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globals_c.html
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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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<meta name="generator" content="Doxygen 1.8.12"/>
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<title>CAFE: Globals</title>
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<tr style="height: 56px;">
<td id="projectalign" style="padding-left: 0.5em;">
<div id="projectname">CAFE
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</tr>
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<div class="contents">
<div class="textblock">Here is a list of all functions, variables, defines, enums, and typedefs with links to the files they belong to:</div>
<h3><a id="index_c"></a>- c -</h3><ul>
<li>cache
: <a class="el" href="birthdeath_8c.html#a018ffb515cded9e77be4179f12b3aca6">birthdeath.c</a>
</li>
<li>cafe_best_lambda_by_fminsearch()
: <a class="el" href="cafe_8h.html#a6276b68a56c6403d815d512080dc46a4">cafe.h</a>
, <a class="el" href="cafe__main_8c.html#a6276b68a56c6403d815d512080dc46a4">cafe_main.c</a>
</li>
<li>cafe_best_lambda_mu_by_fminsearch()
: <a class="el" href="cafe_8h.html#ac44e4ab06944b45e4a1cfd923c8eb9cb">cafe.h</a>
, <a class="el" href="cafe__main_8c.html#ac44e4ab06944b45e4a1cfd923c8eb9cb">cafe_main.c</a>
</li>
<li>cafe_best_lambda_mu_eqbg_by_fminsearch()
: <a class="el" href="cafe_8h.html#a60fc1de991d240a8cb40ab7a98a06a91">cafe.h</a>
</li>
<li>cafe_branch_cutting()
: <a class="el" href="cafe__main_8c.html#adf53bc2a22b3f10d28b5bf5c226b371d">cafe_main.c</a>
, <a class="el" href="cafe_8h.html#adf53bc2a22b3f10d28b5bf5c226b371d">cafe.h</a>
</li>
<li>cafe_cmd
: <a class="el" href="cafe__shell_8c.html#a2a7dd10e437aaa34998d08c16965d4ab">cafe_shell.c</a>
, <a class="el" href="cafe__shell_8h.html#a2a7dd10e437aaa34998d08c16965d4ab">cafe_shell.h</a>
</li>
<li>cafe_cmd_atoi()
: <a class="el" href="test_8cpp.html#aeefb1a71eefbb474b2507c0a01f70326">test.cpp</a>
</li>
<li>cafe_cmd_branchlength()
: <a class="el" href="cafe__shell_8c.html#ab7b88336a604d317c2eea7ebcb1371e8">cafe_shell.c</a>
, <a class="el" href="cafe__shell_8h.html#ab7b88336a604d317c2eea7ebcb1371e8">cafe_shell.h</a>
</li>
<li>cafe_cmd_crossvalidation_by_family()
: <a class="el" href="cafe__shell_8c.html#a8c9eeffa3b9732dd1a46b30475e86ff5">cafe_shell.c</a>
, <a class="el" href="cafe__shell_8h.html#a8c9eeffa3b9732dd1a46b30475e86ff5">cafe_shell.h</a>
</li>
<li>cafe_cmd_crossvalidation_by_species()
: <a class="el" href="cafe__shell_8c.html#a9303ebc40d4020bdf2d539dd76d59c7e">cafe_shell.c</a>
, <a class="el" href="cafe__shell_8h.html#a9303ebc40d4020bdf2d539dd76d59c7e">cafe_shell.h</a>
</li>
<li>cafe_cmd_date()
: <a class="el" href="cafe__commands_8cpp.html#a0fee3d7bb08141c8cdd09ea75259c80d">cafe_commands.cpp</a>
, <a class="el" href="cafe__commands_8h.html#a12e6bbaf64d232b049afc8320e618e12">cafe_commands.h</a>
</li>
<li>cafe_cmd_echo()
: <a class="el" href="cafe__commands_8cpp.html#a2e2e57f336f5adbb29963d50d209d95e">cafe_commands.cpp</a>
, <a class="el" href="cafe__commands_8h.html#a8b2fc001384e0d3c6b9be92650296efe">cafe_commands.h</a>
</li>
<li>cafe_cmd_error_model()
: <a class="el" href="cafe__shell_8c.html#aadf1c94ef1f1c3b60b5423e130dc992e">cafe_shell.c</a>
, <a class="el" href="cafe__shell_8h.html#aadf1c94ef1f1c3b60b5423e130dc992e">cafe_shell.h</a>
</li>
<li>cafe_cmd_esterror()
: <a class="el" href="cafe__shell_8c.html#a76c01528f87cf7e6476970494839e071">cafe_shell.c</a>
, <a class="el" href="cafe__shell_8h.html#a76c01528f87cf7e6476970494839e071">cafe_shell.h</a>
</li>
<li>cafe_cmd_exit()
: <a class="el" href="cafe__commands_8cpp.html#ac716e78d309f12bdad68adf8c615fc33">cafe_commands.cpp</a>
, <a class="el" href="cafe__commands_8h.html#a92f695a37bd42b626b1bd43c2daa2d7e">cafe_commands.h</a>
</li>
<li>cafe_cmd_extinct()
: <a class="el" href="group__Commands.html#ga92a5e46c97a72fdc0e6201f093fdfd6f">cafe_shell.c</a>
, <a class="el" href="group__Commands.html#ga92a5e46c97a72fdc0e6201f093fdfd6f">cafe_shell.h</a>
</li>
<li>cafe_cmd_family()
: <a class="el" href="cafe__shell_8c.html#a412249d0e5fa5ca96da764607f38b6b3">cafe_shell.c</a>
, <a class="el" href="cafe__shell_8h.html#a412249d0e5fa5ca96da764607f38b6b3">cafe_shell.h</a>
</li>
<li>cafe_cmd_gainloss()
: <a class="el" href="cafe__commands_8cpp.html#a3d8c232706e37588381ac7c2293ca81a">cafe_commands.cpp</a>
, <a class="el" href="cafe__commands_8h.html#a83bf15faf005ce18f8207893de62b2ce">cafe_commands.h</a>
</li>
<li>cafe_cmd_generate_random_family()
: <a class="el" href="cafe__commands_8cpp.html#a97ee2f4aac2ea946025528289dabb332">cafe_commands.cpp</a>
, <a class="el" href="cafe__commands_8h.html#ac1ed4ef75f3a0677cea6a5f35fc0f83e">cafe_commands.h</a>
</li>
<li>cafe_cmd_lambda()
: <a class="el" href="lambda_8cpp.html#a2202b68042bcc0f0e0426fc222e25d1e">lambda.cpp</a>
, <a class="el" href="lambda_8h.html#a8ecc5bfbbd1d0ac61689fa3fce598ff2">lambda.h</a>
</li>
<li>cafe_cmd_lambda_mu()
: <a class="el" href="cafe__shell_8c.html#a72ba1fc4c9e0e0d85b1a9db4712ba9e2">cafe_shell.c</a>
, <a class="el" href="cafe__shell_8h.html#a72ba1fc4c9e0e0d85b1a9db4712ba9e2">cafe_shell.h</a>
</li>
<li>cafe_cmd_lh_test()
: <a class="el" href="cafe__shell_8c.html#a1662205f714c446de8c6e470a9fb625a">cafe_shell.c</a>
, <a class="el" href="cafe__shell_8h.html#a1662205f714c446de8c6e470a9fb625a">cafe_shell.h</a>
</li>
<li>cafe_cmd_list()
: <a class="el" href="cafe__commands_8cpp.html#acc2cbf09211f152407d6d2b85ef94fae">cafe_commands.cpp</a>
, <a class="el" href="cafe__commands_8h.html#ac1ff1844757ace68bee073533a83a55a">cafe_commands.h</a>
</li>
<li>cafe_cmd_load()
: <a class="el" href="cafe__shell_8c.html#a135a720eb39deef29c04097793ceb20e">cafe_shell.c</a>
, <a class="el" href="cafe__shell_8h.html#a135a720eb39deef29c04097793ceb20e">cafe_shell.h</a>
</li>
<li>cafe_cmd_log()
: <a class="el" href="group__Commands.html#gae4ff9c32d2375ec8487fd99d140d9134">cafe_shell.c</a>
, <a class="el" href="group__Commands.html#gae4ff9c32d2375ec8487fd99d140d9134">cafe_shell.h</a>
</li>
<li>cafe_cmd_no_error_model()
: <a class="el" href="cafe__shell_8c.html#a5042da408e75bc07b76173def161b9fb">cafe_shell.c</a>
, <a class="el" href="cafe__shell_8h.html#a5042da408e75bc07b76173def161b9fb">cafe_shell.h</a>
</li>
<li>cafe_cmd_print_param()
: <a class="el" href="cafe__shell_8c.html#a3610b289bae55dc6033b293591ec9662">cafe_shell.c</a>
, <a class="el" href="cafe__shell_8h.html#a3610b289bae55dc6033b293591ec9662">cafe_shell.h</a>
</li>
<li>cafe_cmd_pvalue()
: <a class="el" href="cafe__shell_8c.html#a3041a622c7035c1e3bcf48bd5c9609ea">cafe_shell.c</a>
, <a class="el" href="cafe__shell_8h.html#a3041a622c7035c1e3bcf48bd5c9609ea">cafe_shell.h</a>
</li>
<li>cafe_cmd_reconstruction_accuracy()
: <a class="el" href="cafe__shell_8c.html#a938b50ea7ad7ec3b3753c876025d3337">cafe_shell.c</a>
, <a class="el" href="cafe__shell_8h.html#a938b50ea7ad7ec3b3753c876025d3337">cafe_shell.h</a>
</li>
<li>cafe_cmd_report()
: <a class="el" href="reports_8cpp.html#a26da30e3825a05dd824a262d3bad7c9d">reports.cpp</a>
, <a class="el" href="reports_8h.html#a26da30e3825a05dd824a262d3bad7c9d">reports.h</a>
</li>
<li>cafe_cmd_retrieve()
: <a class="el" href="cafe__shell_8c.html#a7486ee9a8e4fc6f64458540628e3026f">cafe_shell.c</a>
, <a class="el" href="cafe__shell_8h.html#a7486ee9a8e4fc6f64458540628e3026f">cafe_shell.h</a>
</li>
<li>cafe_cmd_root_dist()
: <a class="el" href="group__Commands.html#gadce5da31072dab7c010d7e7e4d39320c">cafe_shell.c</a>
, <a class="el" href="group__Commands.html#gadce5da31072dab7c010d7e7e4d39320c">cafe_shell.h</a>
</li>
<li>cafe_cmd_save()
: <a class="el" href="cafe__shell_8c.html#aae07af4b31abc31ec549e9e95b1a1cfc">cafe_shell.c</a>
, <a class="el" href="cafe__shell_8h.html#aae07af4b31abc31ec549e9e95b1a1cfc">cafe_shell.h</a>
</li>
<li>cafe_cmd_score()
: <a class="el" href="cafe__shell_8c.html#a58d8686f881b69565a59206239f5d3da">cafe_shell.c</a>
, <a class="el" href="cafe__shell_8h.html#a58d8686f881b69565a59206239f5d3da">cafe_shell.h</a>
</li>
<li>cafe_cmd_sim_extinct()
: <a class="el" href="group__Commands.html#ga1f8d08708948fe6cc47a16d64cff2d4d">cafe_shell.c</a>
, <a class="el" href="group__Commands.html#ga1f8d08708948fe6cc47a16d64cff2d4d">cafe_shell.h</a>
</li>
<li>cafe_cmd_simerror()
: <a class="el" href="cafe__shell_8c.html#abbe36aca1d1e9b22cc4ec3c2e56012ca">cafe_shell.c</a>
, <a class="el" href="cafe__shell_8h.html#abbe36aca1d1e9b22cc4ec3c2e56012ca">cafe_shell.h</a>
</li>
<li>cafe_cmd_source()
: <a class="el" href="cafe__commands_8cpp.html#aeb4bec27e73c830de804198a76b0b285">cafe_commands.cpp</a>
, <a class="el" href="cafe__commands_8h.html#a1d7bfdc8357f1dd1aab426ce78fb69e3">cafe_commands.h</a>
</li>
<li>cafe_cmd_test
: <a class="el" href="test_8cpp.html#abceefb643f648b5e7d0a4076bde92a60">test.cpp</a>
</li>
<li>cafe_cmd_tree()
: <a class="el" href="cafe__shell_8c.html#a18d0bfb6dae3e9520ffb9c5a534d1aa5">cafe_shell.c</a>
, <a class="el" href="cafe__shell_8h.html#a18d0bfb6dae3e9520ffb9c5a534d1aa5">cafe_shell.h</a>
</li>
<li>cafe_cmd_version()
: <a class="el" href="cafe__shell_8c.html#a633fa681f5ff83b688c7666bf36892a4">cafe_shell.c</a>
, <a class="el" href="cafe__shell_8h.html#a633fa681f5ff83b688c7666bf36892a4">cafe_shell.h</a>
</li>
<li>cafe_cmd_viterbi()
: <a class="el" href="cafe__shell_8c.html#a32ece228b3ba07db144f79452afdb125">cafe_shell.c</a>
, <a class="el" href="cafe__shell_8h.html#a32ece228b3ba07db144f79452afdb125">cafe_shell.h</a>
</li>
<li>cafe_command
: <a class="el" href="cafe__shell_8h.html#a51ff5547bac4f92fa086dc7357394899">cafe_shell.h</a>
</li>
<li>cafe_command2
: <a class="el" href="cafe__commands_8cpp.html#a549a72f5f7e18b4eec1906be169d1bd5">cafe_commands.cpp</a>
</li>
<li>cafe_conditional_distribution()
: <a class="el" href="cafe_8h.html#a28b01083e12d908b4a3d54a7d1d02726">cafe.h</a>
, <a class="el" href="cafe__main_8c.html#a28b01083e12d908b4a3d54a7d1d02726">cafe_main.c</a>
</li>
<li>cafe_copy_parameters()
: <a class="el" href="cafe_8h.html#a0a54e602c59702bd6cc844332b6c2a7a">cafe.h</a>
, <a class="el" href="cafe__main_8c.html#a0a54e602c59702bd6cc844332b6c2a7a">cafe_main.c</a>
</li>
<li>cafe_do_report()
: <a class="el" href="reports_8cpp.html#aec15be77e9f103422ad291915530eff8">reports.cpp</a>
</li>
<li>cafe_each_best_lambda_by_fminsearch()
: <a class="el" href="cafe_8h.html#abc6a1f95000e9407117ed11904be6864">cafe.h</a>
, <a class="el" href="cafe__main_8c.html#abc6a1f95000e9407117ed11904be6864">cafe_main.c</a>
</li>
<li>cafe_family_add_item()
: <a class="el" href="cafe_8h.html#a8040846f0c636e51a56193028a1ff59c">cafe.h</a>
, <a class="el" href="cafe__family_8c.html#a8040846f0c636e51a56193028a1ff59c">cafe_family.c</a>
</li>
<li>cafe_family_clean_cvfiles_byfamily()
: <a class="el" href="cafe_8h.html#a3d85789c6ea2856d46189f9c9fa1d646">cafe.h</a>
, <a class="el" href="cafe__family_8c.html#a3d85789c6ea2856d46189f9c9fa1d646">cafe_family.c</a>
</li>
<li>cafe_family_clean_cvfiles_byspecies()
: <a class="el" href="cafe_8h.html#a77b40a8fbd5a7221a2b3003ba8317b7f">cafe.h</a>
, <a class="el" href="cafe__family_8c.html#a77b40a8fbd5a7221a2b3003ba8317b7f">cafe_family.c</a>
</li>
<li>cafe_family_filter()
: <a class="el" href="cafe_8h.html#a3c807482b5b5d8c827b53fcd6b55c29f">cafe.h</a>
, <a class="el" href="cafe__family_8c.html#a3c807482b5b5d8c827b53fcd6b55c29f">cafe_family.c</a>
</li>
<li>cafe_family_free()
: <a class="el" href="cafe_8h.html#a5c952ff06eb0153eb4021557da22005d">cafe.h</a>
, <a class="el" href="cafe__family_8c.html#a5c952ff06eb0153eb4021557da22005d">cafe_family.c</a>
</li>
<li>cafe_family_get_family_item()
: <a class="el" href="cafe_8h.html#ad87d747e20a51592e6ce2920b32632c3">cafe.h</a>
, <a class="el" href="cafe__family_8c.html#ad87d747e20a51592e6ce2920b32632c3">cafe_family.c</a>
</li>
<li>cafe_family_get_index()
: <a class="el" href="cafe_8h.html#aadf7360c79f3684e025281f746be2c6e">cafe.h</a>
, <a class="el" href="cafe__family_8c.html#aadf7360c79f3684e025281f746be2c6e">cafe_family.c</a>
</li>
<li>cafe_family_get_species_index()
: <a class="el" href="cafe_8h.html#ab4b6f407abda4eaea384743c2b1f9a02">cafe.h</a>
, <a class="el" href="cafe__family_8c.html#ab4b6f407abda4eaea384743c2b1f9a02">cafe_family.c</a>
</li>
<li>cafe_family_init()
: <a class="el" href="cafe_8h.html#ac14285c2a2a32972442da6f3e6503e7a">cafe.h</a>
, <a class="el" href="cafe__family_8c.html#ac14285c2a2a32972442da6f3e6503e7a">cafe_family.c</a>
</li>
<li>cafe_family_item_free()
: <a class="el" href="cafe_8h.html#a2b38ef57e2463389db47965232c5ac98">cafe.h</a>
, <a class="el" href="cafe__family_8c.html#a2b38ef57e2463389db47965232c5ac98">cafe_family.c</a>
</li>
<li>cafe_family_new()
: <a class="el" href="cafe_8h.html#a5551576d8d41b117a0b48b346a96fece">cafe.h</a>
, <a class="el" href="cafe__family_8c.html#a5551576d8d41b117a0b48b346a96fece">cafe_family.c</a>
</li>
<li>cafe_family_print_cluster_membership()
: <a class="el" href="cafe_8h.html#ae881b40f3dab7d87a0db2d6bfb74653f">cafe.h</a>
, <a class="el" href="cafe__family_8c.html#ae881b40f3dab7d87a0db2d6bfb74653f">cafe_family.c</a>
</li>
<li>cafe_family_read_cvquery()
: <a class="el" href="cafe__family_8c.html#a3fd75aa9642276bb88e81e75e32a69df">cafe_family.c</a>
</li>
<li>cafe_family_read_query_family()
: <a class="el" href="cafe_8h.html#a5676d8efaccbc638b19e6028ab859e34">cafe.h</a>
, <a class="el" href="cafe__family_8c.html#a5676d8efaccbc638b19e6028ab859e34">cafe_family.c</a>
</li>
<li>cafe_family_read_validate_species()
: <a class="el" href="cafe_8h.html#a9a579f7aa906dda3855e76e0c966bace">cafe.h</a>
, <a class="el" href="cafe__family_8c.html#a9a579f7aa906dda3855e76e0c966bace">cafe_family.c</a>
</li>
<li>cafe_family_reset_maxlh()
: <a class="el" href="cafe_8h.html#ae3f218b4542078f06e79492ffa8f42e7">cafe.h</a>
, <a class="el" href="cafe__family_8c.html#ae3f218b4542078f06e79492ffa8f42e7">cafe_family.c</a>
</li>
<li>cafe_family_set_size()
: <a class="el" href="cafe_8h.html#ad44ab3a046a4ffa4ea72ccbb024a83c1">cafe.h</a>
, <a class="el" href="cafe__family_8c.html#ad44ab3a046a4ffa4ea72ccbb024a83c1">cafe_family.c</a>
</li>
<li>cafe_family_set_size_by_species()
: <a class="el" href="cafe_8h.html#a3f6a9deb3b221594e1357c270c3e31f4">cafe.h</a>
, <a class="el" href="cafe__family_8c.html#a3f6a9deb3b221594e1357c270c3e31f4">cafe_family.c</a>
</li>
<li>cafe_family_set_size_for_split()
: <a class="el" href="cafe_8h.html#a26c9f424ab9c48359becc47840ec6776">cafe.h</a>
, <a class="el" href="cafe__family_8c.html#a26c9f424ab9c48359becc47840ec6776">cafe_family.c</a>
</li>
<li>cafe_family_set_size_with_family()
: <a class="el" href="cafe_8h.html#a671e8a36c74d72e2f7e9427ef48e0418">cafe.h</a>
, <a class="el" href="cafe__family_8c.html#a671e8a36c74d72e2f7e9427ef48e0418">cafe_family.c</a>
</li>
<li>cafe_family_set_size_with_family_forced()
: <a class="el" href="cafe__family_8c.html#acb02e7cc3e369942626ca994ff0c823d">cafe_family.c</a>
, <a class="el" href="cafe_8h.html#acb02e7cc3e369942626ca994ff0c823d">cafe.h</a>
</li>
<li>cafe_family_set_species_index()
: <a class="el" href="cafe_8h.html#a5d2f54e37c36caf8d59811800f4f559b">cafe.h</a>
, <a class="el" href="cafe__family_8c.html#a5d2f54e37c36caf8d59811800f4f559b">cafe_family.c</a>
</li>
<li>cafe_family_set_truesize_with_family()
: <a class="el" href="cafe_8h.html#a1d18390e5a79329e67b3278e174c473d">cafe.h</a>
, <a class="el" href="cafe__family_8c.html#a1d18390e5a79329e67b3278e174c473d">cafe_family.c</a>
</li>
<li>cafe_family_split_cvfiles_byfamily()
: <a class="el" href="cafe_8h.html#ac195a0fc4ae61c03289db9cd8da09a63">cafe.h</a>
, <a class="el" href="cafe__family_8c.html#ac195a0fc4ae61c03289db9cd8da09a63">cafe_family.c</a>
</li>
<li>cafe_family_split_cvfiles_byspecies()
: <a class="el" href="cafe_8h.html#afba87dc49ad3f7b86e5306b9c7ea5208">cafe.h</a>
, <a class="el" href="cafe__family_8c.html#afba87dc49ad3f7b86e5306b9c7ea5208">cafe_family.c</a>
</li>
<li>cafe_free_birthdeath_cache()
: <a class="el" href="cafe_8h.html#af2ed23d5716b6075fa222a6b6cf326a8">cafe.h</a>
, <a class="el" href="cafe__main_8c.html#af2ed23d5716b6075fa222a6b6cf326a8">cafe_main.c</a>
</li>
<li>cafe_free_copy_parameters()
: <a class="el" href="cafe_8h.html#a72db0fc19498016c5023420f510bad9c">cafe.h</a>
, <a class="el" href="cafe__main_8c.html#a72db0fc19498016c5023420f510bad9c">cafe_main.c</a>
</li>
<li>cafe_get_clustered_posterior()
: <a class="el" href="cafe__main_8c.html#a68b1cb11f1e2231ed8e6f02864982471">cafe_main.c</a>
</li>
<li>cafe_get_posterior()
: <a class="el" href="cafe_8h.html#af1e282522a8c75ed3ea3a186ccbba962">cafe.h</a>
, <a class="el" href="cafe__main_8c.html#af1e282522a8c75ed3ea3a186ccbba962">cafe_main.c</a>
</li>
<li>cafe_lambda_distribution()
: <a class="el" href="cafe_8h.html#a40e1fa38255505c9a57ad590afed6ddb">cafe.h</a>
, <a class="el" href="cafe__main_8c.html#a40e1fa38255505c9a57ad590afed6ddb">cafe_main.c</a>
</li>
<li>cafe_lambda_set_default()
: <a class="el" href="cafe_8h.html#a4a269c2694070c23c8dd643d7bf219e1">cafe.h</a>
, <a class="el" href="cafe__main_8c.html#a4a269c2694070c23c8dd643d7bf219e1">cafe_main.c</a>
</li>
<li>cafe_lhr_for_diff_lambdas()
: <a class="el" href="likelihood__ratio_8cpp.html#a3a818db13b41bd861132bd0aab6f1d9d">likelihood_ratio.cpp</a>
, <a class="el" href="likelihood__ratio_8h.html#a3a818db13b41bd861132bd0aab6f1d9d">likelihood_ratio.h</a>
</li>
<li>cafe_likelihood_ratio_test()
: <a class="el" href="cafe_8h.html#abc9d347c972a12d7a86277efdd4c6b9d">cafe.h</a>
, <a class="el" href="cafe__main_8c.html#abc9d347c972a12d7a86277efdd4c6b9d">cafe_main.c</a>
</li>
<li>cafe_log()
: <a class="el" href="cafe_8h.html#a41fd4a22d96314d20f0c9192c6f02339">cafe.h</a>
, <a class="el" href="cafe__commands_8cpp.html#a41fd4a22d96314d20f0c9192c6f02339">cafe_commands.cpp</a>
, <a class="el" href="cafe__main_8c.html#a41fd4a22d96314d20f0c9192c6f02339">cafe_main.c</a>
</li>
<li>cafe_param
: <a class="el" href="cafe__commands_8cpp.html#a52bf660ab9a3b7f0206fbd8d8311d24b">cafe_commands.cpp</a>
, <a class="el" href="cafe__shell_8c.html#a52bf660ab9a3b7f0206fbd8d8311d24b">cafe_shell.c</a>
, <a class="el" href="lambda_8cpp.html#a52bf660ab9a3b7f0206fbd8d8311d24b">lambda.cpp</a>
, <a class="el" href="main_8cpp.html#a52bf660ab9a3b7f0206fbd8d8311d24b">main.cpp</a>
, <a class="el" href="lambda__tests_8cpp.html#a52bf660ab9a3b7f0206fbd8d8311d24b">lambda_tests.cpp</a>
</li>
<li>cafe_pCD
: <a class="el" href="cafe__commands_8cpp.html#aebb9c135bfafbe439ffc6c5dcc7b1ec2">cafe_commands.cpp</a>
, <a class="el" href="cafe__shell_8c.html#aebb9c135bfafbe439ffc6c5dcc7b1ec2">cafe_shell.c</a>
, <a class="el" href="reports_8cpp.html#aebb9c135bfafbe439ffc6c5dcc7b1ec2">reports.cpp</a>
</li>
<li>cafe_report()
: <a class="el" href="cafe_8h.html#ad5b326684624583b7c4274b9dd36b048">cafe.h</a>
, <a class="el" href="cafe__report_8c.html#ad5b326684624583b7c4274b9dd36b048">cafe_report.c</a>
</li>
<li>CAFE_REPORT_HTML
: <a class="el" href="cafe_8h.html#a941d27c486c2ae1ffb39a864a7ec5cc4a1ad4b84850cdafe9597dd8000dc7f248">cafe.h</a>
</li>
<li>cafe_report_load_bc_or_lhr_list()
: <a class="el" href="cafe__report_8c.html#a7ef121ec6039843318c41056085c1df9">cafe_report.c</a>
</li>
<li>cafe_report_load_data_double_list()
: <a class="el" href="cafe__report_8c.html#a59e468789130db9667f1566824f51ce6">cafe_report.c</a>
</li>
<li>cafe_report_load_data_double_pairs()
: <a class="el" href="cafe__report_8c.html#a84fae6026fc17195c25c25bdcae6cf63">cafe_report.c</a>
</li>
<li>cafe_report_load_data_int_pairs()
: <a class="el" href="cafe__report_8c.html#a3f377593c99ab70f58db44638e3ae95a">cafe_report.c</a>
</li>
<li>cafe_report_load_viterbi_pvalue()
: <a class="el" href="cafe__report_8c.html#a547772d7a4fff301ee74f9c2315070b8">cafe_report.c</a>
</li>
<li>cafe_report_mp_annotation()
: <a class="el" href="cafe__report_8c.html#a12576ecb85402535c67b905f3db47684">cafe_report.c</a>
</li>
<li>cafe_report_mp_remark()
: <a class="el" href="cafe__report_8c.html#a35f7648dab74a561f3a0dab1da93f4dc">cafe_report.c</a>
</li>
<li>cafe_report_mp_summary()
: <a class="el" href="cafe__report_8c.html#adcbf4b0daa3d4c75ddf75a18c4ea963d">cafe_report.c</a>
</li>
<li>cafe_report_pdf()
: <a class="el" href="cafe__report_8c.html#aa1cf20aee3a75b4db9261400c08d62ac">cafe_report.c</a>
</li>
<li>CAFE_REPORT_PDF
: <a class="el" href="cafe_8h.html#a941d27c486c2ae1ffb39a864a7ec5cc4a8c91521fc74032cd1d6013092f96a3dd">cafe.h</a>
</li>
<li>cafe_report_retrieve_data()
: <a class="el" href="cafe_8h.html#a1f28d19d9122353dbfba5f4091368a8e">cafe.h</a>
, <a class="el" href="cafe__report_8c.html#a1f28d19d9122353dbfba5f4091368a8e">cafe_report.c</a>
</li>
<li>cafe_report_set_viterbi()
: <a class="el" href="cafe__report_8c.html#af6fa46be637c881b86dc0ab1f2dbaaa5">cafe_report.c</a>
</li>
<li>cafe_report_summary_metapost()
: <a class="el" href="cafe__report_8c.html#a783a1f0a59d59b0ca935530dd9da4c99">cafe_report.c</a>
</li>
<li>cafe_report_text()
: <a class="el" href="cafe__report_8c.html#af532325c6796eda3b26ef31e03356498">cafe_report.c</a>
</li>
<li>CAFE_REPORT_TEXT
: <a class="el" href="cafe_8h.html#a941d27c486c2ae1ffb39a864a7ec5cc4af665c1b9f44643486f81aa6d78ac8957">cafe.h</a>
</li>
<li>cafe_set_birthdeath_cache()
: <a class="el" href="cafe__main_8c.html#aeb4ab292a60df57301d00e11cfd01822">cafe_main.c</a>
, <a class="el" href="cafe_8h.html#aeb4ab292a60df57301d00e11cfd01822">cafe.h</a>
</li>
<li>cafe_set_birthdeath_cache_thread()
: <a class="el" href="cafe_8h.html#a41e16620ee39f8c3fcfcdfce15f8f874">cafe.h</a>
, <a class="el" href="cafe__main_8c.html#a41e16620ee39f8c3fcfcdfce15f8f874">cafe_main.c</a>
</li>
<li>cafe_set_prior_rfsize_empirical()
: <a class="el" href="cafe__main_8c.html#af9ae3976765e29062e2d678af52322da">cafe_main.c</a>
, <a class="el" href="cafe_8h.html#af9ae3976765e29062e2d678af52322da">cafe.h</a>
</li>
<li>cafe_set_prior_rfsize_poisson_lambda()
: <a class="el" href="cafe__main_8c.html#ac7cc56df589132d2e2d9306da6413497">cafe_main.c</a>
</li>
<li>cafe_shell_build_argument()
: <a class="el" href="cafe__shell_8c.html#a3adf5f4770c6c89b152417ee4b03e360">cafe_shell.c</a>
, <a class="el" href="cafe__shell_8h.html#a3adf5f4770c6c89b152417ee4b03e360">cafe_shell.h</a>
</li>
<li>cafe_shell_clear_param()
: <a class="el" href="cafe__commands_8cpp.html#a3a0b1c333839b083bf301f9418d44a40">cafe_commands.cpp</a>
, <a class="el" href="cafe__shell_8c.html#a3a0b1c333839b083bf301f9418d44a40">cafe_shell.c</a>
</li>
<li>cafe_shell_create_error_matrix_from_estimate()
: <a class="el" href="cafe__shell_8c.html#accafdef1ab81d1d542aa0f51eca4a2bc">cafe_shell.c</a>
</li>
<li>cafe_shell_dispatch_command()
: <a class="el" href="cafe__commands_8cpp.html#aa8a41a2eb004f7f58059a2f76c1ae979">cafe_commands.cpp</a>
, <a class="el" href="cafe__commands_8h.html#aa8a41a2eb004f7f58059a2f76c1ae979">cafe_commands.h</a>
</li>
<li>cafe_shell_dispatch_commandf()
: <a class="el" href="cafe__commands_8cpp.html#a41a58278ae144c504961cd76cc907ccd">cafe_commands.cpp</a>
, <a class="el" href="cafe__shell_8c.html#a41a58278ae144c504961cd76cc907ccd">cafe_shell.c</a>
</li>
<li>cafe_shell_estimate_error_double_measure()
: <a class="el" href="cafe__shell_8c.html#a02df56f228387e09be7ff8c46dd74aeb">cafe_shell.c</a>
</li>
<li>cafe_shell_estimate_error_true_measure()
: <a class="el" href="cafe__shell_8c.html#af88911447cbda363544a8d48332dd59c">cafe_shell.c</a>
</li>
<li>CAFE_SHELL_EXIT
: <a class="el" href="cafe__shell_8h.html#a938245e829e8fe18be69f63031bd3b7da47d68f1580d224f79e73d03276db8bbc">cafe_shell.h</a>
</li>
<li>cafe_shell_free_error_model()
: <a class="el" href="cafe__shell_8c.html#a13b0da905f042219729619992e9aa70f">cafe_shell.c</a>
</li>
<li>cafe_shell_free_errorstruct()
: <a class="el" href="cafe__shell_8c.html#a30d43878ad983c12064b6cf045bf527f">cafe_shell.c</a>
</li>
<li>cafe_shell_get_argument()
: <a class="el" href="cafe__shell_8c.html#a288f5f2ddc4acf86d785deff10ed8e21">cafe_shell.c</a>
</li>
<li>cafe_shell_init()
: <a class="el" href="cafe__shell_8c.html#a6f6ca009bdfa80e59a3e2550412abfe4">cafe_shell.c</a>
, <a class="el" href="cafe__shell_8h.html#a6f6ca009bdfa80e59a3e2550412abfe4">cafe_shell.h</a>
</li>
<li>cafe_shell_likelihood()
: <a class="el" href="cafe__shell_8c.html#a1c9350e1a590d596153b08dc28e111cd">cafe_shell.c</a>
</li>
<li>CAFE_SHELL_NO_COMMAND
: <a class="el" href="cafe__shell_8h.html#a938245e829e8fe18be69f63031bd3b7da1f99d7b11913e364c56c5c877dc3170a">cafe_shell.h</a>
</li>
<li>cafe_shell_parse_branchlength()
: <a class="el" href="cafe__shell_8c.html#abb4e63e9f0ba2ca2b3011271f04f6548">cafe_shell.c</a>
</li>
<li>cafe_shell_parse_familysize()
: <a class="el" href="cafe__shell_8c.html#af4aaab71abb20ea8e727b6a92361db89">cafe_shell.c</a>
</li>
<li>cafe_shell_prompt()
: <a class="el" href="cafe__shell_8c.html#adbb978cbbd721d21fcecfd372604af76">cafe_shell.c</a>
, <a class="el" href="cafe__shell_8h.html#adbb978cbbd721d21fcecfd372604af76">cafe_shell.h</a>
</li>
<li>cafe_shell_read_error_double_measure()
: <a class="el" href="cafe__shell_8c.html#afe1be43cf6e0bc3becc948e1e9231a26">cafe_shell.c</a>
</li>
<li>cafe_shell_read_error_true_measure()
: <a class="el" href="cafe__shell_8c.html#a03c463d0c1e8479e831db068ea6d1276">cafe_shell.c</a>
</li>
<li>cafe_shell_read_freq_from_measures()
: <a class="el" href="cafe__shell_8c.html#a8faa4a95fff0566664ffdd9dadedce5f">cafe_shell.c</a>
</li>
<li>cafe_shell_rm_error_model()
: <a class="el" href="cafe__shell_8c.html#aa6f2686752c07b5e1502704a1d6d21e1">cafe_shell.c</a>
</li>
<li>cafe_shell_score()
: <a class="el" href="cafe__shell_8c.html#a7cffc0eb3c396c12222d50a19817fe25">cafe_shell.c</a>
, <a class="el" href="cafe__shell_8h.html#a7cffc0eb3c396c12222d50a19817fe25">cafe_shell.h</a>
</li>
<li>cafe_shell_set_branchlength()
: <a class="el" href="cafe__shell_8c.html#a9e168dbad3b30a2312440acf17f57d60">cafe_shell.c</a>
</li>
<li>cafe_shell_set_error_matrix()
: <a class="el" href="cafe__shell_8c.html#ad85c878199f80b6f7ffab0d3f5f8a4a2">cafe_shell.c</a>
</li>
<li>cafe_shell_set_error_matrix_from_file()
: <a class="el" href="cafe__shell_8c.html#a383eb9ca3d5d416552d544744f31b893">cafe_shell.c</a>
</li>
<li>cafe_shell_set_familysize()
: <a class="el" href="cafe__shell_8c.html#afe9a3e66ef89dac3abaa6a96b694774c">cafe_shell.c</a>
</li>
<li>cafe_shell_set_lambda()
: <a class="el" href="cafe__shell_8c.html#aa4d4e91f878146701ebbb2a9bdec0e58">cafe_shell.c</a>
, <a class="el" href="reports_8cpp.html#aa4d4e91f878146701ebbb2a9bdec0e58">reports.cpp</a>
, <a class="el" href="lambda__tests_8cpp.html#af74ec7bed406c53726038319912602c7">lambda_tests.cpp</a>
, <a class="el" href="lambda_8cpp.html#af74ec7bed406c53726038319912602c7">lambda.cpp</a>
</li>
<li>cafe_shell_set_lambda_mu()
: <a class="el" href="cafe__shell_8c.html#a69136530face607391c301737ac59a50">cafe_shell.c</a>
</li>
<li>cafe_shell_set_sizes()
: <a class="el" href="cafe__shell_8c.html#a82e7144c7b62a989a5fd3d855a1500a8">cafe_shell.c</a>
, <a class="el" href="cafe__shell_8h.html#a82e7144c7b62a989a5fd3d855a1500a8">cafe_shell.h</a>
</li>
<li>cafe_shell_write_error_matrix()
: <a class="el" href="cafe__shell_8c.html#ad86d30da8444f046395a602442e54ce6">cafe_shell.c</a>
</li>
<li>cafe_tree_clustered_likelihood()
: <a class="el" href="cafe_8h.html#a15e83cea0140d989624ca021fc1316ee">cafe.h</a>
, <a class="el" href="cafe__tree_8c.html#a15e83cea0140d989624ca021fc1316ee">cafe_tree.c</a>
</li>
<li>cafe_tree_clustered_viterbi()
: <a class="el" href="cafe__tree_8c.html#ae7993697889a09c5f071cf1fa7563da1">cafe_tree.c</a>
, <a class="el" href="cafe_8h.html#ae7993697889a09c5f071cf1fa7563da1">cafe.h</a>
</li>
<li>cafe_tree_conditional_distribution()
: <a class="el" href="cafe_8h.html#a45d46d04142f35bd3b8ad2b106719976">cafe.h</a>
, <a class="el" href="cafe__tree_8c.html#a45d46d04142f35bd3b8ad2b106719976">cafe_tree.c</a>
</li>
<li>cafe_tree_copy()
: <a class="el" href="cafe__tree_8c.html#aaacc74335f3e18b9aae2dce03ca3ba95">cafe_tree.c</a>
, <a class="el" href="cafe_8h.html#aaacc74335f3e18b9aae2dce03ca3ba95">cafe.h</a>
</li>
<li>cafe_tree_free()
: <a class="el" href="cafe_8h.html#a399b895da5463457ea8dcd62b31131dd">cafe.h</a>
, <a class="el" href="cafe__tree_8c.html#a399b895da5463457ea8dcd62b31131dd">cafe_tree.c</a>
</li>
<li>cafe_tree_get_default_mpconfig()
: <a class="el" href="cafe_8h.html#a5095cbb3b4652801b2da11512d0aadb0">cafe.h</a>
, <a class="el" href="cafe__tree_8c.html#a5095cbb3b4652801b2da11512d0aadb0">cafe_tree.c</a>
</li>
<li>cafe_tree_likelihood()
: <a class="el" href="cafe__tree_8c.html#a0e6b1095efd5b1cbccf38139848de2f5">cafe_tree.c</a>
, <a class="el" href="cafe_8h.html#a0e6b1095efd5b1cbccf38139848de2f5">cafe.h</a>
</li>
<li>cafe_tree_metapost()
: <a class="el" href="cafe__tree_8c.html#ab02dad48034bd27652cf2d011b71e98e">cafe_tree.c</a>
, <a class="el" href="cafe_8h.html#ab02dad48034bd27652cf2d011b71e98e">cafe.h</a>
</li>
<li>cafe_tree_mp_annotation()
: <a class="el" href="cafe__tree_8c.html#aa801f48d06f60d6a7f22695ea0f2fc1e">cafe_tree.c</a>
, <a class="el" href="cafe_8h.html#a583f3346ac4cd4ac0da2d295ab798631">cafe.h</a>
</li>
<li>cafe_tree_mp_remark()
: <a class="el" href="cafe__shell_8c.html#ab994a6c910f779f783ab58d245c1c5d7">cafe_shell.c</a>
, <a class="el" href="cafe__tree_8c.html#ab994a6c910f779f783ab58d245c1c5d7">cafe_tree.c</a>
, <a class="el" href="cafe_8h.html#a06ef016855f349979f4cef37ac196b1d">cafe.h</a>
</li>
<li>cafe_tree_new()
: <a class="el" href="cafe_8h.html#ab108f5d959d962bcfea2cbaab0a9fd10">cafe.h</a>
, <a class="el" href="cafe__tree_8c.html#ab108f5d959d962bcfea2cbaab0a9fd10">cafe_tree.c</a>
</li>
<li>cafe_tree_new_empty_node()
: <a class="el" href="cafe_8h.html#abf94be4e512caec06b7bbe6391c054a5">cafe.h</a>
, <a class="el" href="cafe__tree_8c.html#a011da805ee2cfebac9290554242a8355">cafe_tree.c</a>
</li>
<li>cafe_tree_node_copy()
: <a class="el" href="cafe__tree_8c.html#a00cfedbd547c6db177c1f88bfd8210be">cafe_tree.c</a>
</li>
<li>cafe_tree_node_free_clustered_likelihoods()
: <a class="el" href="cafe_8h.html#a376f0defba082c9243fe89ccb93de0fa">cafe.h</a>
, <a class="el" href="cafe__tree_8c.html#a376f0defba082c9243fe89ccb93de0fa">cafe_tree.c</a>
</li>
<li>cafe_tree_p_values()
: <a class="el" href="cafe__tree_8c.html#ac4a9ad319cf10a53ac37115183946951">cafe_tree.c</a>
, <a class="el" href="cafe_8h.html#a0b50a33f038ffa9a07ce30621f2cac77">cafe.h</a>
</li>
<li>cafe_tree_p_values_of_two_trees()
: <a class="el" href="cafe_8h.html#a31b86ce1fc4f0db908fe9fa7fc7fb2f3">cafe.h</a>
, <a class="el" href="cafe__tree_8c.html#a8251dabcb52172da3776385b9fef0158">cafe_tree.c</a>
</li>
<li>cafe_tree_parse_node()
: <a class="el" href="cafe__tree_8c.html#ad08d95479c047e932edc6ec7bf7aef3a">cafe_tree.c</a>
</li>
<li>cafe_tree_random_familysize()
: <a class="el" href="cafe__tree_8c.html#ab203b685b05382fbb18d1dd78f81fafb">cafe_tree.c</a>
, <a class="el" href="cafe_8h.html#ab203b685b05382fbb18d1dd78f81fafb">cafe.h</a>
</li>
<li>cafe_tree_random_probabilities()
: <a class="el" href="cafe__tree_8c.html#a2890c7c910b5839063244d54b5896dd3">cafe_tree.c</a>
, <a class="el" href="cafe_8h.html#a2890c7c910b5839063244d54b5896dd3">cafe.h</a>
</li>
<li>cafe_tree_set_birthdeath()
: <a class="el" href="family_8h.html#a41fd9c8764418b4ce51f6b66a2471553">family.h</a>
, <a class="el" href="cafe__tree_8c.html#a41fd9c8764418b4ce51f6b66a2471553">cafe_tree.c</a>
</li>
<li>cafe_tree_set_parameters()
: <a class="el" href="cafe_8h.html#a4a9ceeeaec1f37178a4ad6519f815ad6">cafe.h</a>
, <a class="el" href="cafe__tree_8c.html#a4a9ceeeaec1f37178a4ad6519f815ad6">cafe_tree.c</a>
</li>
<li>cafe_tree_split()
: <a class="el" href="cafe__tree_8c.html#a59a369f120ab05629245fb707dabe441">cafe_tree.c</a>
, <a class="el" href="cafe_8h.html#a59a369f120ab05629245fb707dabe441">cafe.h</a>
</li>
<li>cafe_tree_string()
: <a class="el" href="cafe_8h.html#a9a17222518181cb6ac05c07aaf5e24ca">cafe.h</a>
, <a class="el" href="cafe__tree_8c.html#a9a17222518181cb6ac05c07aaf5e24ca">cafe_tree.c</a>
</li>
<li>cafe_tree_string_familysize()
: <a class="el" href="cafe__tree_8c.html#a1153877204eeb1a10be18ce0b1f8441d">cafe_tree.c</a>
</li>
<li>cafe_tree_string_familysize_lambda()
: <a class="el" href="cafe__tree_8c.html#af4fdb853fab02b6c7ebbc7595f6ce87d">cafe_tree.c</a>
</li>
<li>cafe_tree_string_id()
: <a class="el" href="cafe__tree_8c.html#a3965d669f5f3e118547696bdf6d28def">cafe_tree.c</a>
</li>
<li>cafe_tree_string_lambda()
: <a class="el" href="cafe__tree_8c.html#ad3436926d8fb0a0119e3686c0e4709f1">cafe_tree.c</a>
</li>
<li>cafe_tree_string_name()
: <a class="el" href="cafe__tree_8c.html#a311afa341f0108d84af1366cec16779c">cafe_tree.c</a>
, <a class="el" href="cafe_8h.html#a311afa341f0108d84af1366cec16779c">cafe.h</a>
</li>
<li>cafe_tree_string_print()
: <a class="el" href="cafe_8h.html#a9ef8856ece7dbaba92fde32c4107a72c">cafe.h</a>
, <a class="el" href="cafe__tree_8c.html#a9ef8856ece7dbaba92fde32c4107a72c">cafe_tree.c</a>
</li>
<li>cafe_tree_string_with_familysize()
: <a class="el" href="cafe_8h.html#a75e35397e2535cef3466c37ab9c2cb8f">cafe.h</a>
, <a class="el" href="cafe__tree_8c.html#a75e35397e2535cef3466c37ab9c2cb8f">cafe_tree.c</a>
</li>
<li>cafe_tree_string_with_familysize_lambda()
: <a class="el" href="cafe__tree_8c.html#a2b97ef12468c64ad91fe9ee06a225e4b">cafe_tree.c</a>
, <a class="el" href="cafe_8h.html#a2b97ef12468c64ad91fe9ee06a225e4b">cafe.h</a>
</li>
<li>cafe_tree_string_with_id()
: <a class="el" href="cafe__tree_8c.html#ad446b2b7910dffecb400baa082f1c3ff">cafe_tree.c</a>
, <a class="el" href="cafe_8h.html#ad446b2b7910dffecb400baa082f1c3ff">cafe.h</a>
</li>
<li>cafe_tree_string_with_lambda()
: <a class="el" href="cafe__tree_8c.html#a539b2a7307047507d08628f9232dbf8a">cafe_tree.c</a>
, <a class="el" href="cafe_8h.html#a539b2a7307047507d08628f9232dbf8a">cafe.h</a>
</li>
<li>cafe_tree_viterbi()
: <a class="el" href="cafe_8h.html#ad797e3a6bd04c8fcaab1209548b4f5ef">cafe.h</a>
, <a class="el" href="cafe__tree_8c.html#ad797e3a6bd04c8fcaab1209548b4f5ef">cafe_tree.c</a>
</li>
<li>cafe_tree_viterbi_posterior()
: <a class="el" href="cafe__tree_8c.html#a86b7d92c6d9843ce4010340025eecf42">cafe_tree.c</a>
, <a class="el" href="cafe_8h.html#a86b7d92c6d9843ce4010340025eecf42">cafe.h</a>
</li>
<li>cafe_viterbi()
: <a class="el" href="cafe__main_8c.html#a50a8afe408546920e6a0920cec164ed2">cafe_main.c</a>
, <a class="el" href="cafe_8h.html#a50a8afe408546920e6a0920cec164ed2">cafe.h</a>
</li>
<li>cafe_viterbi_print()
: <a class="el" href="cafe__main_8c.html#a2a37b9a22b8a43e5331507752fae96b2">cafe_main.c</a>
</li>
<li>CafeParam
: <a class="el" href="family_8h.html#a26254f945d1f4c483aea4cd5e96324d1">family.h</a>
</li>
<li>chi2cdf()
: <a class="el" href="mathfunc_8c.html#a95ae3d35765701d3d63e6c6438c91a3f">mathfunc.c</a>
, <a class="el" href="mathfunc_8h.html#a95ae3d35765701d3d63e6c6438c91a3f">mathfunc.h</a>
</li>
<li>chi2pdf()
: <a class="el" href="mathfunc_8h.html#a10366590c5864e55816da5823be8e554">mathfunc.h</a>
, <a class="el" href="mathfunc_8c.html#a10366590c5864e55816da5823be8e554">mathfunc.c</a>
</li>
<li>choose()
: <a class="el" href="mathfunc_8c.html#a707a5cc89fcff7a0fef6f65c4d64b473">mathfunc.c</a>
, <a class="el" href="mathfunc_8h.html#a707a5cc89fcff7a0fef6f65c4d64b473">mathfunc.h</a>
</li>
<li>chooseln()
: <a class="el" href="mathfunc_8h.html#a981cdf6ae1abe4e62961f9be4bd800e8">mathfunc.h</a>
, <a class="el" href="mathfunc_8c.html#a981cdf6ae1abe4e62961f9be4bd800e8">mathfunc.c</a>
</li>
<li>chooseln_cache_free()
: <a class="el" href="birthdeath_8h.html#accc6679ce0e73edbf1b3065eacb2bd61">birthdeath.h</a>
, <a class="el" href="birthdeath_8c.html#accc6679ce0e73edbf1b3065eacb2bd61">birthdeath.c</a>
</li>
<li>chooseln_cache_free2()
: <a class="el" href="chooseln__cache_8h.html#a72c55174fbca89e417a369c58a3c2bef">chooseln_cache.h</a>
, <a class="el" href="chooseln__cache_8c.html#a72c55174fbca89e417a369c58a3c2bef">chooseln_cache.c</a>
</li>
<li>chooseln_cache_init()
: <a class="el" href="birthdeath_8h.html#a4e2bebf13208d2df0bba306e360c53b2">birthdeath.h</a>
, <a class="el" href="birthdeath_8c.html#a4e2bebf13208d2df0bba306e360c53b2">birthdeath.c</a>
</li>
<li>chooseln_cache_init2()
: <a class="el" href="chooseln__cache_8h.html#af35e9032479ce4d487f05b818d1d4617">chooseln_cache.h</a>
, <a class="el" href="chooseln__cache_8c.html#af35e9032479ce4d487f05b818d1d4617">chooseln_cache.c</a>
</li>
<li>chooseln_cache_preset()
: <a class="el" href="chooseln__cache_8c.html#a46a05454a50ecfde39170bd983eec1ee">chooseln_cache.c</a>
</li>
<li>chooseln_cache_resize()
: <a class="el" href="birthdeath_8h.html#ab2c5d1b9de4e210bd5c7a01f0ea134db">birthdeath.h</a>
, <a class="el" href="birthdeath_8c.html#ab2c5d1b9de4e210bd5c7a01f0ea134db">birthdeath.c</a>
</li>
<li>chooseln_cache_resize2()
: <a class="el" href="chooseln__cache_8h.html#a53c8975bc57db35246f3054cf87a3752">chooseln_cache.h</a>
, <a class="el" href="chooseln__cache_8c.html#a53c8975bc57db35246f3054cf87a3752">chooseln_cache.c</a>
</li>
<li>chooseln_cache_size
: <a class="el" href="cafe__main_8c.html#ab022c096f87385cf60838c6d14634b61">cafe_main.c</a>
</li>
<li>chooseln_get()
: <a class="el" href="birthdeath_8c.html#a5e79f9fd4597837276dba3f31f922073">birthdeath.c</a>
</li>
<li>chooseln_is_init()
: <a class="el" href="birthdeath_8h.html#a7d8009f8674aba748af4967df333eb19">birthdeath.h</a>
, <a class="el" href="birthdeath_8c.html#a7d8009f8674aba748af4967df333eb19">birthdeath.c</a>
</li>
<li>chooseln_is_init2()
: <a class="el" href="chooseln__cache_8c.html#a67fdc1eb280c631c487c2c7d129fd428">chooseln_cache.c</a>
, <a class="el" href="chooseln__cache_8h.html#a67fdc1eb280c631c487c2c7d129fd428">chooseln_cache.h</a>
</li>
<li>clear_node_viterbis()
: <a class="el" href="cafe__commands_8cpp.html#a1bded1aae62b13ed6b6fb6eb4a7ffe5f">cafe_commands.cpp</a>
</li>
<li>clear_tree_viterbis()
: <a class="el" href="cafe__commands_8cpp.html#a43d02eb548a90ec237f858ba70cd5113">cafe_commands.cpp</a>
, <a class="el" href="cafe__commands_8h.html#aa815aa35cb1ab8394c7107036deae1eb">cafe_commands.h</a>
</li>
<li>cmp_paired_t_test()
: <a class="el" href="mathfunc_8h.html#a2642aeb3f1225708f01579799271a881">mathfunc.h</a>
, <a class="el" href="grpcmp_8c.html#a2642aeb3f1225708f01579799271a881">grpcmp.c</a>
</li>
<li>cmp_two_indep_chi2test()
: <a class="el" href="grpcmp_8c.html#acc849b13f45bc17f02f9e5e633bc20f7">grpcmp.c</a>
, <a class="el" href="mathfunc_8h.html#acc849b13f45bc17f02f9e5e633bc20f7">mathfunc.h</a>
</li>
<li>cmp_two_indep_t_test()
: <a class="el" href="grpcmp_8c.html#a163870569c3ec80ae9c5351613df9fc7">grpcmp.c</a>
, <a class="el" href="mathfunc_8h.html#a163870569c3ec80ae9c5351613df9fc7">mathfunc.h</a>
</li>
<li>comp_double()
: <a class="el" href="mathfunc_8c.html#a8a8cf00084684d31bd1385a85ec4b63f">mathfunc.c</a>
, <a class="el" href="mathfunc_8h.html#a8a8cf00084684d31bd1385a85ec4b63f">mathfunc.h</a>
</li>
<li>compute_birthdeath_rates()
: <a class="el" href="birthdeath_8c.html#ab81fd61e47717a7a47f7b6e0855ff7ea">birthdeath.c</a>
, <a class="el" href="birthdeath_8h.html#ab81fd61e47717a7a47f7b6e0855ff7ea">birthdeath.h</a>
</li>
<li>compute_internal_node_likelihood()
: <a class="el" href="cafe__tree_8c.html#af9688d286dddb037fabf069aa7209b86">cafe_tree.c</a>
, <a class="el" href="cafe_8h.html#af9688d286dddb037fabf069aa7209b86">cafe.h</a>
</li>
<li>compute_leaf_node_likelihood()
: <a class="el" href="cafe__tree_8c.html#a513624edfd78aba059fa55835275f11d">cafe_tree.c</a>
, <a class="el" href="cafe_8h.html#a513624edfd78aba059fa55835275f11d">cafe.h</a>
</li>
<li>compute_likelihood()
: <a class="el" href="cafe_8h.html#a64a3240a3e126af2fed45b08cde3d2c0">cafe.h</a>
, <a class="el" href="cafe__tree_8c.html#a64a3240a3e126af2fed45b08cde3d2c0">cafe_tree.c</a>
</li>
</ul>
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