef89dac3abaa6a96b694774c"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:abb4e63e9f0ba2ca2b3011271f04f6548"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#abb4e63e9f0ba2ca2b3011271f04f6548">cafe_shell_parse_branchlength</a> (int argc, char *argv[])</td></tr>
<tr class="separator:abb4e63e9f0ba2ca2b3011271f04f6548"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a9e168dbad3b30a2312440acf17f57d60"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#a9e168dbad3b30a2312440acf17f57d60">cafe_shell_set_branchlength</a> ()</td></tr>
<tr class="separator:a9e168dbad3b30a2312440acf17f57d60"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a1c9350e1a590d596153b08dc28e111cd"><td class="memItemLeft" align="right" valign="top">double * </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#a1c9350e1a590d596153b08dc28e111cd">cafe_shell_likelihood</a> (int max)</td></tr>
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<tr class="memitem:a6f6ca009bdfa80e59a3e2550412abfe4"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#a6f6ca009bdfa80e59a3e2550412abfe4">cafe_shell_init</a> (int quiet)</td></tr>
<tr class="memdesc:a6f6ca009bdfa80e59a3e2550412abfe4"><td class="mdescLeft"> </td><td class="mdescRight">Initializes the global <a class="el" href="lambda__tests_8cpp.html#a52bf660ab9a3b7f0206fbd8d8311d24b">cafe_param</a> that holds the data acted upon by cafe. Called at program startup. <a href="#a6f6ca009bdfa80e59a3e2550412abfe4">More...</a><br /></td></tr>
<tr class="separator:a6f6ca009bdfa80e59a3e2550412abfe4"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a18d0bfb6dae3e9520ffb9c5a534d1aa5"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#a18d0bfb6dae3e9520ffb9c5a534d1aa5">cafe_cmd_tree</a> (int argc, char *argv[])</td></tr>
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<tr class="memitem:a2d2f426bc8a7977d29ac453e5876a6c3"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#a2d2f426bc8a7977d29ac453e5876a6c3">phylogeny_lambda_parse_func</a> (<a class="el" href="tree_8h.html#ac1eda65f4edbb85d380203ffae716b53">pTree</a> ptree, <a class="el" href="tree_8h.html#aebe844e39a68ff02d3a2526ab3e719be">pTreeNode</a> ptnode)</td></tr>
<tr class="separator:a2d2f426bc8a7977d29ac453e5876a6c3"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ae3736805ef81da58a9ec2da6a8fca24a"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#ae3736805ef81da58a9ec2da6a8fca24a">__cafe_cmd_lambda_tree</a> (<a class="el" href="cafe__shell_8h.html#ac5a9bebec6d47b2a769221139a167876">pArgument</a> parg)</td></tr>
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<tr class="memitem:a72ba1fc4c9e0e0d85b1a9db4712ba9e2"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#a72ba1fc4c9e0e0d85b1a9db4712ba9e2">cafe_cmd_lambda_mu</a> (int argc, char *argv[])</td></tr>
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<tr class="memitem:a286c4de17031ff6848ae67e249d87006"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#a286c4de17031ff6848ae67e249d87006">__cafe_cmd_viterbi_print</a> (int max)</td></tr>
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<tr class="memitem:a7d64e80e883bf02bd5682640518142a7"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#a7d64e80e883bf02bd5682640518142a7">__cafe_cmd_viterbi_family_print</a> (int idx)</td></tr>
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<tr class="memitem:a32ece228b3ba07db144f79452afdb125"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#a32ece228b3ba07db144f79452afdb125">cafe_cmd_viterbi</a> (int argc, char *argv[])</td></tr>
<tr class="separator:a32ece228b3ba07db144f79452afdb125"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a938b50ea7ad7ec3b3753c876025d3337"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#a938b50ea7ad7ec3b3753c876025d3337">cafe_cmd_reconstruction_accuracy</a> (int argc, char *argv[])</td></tr>
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<tr class="memitem:a126800fe1f55608fef53e4766fcc81ef"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#a126800fe1f55608fef53e4766fcc81ef">_cafe_cross_validate_by_family</a> (char *queryfile, char *truthfile, char *errortype)</td></tr>
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<tr class="memitem:a749fae32c89708a04836b0ebfbd2340f"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#a749fae32c89708a04836b0ebfbd2340f">_cafe_cross_validate_by_species</a> (char *validatefile, char *errortype)</td></tr>
<tr class="separator:a749fae32c89708a04836b0ebfbd2340f"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a8c9eeffa3b9732dd1a46b30475e86ff5"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#a8c9eeffa3b9732dd1a46b30475e86ff5">cafe_cmd_crossvalidation_by_family</a> (int argc, char *argv[])</td></tr>
<tr class="separator:a8c9eeffa3b9732dd1a46b30475e86ff5"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a9303ebc40d4020bdf2d539dd76d59c7e"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#a9303ebc40d4020bdf2d539dd76d59c7e">cafe_cmd_crossvalidation_by_species</a> (int argc, char *argv[])</td></tr>
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<tr class="memitem:a135a720eb39deef29c04097793ceb20e"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#a135a720eb39deef29c04097793ceb20e">cafe_cmd_load</a> (int argc, char *argv[])</td></tr>
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<tr class="memitem:aae07af4b31abc31ec549e9e95b1a1cfc"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#aae07af4b31abc31ec549e9e95b1a1cfc">cafe_cmd_save</a> (int argc, char *argv[])</td></tr>
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<tr class="memitem:a3610b289bae55dc6033b293591ec9662"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#a3610b289bae55dc6033b293591ec9662">cafe_cmd_print_param</a> (int argc, char *argv[])</td></tr>
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<tr class="memitem:a633fa681f5ff83b688c7666bf36892a4"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#a633fa681f5ff83b688c7666bf36892a4">cafe_cmd_version</a> (int argc, char *argv[])</td></tr>
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<tr class="memitem:acd4400722dc63e9b68c71dafe59361cd"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#acd4400722dc63e9b68c71dafe59361cd">__cafe_cmd_pvalue_print</a> (int max)</td></tr>
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<tr class="memitem:a3041a622c7035c1e3bcf48bd5c9609ea"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#a3041a622c7035c1e3bcf48bd5c9609ea">cafe_cmd_pvalue</a> (int argc, char *argv[])</td></tr>
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<tr class="memitem:ab7b88336a604d317c2eea7ebcb1371e8"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#ab7b88336a604d317c2eea7ebcb1371e8">cafe_cmd_branchlength</a> (int argc, char *argv[])</td></tr>
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<tr class="memitem:a412249d0e5fa5ca96da764607f38b6b3"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#a412249d0e5fa5ca96da764607f38b6b3">cafe_cmd_family</a> (int argc, char *argv[])</td></tr>
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<tr class="memitem:a782da751318188b58268567d0ef70e2a"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#a782da751318188b58268567d0ef70e2a">__cafe_best_lambda_search</a> (double *plambda, void *args)</td></tr>
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<tr class="memitem:acd71095c160fb97350ce5a4eee381124"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#acd71095c160fb97350ce5a4eee381124">__cafe_best_lambda_mu_search</a> (double *pparams, void *args)</td></tr>
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<tr class="memitem:a5b9eaf87f13fadcb34afc1a96330be9e"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#a5b9eaf87f13fadcb34afc1a96330be9e">__cafe_cluster_lambda_search</a> (double *plambda, void *args)</td></tr>
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<tr class="memitem:ac75fb4cd3489783d289c606c0b5cbd92"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#ac75fb4cd3489783d289c606c0b5cbd92">__cafe_cluster_lambda_mu_search</a> (double *pparams, void *args)</td></tr>
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<tr class="memitem:a7cffc0eb3c396c12222d50a19817fe25"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#a7cffc0eb3c396c12222d50a19817fe25">cafe_shell_score</a> ()</td></tr>
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<tr class="memitem:a58d8686f881b69565a59206239f5d3da"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#a58d8686f881b69565a59206239f5d3da">cafe_cmd_score</a> (int argc, char *argv[])</td></tr>
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<tr class="memitem:a7486ee9a8e4fc6f64458540628e3026f"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#a7486ee9a8e4fc6f64458540628e3026f">cafe_cmd_retrieve</a> (int argc, char *argv[])</td></tr>
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<tr class="memitem:gae4ff9c32d2375ec8487fd99d140d9134"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Commands.html#gae4ff9c32d2375ec8487fd99d140d9134">cafe_cmd_log</a> (int argc, char *argv[])</td></tr>
<tr class="memdesc:gae4ff9c32d2375ec8487fd99d140d9134"><td class="mdescLeft"> </td><td class="mdescRight">Echoes parameters to the current output. <a href="group__Commands.html#gae4ff9c32d2375ec8487fd99d140d9134">More...</a><br /></td></tr>
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<tr class="memitem:a6be819694edd4e80ef93e495c5234a65"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#a6be819694edd4e80ef93e495c5234a65">__cafe_tree_string_gainloss</a> (<a class="el" href="utils__string_8h.html#a7174cd6b53997a74bf1df360153ad7b0">pString</a> pstr, <a class="el" href="tree_8h.html#a47c8b5d175cf4f1946a873dd28b77516">pPhylogenyNode</a> ptnode)</td></tr>
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<tr class="memitem:a30c2f8b518b2587a73bbbc558be7eccd"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#a30c2f8b518b2587a73bbbc558be7eccd">__cafe_tree_string_sum_gainloss</a> (<a class="el" href="utils__string_8h.html#a7174cd6b53997a74bf1df360153ad7b0">pString</a> pstr, <a class="el" href="tree_8h.html#a47c8b5d175cf4f1946a873dd28b77516">pPhylogenyNode</a> ptnode)</td></tr>
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<tr class="memitem:a34c1483ce4852daaad9cbe21652f6318"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#a34c1483ce4852daaad9cbe21652f6318">__cafe_tree_gainloss_mp_annotation</a> (<a class="el" href="utils__string_8h.html#a7174cd6b53997a74bf1df360153ad7b0">pString</a> pstr, <a class="el" href="tree_8h.html#aebe844e39a68ff02d3a2526ab3e719be">pTreeNode</a> pnode, <a class="el" href="tree_8h.html#a72fe5b32d9eed96d3eeb7add5ec78920">pMetapostConfig</a> pmc, va_list ap)</td></tr>
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<tr class="memitem:ab994a6c910f779f783ab58d245c1c5d7"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#ab994a6c910f779f783ab58d245c1c5d7">cafe_tree_mp_remark</a> (<a class="el" href="utils__string_8h.html#a7174cd6b53997a74bf1df360153ad7b0">pString</a> pstr, <a class="el" href="tree_8h.html#ac1eda65f4edbb85d380203ffae716b53">pTree</a> ptree, <a class="el" href="tree_8h.html#a72fe5b32d9eed96d3eeb7add5ec78920">pMetapostConfig</a> pmc, va_list ap1)</td></tr>
<tr class="separator:ab994a6c910f779f783ab58d245c1c5d7"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ac238f1cff2445ecf67db2b13cef2d454"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#ac238f1cff2445ecf67db2b13cef2d454">__cafe_cmd_extinct_count_zero</a> ()</td></tr>
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<tr class="memitem:ga1f8d08708948fe6cc47a16d64cff2d4d"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Commands.html#ga1f8d08708948fe6cc47a16d64cff2d4d">cafe_cmd_sim_extinct</a> (int argc, char *argv[])</td></tr>
<tr class="memdesc:ga1f8d08708948fe6cc47a16d64cff2d4d"><td class="mdescLeft"> </td><td class="mdescRight">Runs a Monte Carlo simulation against the data and reports the number of extinctions that occurred. <a href="group__Commands.html#ga1f8d08708948fe6cc47a16d64cff2d4d">More...</a><br /></td></tr>
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<tr class="memitem:adad5789514cd2867f277154cc4505353"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#adad5789514cd2867f277154cc4505353">__hg_norm_cdf_func</a> (double p, double *args)</td></tr>
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<tr class="memitem:a3ecfe3f073604e17aef011acd664572b"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#a3ecfe3f073604e17aef011acd664572b">__hg_print_sim_extinct</a> (<a class="el" href="mathfunc_8h.html#a77d1d0f2a1af3df93f2884cf22a29075">pHistogram</a> **phist_sim_n, <a class="el" href="mathfunc_8h.html#a77d1d0f2a1af3df93f2884cf22a29075">pHistogram</a> *phist_sim, int r, <a class="el" href="mathfunc_8h.html#a77d1d0f2a1af3df93f2884cf22a29075">pHistogram</a> phist_tmp, double *cnt, int num_trials)</td></tr>
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<tr class="memitem:gadce5da31072dab7c010d7e7e4d39320c"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Commands.html#gadce5da31072dab7c010d7e7e4d39320c">cafe_cmd_root_dist</a> (int argc, char *argv[])</td></tr>
<tr class="memdesc:gadce5da31072dab7c010d7e7e4d39320c"><td class="mdescLeft"> </td><td class="mdescRight">Specify root family size distribution for simulation. <a href="group__Commands.html#gadce5da31072dab7c010d7e7e4d39320c">More...</a><br /></td></tr>
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<tr class="memitem:ga92a5e46c97a72fdc0e6201f093fdfd6f"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Commands.html#ga92a5e46c97a72fdc0e6201f093fdfd6f">cafe_cmd_extinct</a> (int argc, char *argv[])</td></tr>
<tr class="memdesc:ga92a5e46c97a72fdc0e6201f093fdfd6f"><td class="mdescLeft"> </td><td class="mdescRight">Runs a simulation to determine how many families are likely to have gone extinct. <a href="group__Commands.html#ga92a5e46c97a72fdc0e6201f093fdfd6f">More...</a><br /></td></tr>
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<tr class="memitem:a1662205f714c446de8c6e470a9fb625a"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#a1662205f714c446de8c6e470a9fb625a">cafe_cmd_lh_test</a> (int argc, char *argv[])</td></tr>
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<tr class="memitem:accafdef1ab81d1d542aa0f51eca4a2bc"><td class="memItemLeft" align="right" valign="top"><a class="el" href="family_8h.html#a1de673dd9010607687c8ab1bf318c19d">pErrorStruct</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#accafdef1ab81d1d542aa0f51eca4a2bc">cafe_shell_create_error_matrix_from_estimate</a> (<a class="el" href="cafe__shell_8h.html#a7e86eeb5f7fc48869e805c9f1142959e">pErrorMeasure</a> errormeasure)</td></tr>
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<tr class="memitem:a30d43878ad983c12064b6cf045bf527f"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#a30d43878ad983c12064b6cf045bf527f">cafe_shell_free_errorstruct</a> (<a class="el" href="family_8h.html#a1de673dd9010607687c8ab1bf318c19d">pErrorStruct</a> errormodel)</td></tr>
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<tr class="memitem:a8faa4a95fff0566664ffdd9dadedce5f"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#a8faa4a95fff0566664ffdd9dadedce5f">cafe_shell_read_freq_from_measures</a> (char *file1, char *file2, int *sizeFreq)</td></tr>
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<tr class="memitem:afe1be43cf6e0bc3becc948e1e9231a26"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#afe1be43cf6e0bc3becc948e1e9231a26">cafe_shell_read_error_double_measure</a> (char *error1, char *error2, int **observed_pairs, int maxFamilySize)</td></tr>
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<tr class="memitem:a03c463d0c1e8479e831db068ea6d1276"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#a03c463d0c1e8479e831db068ea6d1276">cafe_shell_read_error_true_measure</a> (char *errorfile, char *truefile, int **observed_pairs, int maxFamilySize)</td></tr>
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<tr class="memitem:a4737bceb299747d22acc9fa66e6ef8f4"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#a4737bceb299747d22acc9fa66e6ef8f4">__loglikelihood_pairs_from_double_measure</a> (double *parameters, void *args)</td></tr>
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<tr class="memitem:aa57d692e06a2a8311c3246511ebc4858"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#aa57d692e06a2a8311c3246511ebc4858">__loglikelihood_pairs_from_true_measure</a> (double *parameters, void *args)</td></tr>
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<tr class="memitem:a02df56f228387e09be7ff8c46dd74aeb"><td class="memItemLeft" align="right" valign="top"><a class="el" href="cafe__shell_8h.html#a7e86eeb5f7fc48869e805c9f1142959e">pErrorMeasure</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#a02df56f228387e09be7ff8c46dd74aeb">cafe_shell_estimate_error_double_measure</a> (char *error1, char *error2, int b_symmetric, int max_diff, int b_peakzero)</td></tr>
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<tr class="memitem:af88911447cbda363544a8d48332dd59c"><td class="memItemLeft" align="right" valign="top"><a class="el" href="cafe__shell_8h.html#a7e86eeb5f7fc48869e805c9f1142959e">pErrorMeasure</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#af88911447cbda363544a8d48332dd59c">cafe_shell_estimate_error_true_measure</a> (char *errorfile, char *truefile, int b_symmetric, int max_diff, int b_peakzero)</td></tr>
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<tr class="memitem:ad86d30da8444f046395a602442e54ce6"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#ad86d30da8444f046395a602442e54ce6">cafe_shell_write_error_matrix</a> (<a class="el" href="family_8h.html#a1de673dd9010607687c8ab1bf318c19d">pErrorStruct</a> errormodel, FILE *fp)</td></tr>
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<tr class="memitem:a1433c16be6d8a2d1192dd9f095e8ffaf"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#a1433c16be6d8a2d1192dd9f095e8ffaf">__check_error_model_columnsums</a> (<a class="el" href="family_8h.html#a1de673dd9010607687c8ab1bf318c19d">pErrorStruct</a> errormodel)</td></tr>
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<tr class="memitem:ad85c878199f80b6f7ffab0d3f5f8a4a2"><td class="memItemLeft" align="right" valign="top"><a class="el" href="family_8h.html#a1de673dd9010607687c8ab1bf318c19d">pErrorStruct</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#ad85c878199f80b6f7ffab0d3f5f8a4a2">cafe_shell_set_error_matrix</a> (<a class="el" href="family_8h.html#a1de673dd9010607687c8ab1bf318c19d">pErrorStruct</a> errormodel, char *speciesname)</td></tr>
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<tr class="memitem:a76c01528f87cf7e6476970494839e071"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#a76c01528f87cf7e6476970494839e071">cafe_cmd_esterror</a> (int argc, char *argv[])</td></tr>
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<tr class="memitem:a383eb9ca3d5d416552d544744f31b893"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#a383eb9ca3d5d416552d544744f31b893">cafe_shell_set_error_matrix_from_file</a> (char *filename, char *speciesname)</td></tr>
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<tr class="memitem:aadf1c94ef1f1c3b60b5423e130dc992e"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#aadf1c94ef1f1c3b60b5423e130dc992e">cafe_cmd_error_model</a> (int argc, char *argv[])</td></tr>
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<tr class="memitem:aa6f2686752c07b5e1502704a1d6d21e1"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#aa6f2686752c07b5e1502704a1d6d21e1">cafe_shell_rm_error_model</a> (char *speciesname)</td></tr>
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<tr class="memitem:a13b0da905f042219729619992e9aa70f"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#a13b0da905f042219729619992e9aa70f">cafe_shell_free_error_model</a> ()</td></tr>
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<tr class="memitem:a5042da408e75bc07b76173def161b9fb"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#a5042da408e75bc07b76173def161b9fb">cafe_cmd_no_error_model</a> (int argc, char *argv[])</td></tr>
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<tr class="memitem:a9d491bf96a92a8d04c724e4767ca0e97"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#a9d491bf96a92a8d04c724e4767ca0e97">__backup_original_count</a> ()</td></tr>
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<tr class="memitem:a70b0d690d0b403d1d8149fc8eca22966"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#a70b0d690d0b403d1d8149fc8eca22966">__restore_original_count</a> ()</td></tr>
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<tr class="memitem:a83e8c6105fbfafb06da73dac8e4785e9"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#a83e8c6105fbfafb06da73dac8e4785e9">simulate_misclassification</a> (char *filename)</td></tr>
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<tr class="memitem:a9490772940e906749d3f0721d2b45bd7"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#a9490772940e906749d3f0721d2b45bd7">_cafe_simerror</a> (char *prefix, int repeat)</td></tr>
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<tr class="memitem:abbe36aca1d1e9b22cc4ec3c2e56012ca"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#abbe36aca1d1e9b22cc4ec3c2e56012ca">cafe_cmd_simerror</a> (int argc, char *argv[])</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:a52bf660ab9a3b7f0206fbd8d8311d24b"><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__shell_8c.html#a52bf660ab9a3b7f0206fbd8d8311d24b">cafe_param</a></td></tr>
<tr class="memdesc:a52bf660ab9a3b7f0206fbd8d8311d24b"><td class="mdescLeft"> </td><td class="mdescRight">Holds the global program state that user commands act on. <a href="#a52bf660ab9a3b7f0206fbd8d8311d24b">More...</a><br /></td></tr>
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<tr class="memitem:a727e595e0615190248496afc516bdbef"><td class="memItemLeft" align="right" valign="top"><a class="el" href="tree_8h.html#ac1eda65f4edbb85d380203ffae716b53">pTree</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#a727e595e0615190248496afc516bdbef">tmp_lambda_tree</a></td></tr>
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<tr class="memitem:aebb9c135bfafbe439ffc6c5dcc7b1ec2"><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__shell_8c.html#aebb9c135bfafbe439ffc6c5dcc7b1ec2">cafe_pCD</a></td></tr>
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<tr class="memitem:a2a7dd10e437aaa34998d08c16965d4ab"><td class="memItemLeft" align="right" valign="top"><a class="el" href="structCafeShellCommand.html">CafeShellCommand</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="cafe__shell_8c.html#a2a7dd10e437aaa34998d08c16965d4ab">cafe_cmd</a> []</td></tr>
<tr class="memdesc:a2a7dd10e437aaa34998d08c16965d4ab"><td class="mdescLeft"> </td><td class="mdescRight">Holds the list of commands that are available in Cafe. <a href="#a2a7dd10e437aaa34998d08c16965d4ab">More...</a><br /></td></tr>
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<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><p>Functions corresponding to the commands available in Cafe. </p>
<p>Command list is found in the <a class="el" href="cafe__shell_8c.html#a2a7dd10e437aaa34998d08c16965d4ab" title="Holds the list of commands that are available in Cafe. ">cafe_cmd</a> function </p>
</div><h2 class="groupheader">Macro Definition Documentation</h2>
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<h2 class="memtitle"><span class="permalink"><a href="#a993ec84369cb5e52517ee96843e4aeeb">§ </a></span>STDERR_IF</h2>
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<td class="memname">#define STDERR_IF</td>
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<td></td><td>   if ( a ) { fprintf(stderr,b); return -1; }</td>
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<h2 class="groupheader">Function Documentation</h2>
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<h2 class="memtitle"><span class="permalink"><a href="#a9d491bf96a92a8d04c724e4767ca0e97">§ </a></span>__backup_original_count()</h2>
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<td class="memname">int __backup_original_count </td>
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<h2 class="memtitle"><span class="permalink"><a href="#acd71095c160fb97350ce5a4eee381124">§ </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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<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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<h2 class="memtitle"><span class="permalink"><a href="#ac75fb4cd3489783d289c606c0b5cbd92">§ </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="memname">double __cafe_cluster_lambda_search </td>
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<h2 class="memtitle"><span class="permalink"><a href="#ac238f1cff2445ecf67db2b13cef2d454">§ </a></span>__cafe_cmd_extinct_count_zero()</h2>
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<td class="memname">int __cafe_cmd_extinct_count_zero </td>
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<td class="memname">int __cafe_cmd_lambda_tree </td>
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<h2 class="memtitle"><span class="permalink"><a href="#af9debf3a25638315c5449502247170e8">§ </a></span>__cafe_cmd_log()</h2>
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<h2 class="memtitle"><span class="permalink"><a href="#acd4400722dc63e9b68c71dafe59361cd">§ </a></span>__cafe_cmd_pvalue_print()</h2>
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<td class="memname">void __cafe_cmd_pvalue_print </td>
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<h2 class="memtitle"><span class="permalink"><a href="#a7d64e80e883bf02bd5682640518142a7">§ </a></span>__cafe_cmd_viterbi_family_print()</h2>
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<td class="memname">void __cafe_cmd_viterbi_family_print </td>
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<h2 class="memtitle"><span class="permalink"><a href="#a286c4de17031ff6848ae67e249d87006">§ </a></span>__cafe_cmd_viterbi_print()</h2>
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<td class="memname">void __cafe_cmd_viterbi_print </td>
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<td class="paramname"><em>max</em></td><td>)</td>
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<h2 class="memtitle"><span class="permalink"><a href="#a34c1483ce4852daaad9cbe21652f6318">§ </a></span>__cafe_tree_gainloss_mp_annotation()</h2>
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<td class="memname">double __cafe_tree_gainloss_mp_annotation </td>
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<td class="paramtype"><a class="el" href="utils__string_8h.html#a7174cd6b53997a74bf1df360153ad7b0">pString</a> </td>
<td class="paramname"><em>pstr</em>, </td>
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<td class="paramtype"><a class="el" href="tree_8h.html#aebe844e39a68ff02d3a2526ab3e719be">pTreeNode</a> </td>
<td class="paramname"><em>pnode</em>, </td>
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<td class="paramtype"><a class="el" href="tree_8h.html#a72fe5b32d9eed96d3eeb7add5ec78920">pMetapostConfig</a> </td>
<td class="paramname"><em>pmc</em>, </td>
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<td class="paramtype">va_list </td>
<td class="paramname"><em>ap</em> </td>
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<h2 class="memtitle"><span class="permalink"><a href="#a6be819694edd4e80ef93e495c5234a65">§ </a></span>__cafe_tree_string_gainloss()</h2>
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<td class="memname">void __cafe_tree_string_gainloss </td>
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<td class="paramtype"><a class="el" href="utils__string_8h.html#a7174cd6b53997a74bf1df360153ad7b0">pString</a> </td>
<td class="paramname"><em>pstr</em>, </td>
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<td class="paramtype"><a class="el" href="tree_8h.html#a47c8b5d175cf4f1946a873dd28b77516">pPhylogenyNode</a> </td>
<td class="paramname"><em>ptnode</em> </td>
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<h2 class="memtitle"><span class="permalink"><a href="#a30c2f8b518b2587a73bbbc558be7eccd">§ </a></span>__cafe_tree_string_sum_gainloss()</h2>
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<td class="memname">void __cafe_tree_string_sum_gainloss </td>
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<td class="paramtype"><a class="el" href="utils__string_8h.html#a7174cd6b53997a74bf1df360153ad7b0">pString</a> </td>
<td class="paramname"><em>pstr</em>, </td>
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<td class="paramtype"><a class="el" href="tree_8h.html#a47c8b5d175cf4f1946a873dd28b77516">pPhylogenyNode</a> </td>
<td class="paramname"><em>ptnode</em> </td>
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<h2 class="memtitle"><span class="permalink"><a href="#a1433c16be6d8a2d1192dd9f095e8ffaf">§ </a></span>__check_error_model_columnsums()</h2>
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<td class="memname">int __check_error_model_columnsums </td>
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<td class="paramtype"><a class="el" href="family_8h.html#a1de673dd9010607687c8ab1bf318c19d">pErrorStruct</a> </td>
<td class="paramname"><em>errormodel</em></td><td>)</td>
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<h2 class="memtitle"><span class="permalink"><a href="#adad5789514cd2867f277154cc4505353">§ </a></span>__hg_norm_cdf_func()</h2>
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<td class="memname">double __hg_norm_cdf_func </td>
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<td class="paramtype">double </td>
<td class="paramname"><em>p</em>, </td>
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<h2 class="memtitle"><span class="permalink"><a href="#a3ecfe3f073604e17aef011acd664572b">§ </a></span>__hg_print_sim_extinct()</h2>
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<td class="memname">void __hg_print_sim_extinct </td>
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<td class="paramtype"><a class="el" href="mathfunc_8h.html#a77d1d0f2a1af3df93f2884cf22a29075">pHistogram</a> ** </td>
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<td class="paramtype"><a class="el" href="mathfunc_8h.html#a77d1d0f2a1af3df93f2884cf22a29075">pHistogram</a> * </td>
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<td class="paramtype"><a class="el" href="mathfunc_8h.html#a77d1d0f2a1af3df93f2884cf22a29075">pHistogram</a> </td>
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<td class="paramname"><em>num_trials</em> </td>
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<h2 class="memtitle"><span class="permalink"><a href="#a4737bceb299747d22acc9fa66e6ef8f4">§ </a></span>__loglikelihood_pairs_from_double_measure()</h2>
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<td class="memname">double __loglikelihood_pairs_from_double_measure </td>
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<h2 class="memtitle"><span class="permalink"><a href="#aa57d692e06a2a8311c3246511ebc4858">§ </a></span>__loglikelihood_pairs_from_true_measure()</h2>
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<h2 class="memtitle"><span class="permalink"><a href="#a126800fe1f55608fef53e4766fcc81ef">§ </a></span>_cafe_cross_validate_by_family()</h2>
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<h2 class="memtitle"><span class="permalink"><a href="#a749fae32c89708a04836b0ebfbd2340f">§ </a></span>_cafe_cross_validate_by_species()</h2>
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<h2 class="memtitle"><span class="permalink"><a href="#a9490772940e906749d3f0721d2b45bd7">§ </a></span>_cafe_simerror()</h2>
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<p>to check how simex is working generate data with additional error (Ystar) by applying the misclassification matrix to the true data ( random sampling of true factors=f, with probabilities following the column=f of the misclassification matrix ) then run simex on the variable with error (Ystar), and compare it with the true model (based on Y) and the naive model(based on Ystar).</p>
<p>first find the naive estimator by assuming there is no error in the data. then we will add even more error and store the estimates for each dataset with increasing error (k = 0.5, 1, 1.5, 2) so in the end we have (1+number of lambda) * (number of parameters) estimates. for each i = k we run the estimate j = B number of times. each time add error by applying the misclassification matrix = errormatrix^k update the estimates based on error added data, store the mean estimates for all B runs. then predict the estimates at k=-1 </p>
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<h2 class="memtitle"><span class="permalink"><a href="#ab7b88336a604d317c2eea7ebcb1371e8">§ </a></span>cafe_cmd_branchlength()</h2>
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<h2 class="memtitle"><span class="permalink"><a href="#a8c9eeffa3b9732dd1a46b30475e86ff5">§ </a></span>cafe_cmd_crossvalidation_by_family()</h2>
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<h2 class="memtitle"><span class="permalink"><a href="#a9303ebc40d4020bdf2d539dd76d59c7e">§ </a></span>cafe_cmd_crossvalidation_by_species()</h2>
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<h2 class="memtitle"><span class="permalink"><a href="#aadf1c94ef1f1c3b60b5423e130dc992e">§ </a></span>cafe_cmd_error_model()</h2>
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