26040088c562a25829edd6fb9ac71417 *DESCRIPTION
9f59d56f4fe7d696650e1ac68baadb2d *NAMESPACE
fb812544cfbc62692fd7569ea5cb3987 *R/are_clock_models.R
c4e3c712ff99348024c8f701adef93a4 *R/are_equal_mcmcs.R
4f9bdbc7bd0c3ea02d2298fec9a61b58 *R/are_equal_screenlogs.R
ed8eb9df166064c320087494f845e82e *R/are_equal_tracelogs.R
ffef5593565613d0e9f62e69c0266041 *R/are_equal_treelogs.R
db21ea5683c7940c66b5c75b42cdc832 *R/are_equal_xml_files.R
087b0076a0ccfe19323d0ae305331879 *R/are_equal_xml_lines.R
f1ca40e197537633bd754cf2b3537a23 *R/are_equivalent_xmls.R
48ddff92ff6a023cead3db7050229763 *R/are_fasta_filenames.R
e0c7ac9d3c83efbecf6ae73bdba6394d *R/are_ids.R
fc1ddaa896b0923ebcfc37a4ba9dc69f *R/are_init_clock_models.R
677b1473a90bd6ac84653ee114803b83 *R/are_init_mrca_priors.R
934103fc55107a8c564b076c5f2535f5 *R/are_init_site_models.R
572913943c0eceb0b982e2b56f0f444f *R/are_init_tree_priors.R
68f5e8afb463912ed2607c0a912f6200 *R/are_mrca_align_ids_in_fasta.R
a03079b9d1d06f5fb6273d797e534fc5 *R/are_mrca_priors.R
f62baabc894eb9d030fc3cf802242d59 *R/are_mrca_taxon_names_in_fasta.R
4a0cc21ee8da11c22acdfc48db824fe5 *R/are_site_models.R
9a0fc18c79fcbe7a696b7def69848fdb *R/are_tree_priors.R
1c175f133514bdeb6b73b13ac968146d *R/beautier.R
7c49dcfb65e70be96d0fd92cdd988f1e *R/check_alignment_id.R
45cc86f1bf73cf16d5b778f3debbf62a *R/check_beauti_options.R
c124e6584e97d146a902a1152536ae79 *R/check_clock_model.R
43f4323ac85dc7567884204faa41d41c *R/check_clock_models.R
91f69cb70c2db7e2d1ad814f501423e1 *R/check_file_and_model_agree.R
3f0671723ea8288bec64e8607e0da3a0 *R/check_file_exists.R
3e5a9da48068bef55f44c18c8ba13b7b *R/check_gamma_site_model.R
afae6bab446e03476ed0cd4db259092c *R/check_inference_model.R
b3707ecf7223a0cd02f8ba65653b293c *R/check_inference_models.R
b9fa27545f0c455a6eaa5bae56f4f3e7 *R/check_is_monophyletic.R
4b81424b00ab783f565013b80de9175c *R/check_log_mode.R
0e4ee2a4fdb6334aca20b5de83e54913 *R/check_log_sort.R
48135a30ae4b6232c77c28a72c27dcc7 *R/check_mcmc.R
8a111980ddb1d1554b22c251371dd42d *R/check_mcmc_nested_sampling.R
55e9a5134b77c27ddd83403322883649 *R/check_mrca_prior.R
d6d9f37f256c854bac30fd6670861a8f *R/check_mrca_prior_name.R
bbfb7341275ed25396548930a66d29fa *R/check_mrca_prior_taxa_names.R
f772c8d1e1e00de4b6d2bcf38b8376e8 *R/check_phylogeny.R
d2731d8ec81b9ebdc7375d70a0142e35 *R/check_screenlog.R
df9deb96504b0d6420326f1b4135ee67 *R/check_site_model.R
5433a7e12c61a8d7db54322c69eaebae *R/check_site_models.R
fc106e5cfd81d01a7f8f96cb023849ee *R/check_store_every.R
b23881d5d67c944993a327d73322dc31 *R/check_tracelog.R
70995ad7088354be35ef40e2edfcc969 *R/check_tree_prior.R
66bcc4533849fba27eaa91fe3991aa82 *R/check_tree_priors.R
7d2fa9330099963c5248f1f0ed72c2dd *R/check_treelog.R
aaf58d7603bd7ee138c151f7acd54b4e *R/clock_model_to_xml_lh_distr.R
2fc55168a6af75a7382cdd0a977a65f4 *R/clock_model_to_xml_operators.R
a886aaa3985c35482a4cfe1bde85ff75 *R/clock_model_to_xml_prior_distr.R
8e5e0eac722c6af9a846cd2b9929aabc *R/clock_model_to_xml_state.R
96974c4c96ea3ba2359e066e820c139f *R/clock_model_to_xml_tracelog.R
6db8140a57774fa1397d25fb826b4590 *R/clock_model_to_xml_treelogger.R
bbab59e04736568547b3dc139f34578f *R/clock_models_to_xml_operators.R
3ca1515cd0a6e916d30b173f013811d3 *R/clock_models_to_xml_prior_distr.R
de06f98876dceaac9dc9b87f893df407 *R/clock_models_to_xml_state.R
1de3303d30a143422adffe4d705594b5 *R/clock_models_to_xml_tracelog.R
6ac7214a400bb069ea4a2dc0513038c3 *R/compare_lines.R
c26c6e4f014d17b9becc9b8708a178f5 *R/count_trailing_spaces.R
cbe37ebf75f314a4b73de78fb668274b *R/create_beast2_beast_xml.R
4689e7668c055d74e0a47a366c3d33a0 *R/create_beast2_input.R
c38256dd452fc4bd43c9ad6e57f585cc *R/create_beast2_input_beast.R
c39c428af7d4ce4d847bf8656b8629ae *R/create_beast2_input_data.R
1d50492d40a3a56a1f91f40a9612b00b *R/create_beast2_input_data_sequences.R
a200d1b691d78f18ba2220f1db69e494 *R/create_beast2_input_distr.R
9ab02b10f69b37414398bb5113208db1 *R/create_beast2_input_file.R
8e2987171b650054b62547042aee38d7 *R/create_beast2_input_file_from_model.R
26fbfdfc7854270495c79e77d1ab1b88 *R/create_beast2_input_from_model.R
c49974f4ca86525f8f1d1931e298c875 *R/create_beast2_input_init.R
79bbcd544cea305a918b020cac330b5f *R/create_beast2_input_map.R
4d8791438fc656d2d3d69d3f9f6767df *R/create_beast2_input_operators.R
7ecef73d9b41765c1c8df36eb4b05ee3 *R/create_beast2_input_run.R
7316237b7c0f86b093672dbe12a1ee08 *R/create_beast2_input_state.R
12e777c207d7e44d2a02a24e3727700b *R/create_beast2_input_xml.R
a2d1b7f7515fc0c64aa64a3c1976e2a3 *R/create_beauti_options.R
e5ad73b58be2be0c702b9fd256bdc95e *R/create_clock_model.R
3bc6562739c9b28f072ac1edc06fd68a *R/create_clock_model_from_name.R
b75b2c2600f963b4aab90f5113d1a77a *R/create_clock_models.R
ae3c0a990de92cdfe1e3bcbaca8351ef *R/create_clock_models_from_names.R
fceeab0126d184172c9a09540420bbcd *R/create_data_xml.R
2cf1762cf8ddc6759f27f50e35143e5b *R/create_distr.R
78ac5c34d327619c6e5807ec6fd4687e *R/create_gamma_site_model.R
4f6ebcc40106637aa05731c269fa5b90 *R/create_inference_model.R
b69bfc7c1cd5c28a1a0a7e08609d78d6 *R/create_loggers_xml.R
74974561523dd230e2211986b92d7a7a *R/create_mcmc.R
f28a30ddb56a08890f89d1809651c282 *R/create_mcmc_nested_sampling.R
c961fb5ae98fba5da924c05e2f141800 *R/create_mrca_prior.R
1ef2b096adbee03ccc62f5530f69a414 *R/create_param.R
79ebe966cbc8f24ec9258d9e3d190d28 *R/create_screenlog.R
682083bf2ad016a6546ee5ce41ca0215 *R/create_screenlog_xml.R
7d9368587ee2ca7fa04db19354253800 *R/create_site_model.R
a5906a7d9ef3af8c2f27d58b00575a73 *R/create_site_model_from_name.R
491854e41ac89396fa42da9919caedee *R/create_site_models.R
bfedb539f413711b7e61c7a6519b394a *R/create_site_models_from_names.R
efc83ab5d0fa3216d9b2dc2850d50970 *R/create_temp_screenlog_filename.R
c96a91a8ab5e8b6f3c931dfd67d159b8 *R/create_temp_tracelog_filename.R
46fb34602daf962a97ba3c6f6b5c108c *R/create_temp_treelog_filename.R
6fd080c5dfc33042a6dc03b62d13675a *R/create_test_inference_model.R
258e52e495b53e12347face0951addb2 *R/create_test_mcmc.R
af0b4f99bfb06b104969fc4dc87c7fec *R/create_test_ns_inference_model.R
7275002a3734ed5302b5788ed1530eb1 *R/create_test_ns_mcmc.R
11e9098365ec5526179d03ad5fa5a07d *R/create_test_screenlog.R
947aa794ee60191aeaa47a42b8cf27b8 *R/create_test_tracelog.R
429aa19cc9407a944b533e63e9e5ee1b *R/create_test_treelog.R
d644a5872ab472d1a5bd74b02caa6263 *R/create_tracelog.R
81a788117212420a7eb08e5a0cb9c14f *R/create_tracelog_xml.R
7155fa95ae6b8dad7e7b16997d02ee09 *R/create_trait_set_string.R
4fc697cc09daac07d98e2a25688bc5b3 *R/create_tree_prior.R
6f0f47b56614bf36d0bbe5f00e68f1c1 *R/create_tree_priors.R
090f43e58863974f3cd38b624b8122c4 *R/create_treelog.R
c3d2e567dc2aa204969acfd3e3e16c02 *R/create_treelog_xml.R
f2826854b2afe3e17fec3110f7d37767 *R/default_params_doc.R
676538b1ec46646df6ffd815dcc0616c *R/distr_to_xml.R
2c724cd2007244652fefc0f217b1e622 *R/extract_xml_loggers_from_lines.R
2382cbbbc65c270542826c8fbb78abdd *R/extract_xml_operators_from_lines.R
3fbe7d789eaf610f22abbcb0f1ad157a *R/extract_xml_section_from_lines.R
59cd35321be04509ff1c9892d63b6b3a *R/fasta_to_phylo.R
f417a88916f526297944f806aa4975f9 *R/fasta_to_sequences.R
d9da5f48ba1931ceef4998fb351bce98 *R/fastas_to_phylos.R
9dc598365bd6cacdac4e420ede9e8290 *R/find_clock_model.R
a16de56c97e2df439bf454e9ce8af610 *R/find_first_regex_line.R
e9493c32772f9addf460566b4ab82035 *R/find_first_xml_opening_tag_line.R
9f4e5a1c851534772ccf6e49c6008762 *R/find_last_regex_line.R
62ce7511c75bd0b277dec0b755653caa *R/find_last_xml_closing_tag_line.R
31522b293cf6e89d1abd9669bf639a64 *R/freq_equilibrium_to_xml.R
1a4d79004b535cec32688e1358fa444c *R/gamma_site_model_to_xml_prior_distr.R
12eef2e80d78cde875b7857996021280 *R/gamma_site_model_to_xml_state.R
e603a52d6aae71c918548679a24c43bf *R/gamma_site_models_to_xml_prior_distr.R
78d699303db8f8451cfe685cafb0dc7c *R/get_alignment_id.R
b48392b5d26087e668271fcf7c811e88 *R/get_alignment_ids.R
9acc09e4930ded79d7e3978daa1d43fa *R/get_beautier_path.R
db6ca7b250fbac3e536ac4984094a50b *R/get_beautier_paths.R
5d4c22420667672cd36cf1e2ac7114d4 *R/get_clock_model_name.R
391cdc7bcda1c4fe476155d288667b66 *R/get_clock_model_names.R
143bef63f6bbfe68ead128058e56dad6 *R/get_clock_models_ids.R
4f25dbc47d3b7cd5b686221395b6e373 *R/get_crown_age.R
69e88d16671be5a1151a3e66ea4013b3 *R/get_distr_n_params.R
d05c1941ab38838e47d6c57374d49eef *R/get_distr_names.R
c111e92c7522ea984902d040d0ac4d31 *R/get_file_base_sans_ext.R
14631c5a11a67bc80be5daa2700258e4 *R/get_freq_equilibrium_names.R
4003c82bcf76d2a7f528a04dda3fe938 *R/get_gamma_site_model_n_distrs.R
6a276902a1997a1140de32dd8bfa046b *R/get_gamma_site_model_n_params.R
5ff1237a11dc23140f174e77289f9e02 *R/get_has_non_strict_clock_model.R
2bda5bd98b81e56e0915943673d2c299 *R/get_log_modes.R
1d553e38e9acb80ca60cac2c3d16843c *R/get_log_sorts.R
4c954bc483ff851e94f8e34b77e5d492 *R/get_n_taxa.R
0bf710d715b25388b3676834a6f1ab3f *R/get_operator_id_pre.R
1a44b189d3d6ea31ae1a921c72ebc688 *R/get_param_names.R
9a2c501e0d04f8e7a6c31bbede6e46fc *R/get_site_model_n_distrs.R
a61233fe78a48bc348b33931cd31503d *R/get_site_model_n_params.R
f6ff8bb2c71aaaddfa4aa2f9dd0b8ec4 *R/get_site_model_names.R
30b8a509b78fd85314c30b8e36cac3a9 *R/get_site_models_n_distrs.R
2760df075b864be5fe70b3c12bb9bc39 *R/get_site_models_n_params.R
f16cbe315c194fb2474ebc2cbd348e7b *R/get_taxa_names.R
62f40ff25da7f1421ae24170058ccf5a *R/get_test_filenames.R
4f35fde3edfa62708f41458447a19160 *R/get_tree_prior_n_distrs.R
cc018b92f42741e503cf1acc8316f84d *R/get_tree_prior_n_params.R
5d3bf952f6c8a25dbf4183c28a98a24a *R/get_tree_prior_names.R
52a980e1c298961d92a9ba6c1e1e2d09 *R/get_tree_priors_n_distrs.R
869907073d6b7400cf8794bf3f79bf2a *R/get_tree_priors_n_params.R
841a73ab6c47bb8ce3004e196636d9ef *R/get_xml_closing_tag.R
20ab41c1363f596b95a9019bd95b23f8 *R/get_xml_opening_tag.R
d6e27cfcec3b27c295828f513bf8998b *R/has_mrca_prior.R
ba0f9e8d232c574bbfffe82a0d6155f9 *R/has_xml_closing_tag.R
c29267736cdf8c357c8121523f6d9651 *R/has_xml_opening_tag.R
46bbcf5453321cb1d51c60ce704ac282 *R/has_xml_short_closing_tag.R
83e917b9058759fc48a613b24ef186c7 *R/indent.R
9875cd3486800f5b0807c795581fea50 *R/init_clock_models.R
a7f3bf1669b3415b6a302c6bb5e825ec *R/init_distr.R
7da520c756d02e15b719e7a66dbbc963 *R/init_gamma_site_model.R
8f1912b77a914d980e330188851eb161 *R/init_inference_model.R
756f3b5a2c22074776da143d72d3c7a2 *R/init_mrca_prior.R
5aefd404bb8d4641d28e17e0b13b90ae *R/init_mrca_priors.R
d77d0efe19e22be40feb5343ea9de446 *R/init_param.R
b1b53890efaafc6fd3524e2ee9b1936c *R/init_site_models.R
3c7643d364e2c6954a5271be53dfee68 *R/init_tree_priors.R
4086f1819a76b2ab91fab2466a988f76 *R/interspace.R
9a9d5e559dab4bea3604a1ccdb108987 *R/is_beauti_options.R
66325398a7ba692bc8cf4fcae8beac13 *R/is_clock_model.R
69654b64b179612d3cf8c183c3ec6bdc *R/is_clock_model_name.R
d8af1a8d594e33a93c30835f3186aa3f *R/is_default_mcmc.R
e7b163a02b738506f102a354e94203b7 *R/is_distr.R
e3b1fe56d561f577b58b69d913a168e6 *R/is_distr_name.R
7e231fdb6f8ce9a87f9a241720cb3f3b *R/is_freq_equilibrium_name.R
08ee3c82be401680fc0a19fb1e275561 *R/is_gamma_site_model.R
12524e8f33d9c31682e021ec430b391b *R/is_id.R
c61f9dc92d414dbba833d2051eb6a78c *R/is_in_patterns.R
a99e75abff88a230f4380bcad65eddd4 *R/is_inference_model.R
1df937faaa826673a1dbf1ed11866eb9 *R/is_init_clock_model.R
161c736151c08a01d0511c2e9d1ae089 *R/is_init_distr.R
1ab0c1fa97af6ea0218dde6e70c9bb69 *R/is_init_gamma_site_model.R
dfd7e71cb64ac9074db6582566782fed *R/is_init_mrca_prior.R
6a9c4c9c590ba81bed9e37bec1c01fbe *R/is_init_param.R
203f9088263cb014d1b9a019b6cd5c61 *R/is_init_site_model.R
dc73d7fa9da32cc76f3629330df84c09 *R/is_init_tree_prior.R
2fe0854edfbf9a83ea18f1ec6974e060 *R/is_mcmc.R
47d11aa0506556f2ac0e2be14cf81310 *R/is_mrca_align_id_in_fasta.R
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627a36c88a3e0b80cba38c21f9e9aac7 *R/is_mrca_prior.R
a465971d01b235b0e68f9c4c3568ffc8 *R/is_mrca_prior_with_distr.R
c9ce1c51ace3b4b8d891d90f7ea3b2ee *R/is_one_bool.R
06bb1a01854d72e67987b7bc028be9d7 *R/is_one_double.R
68a1ff6c917f46e9249ace890afd308b *R/is_one_int.R
6dadf5534cc39288b7f225ed6bbf8070 *R/is_one_na.R
63836f93778d17f24913da954ce98ea3 *R/is_param.R
208098ab0adedf0a8f426e4bdc4d2c74 *R/is_param_name.R
a85a701bb98600e6dacdb9798b88ad29 *R/is_phylo.R
2128b9ee9c0575b22c0f2d770cbadee3 *R/is_site_model.R
837d0f052a1e7ed0922bade057642007 *R/is_site_model_name.R
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8f41d6778f090e8f208db9f1a031ef63 *R/is_xml.R
3ff6286024fbe7c0ad99ca6d9bb454b2 *R/mcmc_to_xml_run.R
f8f6c692c4ddfa1622925d655319e0b8 *R/mrca_prior_to_xml_lh_distr.R
467f48c210596487167d92ecbe3c22f3 *R/mrca_prior_to_xml_prior_distr.R
b6c91550940c3aa9fcfe633a55dc36ac *R/mrca_prior_to_xml_state.R
8b40e665bf6f10bea4382442901e2586 *R/mrca_prior_to_xml_taxonset.R
4ac552cc769d38619fe75a37a8b56263 *R/mrca_prior_to_xml_tracelog.R
3fe2aa81203de76c5b95538a26e5b715 *R/mrca_priors_to_xml_distr.R
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c3785daec3bf63f5d56c7c58c172187c *R/parameter_to_xml.R
f96266d6b5d3d1bd5fae8224454bce0b *R/phylo_to_xml_state.R
412af75566487b1af1c580750370aa17 *R/remove_empty_lines.R
b6b3639d65031761c20c36e0d9fb3b48 *R/remove_multiline.R
b94e8116d77730d7567d5523326fff29 *R/rln_clock_model_to_xml_mean_rate_prior.R
a6f7b25efd675965c923ebab14b9456e *R/rnd_phylo_xml_init.R
67a2d584c45165a9d7ed6d63d16137ad *R/site_model_to_xml_lh_distr.R
8edb21af9cc817e38a123e5ae498e1f3 *R/site_model_to_xml_operators.R
a3f16f52fe92506ade26a82e4abf2b48 *R/site_model_to_xml_prior.R
534e45c93574652323a31870be652b1f *R/site_model_to_xml_state.R
538446cc884f0d5a6b39fa6e91c45ae6 *R/site_model_to_xml_subst_model.R
4a44b4174c12d9e67c1a9ebcf80a93e8 *R/site_model_to_xml_tracelog.R
75888eae03e6370b00cbfb585fe51c03 *R/site_models_to_xml_operators.R
8746916442ca74da4a186d46e4e70e1b *R/site_models_to_xml_prior_distr.R
032ae0aa52581927363087ac282cba14 *R/site_models_to_xml_state.R
7d823e784f6e2354aecb47c4dcdb993e *R/site_models_to_xml_tracelog.R
01f10cebd8f4cad2c3ec9090d797d8cd *R/taxa_to_xml_tree.R
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