6ee2bcc4b8e70fa0a3e0623ee7054c53 *DESCRIPTION
d42a8a99d4e1ef96667de47dfe4b1bd6 *NAMESPACE
4a0e6711ee28207db7ef74b539f10687 *R/are_clock_models.R
9c050d33db6e368ff8e36e9a1102961c *R/are_equal_mcmcs.R
4f9bdbc7bd0c3ea02d2298fec9a61b58 *R/are_equal_screenlogs.R
ed8eb9df166064c320087494f845e82e *R/are_equal_tracelogs.R
ffef5593565613d0e9f62e69c0266041 *R/are_equal_treelogs.R
ea3f2f39c8802eddc6b4751f54dd88b2 *R/are_equal_xml_files.R
bc9f39b1718416972b98b29ab902dad4 *R/are_equal_xml_lines.R
8537777255453cccc06f5b55d8f88be2 *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
e677a9fb265f9001dc21769e7849b44a *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
f1935df4feb92030bde4b1557a63cd05 *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
6fc798c04a56d9de18def2c487fda9c8 *R/check_gamma_site_model.R
ad758c2cf5b95db58007f23cc0614c6c *R/check_gtr_site_model.R
52d83d29d6b6db7cb9f84db1ad3e87b7 *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
024c83f87f0a3d00487817c74a5609c4 *R/check_mcmc.R
3c351b512650086eb5dbe91e61127965 *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
1a5155534c42ee5103810eb092edd8fe *R/check_param.R
f772c8d1e1e00de4b6d2bcf38b8376e8 *R/check_phylogeny.R
77d151242deaa7d4f60171c15e65b2c0 *R/check_rename_fun.R
9fa0fd926d57ef87b080a90e67308bd1 *R/check_screenlog.R
9470f2129be68afe102bc5c646580e30 *R/check_site_model.R
5433a7e12c61a8d7db54322c69eaebae *R/check_site_models.R
fc106e5cfd81d01a7f8f96cb023849ee *R/check_store_every.R
48b35d880714ec5a95b6a08fa53149b9 *R/check_tn93_site_model.R
dac3060af68f60aebb56aa1815d150ec *R/check_tracelog.R
34ece99a159069b7bbfb4b6c16b7376d *R/check_tree_prior.R
66bcc4533849fba27eaa91fe3991aa82 *R/check_tree_priors.R
b5b35d9753cbaade41d2097c6f095302 *R/check_treelog.R
62f6d45250ca5133ffc9c5d2e962798d *R/clock_model_to_xml_lh_distr.R
3599f81d2bcfdd39c0943117bd4fcf85 *R/clock_model_to_xml_operators.R
2f7429f1065e39dd24675a499b8581e7 *R/clock_model_to_xml_prior_distr.R
5df1ef27d1850f7e357aa72ecb618ec6 *R/clock_model_to_xml_state.R
03100a5ba3ae17fb65f3f78ca5df88a6 *R/clock_model_to_xml_tracelog.R
49b4d830f498b0c49a8dcfaf8b0db0a9 *R/clock_model_to_xml_treelogger.R
6d93c3b3cc5d94d4005ad304aa9a6543 *R/clock_models_to_xml_operators.R
213c050f3a62b8aa634efa6511880825 *R/clock_models_to_xml_prior_distr.R
6328a57b284771e12b831eeeb6d23584 *R/clock_models_to_xml_state.R
adaa7bef7b630636a1bb865b4a78882d *R/clock_models_to_xml_tracelog.R
b43132f4d443949a5ad07135939f4000 *R/compare_lines.R
c26c6e4f014d17b9becc9b8708a178f5 *R/count_trailing_spaces.R
150f76ffd2dc90f70ae122c08247907f *R/create_beast2_beast_xml.R
4689e7668c055d74e0a47a366c3d33a0 *R/create_beast2_input.R
598bf396d1fdb8ea67b87b1c7d11e546 *R/create_beast2_input_beast.R
c39c428af7d4ce4d847bf8656b8629ae *R/create_beast2_input_data.R
b64b2065f1c5d73e4b4283601868a814 *R/create_beast2_input_data_sequences.R
e51fe5a5c19a252ea1c04f5e6ac353fc *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
418ab4b9cae66e820fc4800cea9ac80c *R/create_beast2_input_map.R
b6c94fa051ff63e6de6cae6333b3d59e *R/create_beast2_input_operators.R
2a473d3beeb39a8215aeff222bbaff79 *R/create_beast2_input_run.R
f5125004bfc85501349d3c52f32f7b11 *R/create_beast2_input_state.R
9e0f7dbc73e9d4e71dd75e42079e958b *R/create_beast2_input_xml.R
a2d1b7f7515fc0c64aa64a3c1976e2a3 *R/create_beauti_options.R
7df6c796a95e1c9e431e0ce33a414128 *R/create_clock_model.R
3bc6562739c9b28f072ac1edc06fd68a *R/create_clock_model_from_name.R
4ae6d162b613565cbf172c538178d064 *R/create_clock_models.R
8bc2ab8cc326ef6943de4c1535759ca3 *R/create_clock_models_from_names.R
de1f1b7896d7b60ffeaa6007106ac136 *R/create_data_xml.R
2cf1762cf8ddc6759f27f50e35143e5b *R/create_distr.R
78ac5c34d327619c6e5807ec6fd4687e *R/create_gamma_site_model.R
b823b84346a4da60e8ee4d66a85fec7d *R/create_inference_model.R
b69bfc7c1cd5c28a1a0a7e08609d78d6 *R/create_loggers_xml.R
237e451bdfe358f1782c3ed877d6dff8 *R/create_mcmc.R
dba17802c74647bef3b2cd6a5e1c9c5a *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
f0a6bc56e1dd69b65f1fd0f1e1cdc2d2 *R/create_site_models.R
ca56dc73c6c6e6a896f81d29fb924200 *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
3440f6c9bab886c7f4bcd4518d1b9c44 *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
281e390142d434f4662d15e5fad79ab6 *R/create_tracelog_xml.R
778581086ae1c4485aec98798bcc8460 *R/create_trait_set_string.R
bab76c04e977ff684103992b787f695a *R/create_tree_prior.R
e44e6b5bec07e7f915f30e5c3be96359 *R/create_tree_priors.R
090f43e58863974f3cd38b624b8122c4 *R/create_treelog.R
c3d2e567dc2aa204969acfd3e3e16c02 *R/create_treelog_xml.R
1bb452fe4a345dbf2069c6bef0d0dbe0 *R/default_params_doc.R
6e869859ee063dd774a585d90408268c *R/distr_to_xml.R
7667007bf27c8c039c78f54b9691b090 *R/extract_xml_loggers_from_lines.R
2382cbbbc65c270542826c8fbb78abdd *R/extract_xml_operators_from_lines.R
91125ba5f36d225baa30891ebb9f1895 *R/extract_xml_section_from_lines.R
441b6247b19299f56c8ccd6a3bc534d7 *R/fasta_to_sequences.R
0a64fc506f21338be37a3e2cf6a26691 *R/find_clock_model.R
a16de56c97e2df439bf454e9ce8af610 *R/find_first_regex_line.R
d8c29d4907e9d0ec33706ac949b4b40e *R/find_first_xml_opening_tag_line.R
9f4e5a1c851534772ccf6e49c6008762 *R/find_last_regex_line.R
0485d2bbdae22f869909cec0125bbef0 *R/find_last_xml_closing_tag_line.R
31522b293cf6e89d1abd9669bf639a64 *R/freq_equilibrium_to_xml.R
28f966fa4e76b4365a439d2fb9c76fe3 *R/gamma_site_model_to_xml_prior_distr.R
867a18379bf00a862718165a38b29121 *R/gamma_site_model_to_xml_state.R
69a84bcdc1d4eebe74371b936d47195a *R/gamma_site_models_to_xml_prior_distr.R
78d699303db8f8451cfe685cafb0dc7c *R/get_alignment_id.R
4075f27a4b48ab1b715d96ef8d6d4027 *R/get_alignment_ids.R
e2a119405b7afe61afdfc1ce5a03c8c4 *R/get_beautier_path.R
c874793e8bcfac4cdebfae88c0007a9c *R/get_beautier_paths.R
ef138b2e51f2413dd09714994339cfc4 *R/get_clock_model_name.R
391cdc7bcda1c4fe476155d288667b66 *R/get_clock_model_names.R
e3d3872169f9dd5cc44eb7069b43eea8 *R/get_clock_models_ids.R
4f25dbc47d3b7cd5b686221395b6e373 *R/get_crown_age.R
6d1aa4b3e604db0ae2bc3a2c17b48746 *R/get_distr_n_params.R
d05c1941ab38838e47d6c57374d49eef *R/get_distr_names.R
c111e92c7522ea984902d040d0ac4d31 *R/get_file_base_sans_ext.R
93ff8c72cc924673bcbe25cbb5fcf236 *R/get_freq_equilibrium_names.R
4003c82bcf76d2a7f528a04dda3fe938 *R/get_gamma_site_model_n_distrs.R
6a276902a1997a1140de32dd8bfa046b *R/get_gamma_site_model_n_params.R
325163c41ab281979ea122a0ed157e45 *R/get_has_non_strict_clock_model.R
c3b518410961c1149ac0f62924219cb1 *R/get_inference_model_filenames.R
2bda5bd98b81e56e0915943673d2c299 *R/get_log_modes.R
1d553e38e9acb80ca60cac2c3d16843c *R/get_log_sorts.R
cf67f7ee3eb2d877fdee1bfd4b14a26f *R/get_mcmc_filenames.R
4c954bc483ff851e94f8e34b77e5d492 *R/get_n_taxa.R
d023299a556befa5dd47f6cb8b749a74 *R/get_operator_id_pre.R
fb4f7e71bdcf63fddd99500456ac1a16 *R/get_param_names.R
0bb23423aa289d6dadcf9b379e72319e *R/get_remove_dir_fun.R
6717ad70b2e457bd8b51a00125c3b0c7 *R/get_remove_hex_fun.R
dc1d3ec58b6510e2311e1cf8574d41bd *R/get_replace_dir_fun.R
9a2c501e0d04f8e7a6c31bbede6e46fc *R/get_site_model_n_distrs.R
a61233fe78a48bc348b33931cd31503d *R/get_site_model_n_params.R
f6ff8bb2c71aaaddfa4aa2f9dd0b8ec4 *R/get_site_model_names.R
2cdd0265c8bc5bb6d2d1bbd2f0b5be70 *R/get_site_models_n_distrs.R
2760df075b864be5fe70b3c12bb9bc39 *R/get_site_models_n_params.R
f16cbe315c194fb2474ebc2cbd348e7b *R/get_taxa_names.R
ea008f05b10c4a47a84c4547f1cffc34 *R/get_test_filenames.R
8cc2d367d5eea77b33b9ed84c2939e06 *R/get_tree_prior_n_distrs.R
cc018b92f42741e503cf1acc8316f84d *R/get_tree_prior_n_params.R
43335aa59b85563edd4f7649fd3e76c5 *R/get_tree_prior_names.R
918b397e8265d54b3847952f4b857f81 *R/get_tree_priors_n_distrs.R
e3906a7933a37201d12554d607e7403d *R/get_tree_priors_n_params.R
f930ffeff4a5258bddb2799069889c80 *R/get_xml_closing_tag.R
20f52b277ebcde1f32cf197fd33db2ac *R/get_xml_opening_tag.R
d6e27cfcec3b27c295828f513bf8998b *R/has_mrca_prior.R
ca1f224e1b037bce1599129508f43d4c *R/has_xml_closing_tag.R
9ea6b431e6a2550543ae2d46376228f6 *R/has_xml_opening_tag.R
8a0033f96a02b893a780870bb54c6890 *R/has_xml_short_closing_tag.R
83e917b9058759fc48a613b24ef186c7 *R/indent.R
8a2fd8caf79924fa45188ef1c578ad6c *R/init_clock_models.R
c8b3818a4ad0a7a9486787b33eb174d9 *R/init_distr.R
8f050f30798ed43b1499856d9aecb4e9 *R/init_gamma_site_model.R
db0a6c8e9f1039734dc22fb7fa59858f *R/init_inference_model.R
f0f63147545f1ea44e86fc97de79c2ea *R/init_mrca_prior.R
ae8cb2882b6ebc605397736925ee4dd8 *R/init_mrca_priors.R
d77d0efe19e22be40feb5343ea9de446 *R/init_param.R
55f2fbd0d545f2423892c4b6f2d9c3c8 *R/init_site_models.R
defc65a3a1ba2345c904962ad72b6a41 *R/init_tree_priors.R
4086f1819a76b2ab91fab2466a988f76 *R/interspace.R
f540f8a4835dda3a384c98974dbeaf2b *R/is_beauti_options.R
66325398a7ba692bc8cf4fcae8beac13 *R/is_clock_model.R
69654b64b179612d3cf8c183c3ec6bdc *R/is_clock_model_name.R
adef00eb4aee0b339b5dccd44f9afaba *R/is_default_mcmc.R
0fa075facb09ec0e89cbe7c2f431eb94 *R/is_distr.R
82c71647ec027e16e4981a24ab0c651f *R/is_distr_name.R
7e231fdb6f8ce9a87f9a241720cb3f3b *R/is_freq_equilibrium_name.R
d49ad634799ebe3ce537ac98c2cc1133 *R/is_gamma_site_model.R
c87e42a3151bdd93b91156ae4091cd7e *R/is_id.R
c61f9dc92d414dbba833d2051eb6a78c *R/is_in_patterns.R
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1df937faaa826673a1dbf1ed11866eb9 *R/is_init_clock_model.R
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1ab0c1fa97af6ea0218dde6e70c9bb69 *R/is_init_gamma_site_model.R
dfd7e71cb64ac9074db6582566782fed *R/is_init_mrca_prior.R
6a9c4c9c590ba81bed9e37bec1c01fbe *R/is_init_param.R
52b231f8d4274c922b0ce4a2ce4250aa *R/is_init_site_model.R
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627a36c88a3e0b80cba38c21f9e9aac7 *R/is_mrca_prior.R
158b4ebdb305d966ac422f7b141bf386 *R/is_mrca_prior_with_distr.R
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68a1ff6c917f46e9249ace890afd308b *R/is_one_int.R
6dadf5534cc39288b7f225ed6bbf8070 *R/is_one_na.R
5e9821927e2cf74d016d2236b0774543 *R/is_param.R
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a85a701bb98600e6dacdb9798b88ad29 *R/is_phylo.R
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b235cd3771e876a0cf80ba880451cc07 *R/is_xml.R
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a2a7c835d70c6119e6755ad43f226825 *R/mrca_prior_to_xml_lh_distr.R
c6e1a6778be93d2bdef45dd17328f10d *R/mrca_prior_to_xml_prior_distr.R
b9cdc49d51eabfb2e88ed5c40117de75 *R/mrca_prior_to_xml_state.R
4b7f6296fd94c367f8ae2eb15169a26c *R/mrca_prior_to_xml_taxonset.R
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81650ff79674e2c635ac325c102b002a *R/mrca_priors_to_xml_distr.R
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046ee107ec1c101b8e16b3b00b1f8434 *R/parameter_to_xml.R
363e7b7709a7296b96a87d3308429f22 *R/phylo_to_xml_state.R
aeea35678fb962affb49029895a10f30 *R/remove_empty_lines.R
b617fc9254b897ac6dd36d08c669b55e *R/remove_multiline.R
36fe6bd9f1abf052b9806274ecd321f7 *R/rename_inference_model_filenames.R
690ee0e76ebb45de6a625a9ed596da87 *R/rename_mcmc_filenames.R
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d600794860942bc9f49075f9fe9a906c *R/site_model_to_xml_lh_distr.R
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