3dd6f69dacf2415a9056bddf75ae4904 *DESCRIPTION
56444c195264c91f53534e421ef4fb82 *NAMESPACE
e057b93a0389692b311c6697a866d009 *R/alpha_parameter_to_xml.R
93dae883c839870b6f664560d1c5a0b9 *R/are_clock_models.R
744ebcf1f4594b28862445ac2678c847 *R/are_equal_mcmcs.R
720ee65f5c718164afbb1cd6dfab6fb8 *R/are_equal_screenlogs.R
2cad49877549a8e4de4e550f01d83d02 *R/are_equal_tracelogs.R
d2d8543b67f3171d1ca5b02fcd7dc590 *R/are_equal_treelogs.R
b0190224b64ddcda853dfc42d39bb716 *R/are_equal_xml_files.R
4c53a8b775659decb5ae0c9116cfb8c3 *R/are_equal_xml_lines.R
b3b763262e8b5a12cc7444a12c3d58ef *R/are_equivalent_xmls.R
d22ede24f72fc2c8468695bde9e425d5 *R/are_fasta_filenames.R
613bff7d365525613fdfea2b6fa461cf *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
ae14e16b335b653c8a0638e8198f36d9 *R/are_mrca_align_ids_in_fasta.R
a03079b9d1d06f5fb6273d797e534fc5 *R/are_mrca_priors.R
e677a9fb265f9001dc21769e7849b44a *R/are_mrca_taxon_names_in_fasta.R
bb2373a0f53fcac6f50686af07e667f8 *R/are_site_models.R
ebaeb0a51517b0dbffcc23628679f4e3 *R/are_tree_priors.R
6654bee9011ab26c418ba7df9733a6cd *R/beautier.R
179195cc9885da2b258c05e93d2ca77e *R/beta_parameter_to_xml.R
1f1aee44ba8b69f065ff7baa227efbec *R/ccp_tree_prior_to_xml_state.R
bdac4d78961010fec64bbee1567e6c31 *R/check_alignment_id.R
5f54d57abea4d652833690a4420885f9 *R/check_beauti_options.R
87c3732aa1caa6a4957fa84067706dbe *R/check_clock_model.R
cec68b440908c75540dd0093ad32d8cc *R/check_clock_models.R
eb7db8d6b0cf6d557022872b28e2631d *R/check_empty_beautier_folder.R
91f69cb70c2db7e2d1ad814f501423e1 *R/check_file_and_model_agree.R
34385811822e2b0dcf1afa266db6eb41 *R/check_file_exists.R
5fd7e6a44fbb81ba9fc46fbf2931e7d8 *R/check_filename.R
ed17d8072181c52209bc39df521d8df5 *R/check_gamma_site_model.R
02b820b4ed3da1db794df517264f09ab *R/check_gtr_site_model.R
34daadc50d51ef02ce6cf080d1ddf825 *R/check_inference_model.R
65af5733972dda574a9d23ea8cd0e8e8 *R/check_inference_models.R
b9fa27545f0c455a6eaa5bae56f4f3e7 *R/check_is_monophyletic.R
bab02aa724fc6143d6006bc73c4918bc *R/check_log_mode.R
3f3bd9c6fb082434e6f2e3d0625d2ba6 *R/check_log_sort.R
5e1b0188cacee129aed3c76de4b69df1 *R/check_mcmc.R
3c351b512650086eb5dbe91e61127965 *R/check_mcmc_nested_sampling.R
5a1a2416e401c8d1d50d459d8f2dbbd9 *R/check_mrca_prior.R
d6d9f37f256c854bac30fd6670861a8f *R/check_mrca_prior_name.R
bbfb7341275ed25396548930a66d29fa *R/check_mrca_prior_taxa_names.R
066359715e4fa49e3cbb59d83d82aa3f *R/check_param.R
21834b9f07a84a0241296a78edf95c6f *R/check_phylogeny.R
77d151242deaa7d4f60171c15e65b2c0 *R/check_rename_fun.R
b26903e13ea7cdda1887bad4b9b20544 *R/check_screenlog.R
096ca725b76adde021a2c8d6379229f2 *R/check_site_model.R
a30a20e2176a913d0f9d0db287b88235 *R/check_site_models.R
fc106e5cfd81d01a7f8f96cb023849ee *R/check_store_every.R
675b855eb7672ca11454be1cd0fc33ab *R/check_tn93_site_model.R
34afd05f2582c67af0a2b0967dcce71a *R/check_tracelog.R
4c7e9195245f15a349468f72fd0d29eb *R/check_tree_prior.R
f1dd693d2d9811c1e3f1b6a20f95e906 *R/check_tree_priors.R
27e9870bdf6fe92c3665faa0d62c5445 *R/check_treelog.R
b2ea3ad03cdd1e1c62b22a2a9a47ff6c *R/clock_model_to_xml_operators.R
662da92e404ee50a1d6d0684aa3fb5a4 *R/clock_model_to_xml_prior_distr.R
0ae50a60d5e5f8ece3860fa09931b17e *R/clock_model_to_xml_state.R
34ccdc3c61d52369ab69050fec705bca *R/clock_model_to_xml_tracelog.R
49b4d830f498b0c49a8dcfaf8b0db0a9 *R/clock_model_to_xml_treelogger.R
3dcac0c2ce407f558b3b0f42f2051e90 *R/clock_models_to_xml_operators.R
6e6fc1a354334b5d89c15bc4e7c383b5 *R/clock_models_to_xml_prior_distr.R
dc6e8b047c4098d648e48899342607e6 *R/clock_models_to_xml_state.R
aeca606283b3f0276042c1823101fc71 *R/clock_models_to_xml_tracelog.R
57306768b15fb97f2c9aacc77e7d2b18 *R/clock_rate_param_to_xml.R
e1eac25a5c6deb9e37b3749918e87f1b *R/compare_lines.R
10106f096358dda115347d5628038b82 *R/count_trailing_spaces.R
848c5d3be8885aba479d493600855e43 *R/create_beast2_beast_xml.R
570523cb625ef3a10add9f0791d32e1b *R/create_beast2_input.R
ec3a229c0ff23f44f59fe7b601933777 *R/create_beast2_input_beast.R
cc0794e5bf15e804e07d1d3b12d7e88e *R/create_beast2_input_data.R
2fb0535df995c96fa146a9a5c045db68 *R/create_beast2_input_data_sequences.R
5399dc8cfc56641b5f36cda622d0b683 *R/create_beast2_input_distr.R
75f8ef7b9dedc15a2e48cd7bc809dac6 *R/create_beast2_input_file.R
3381ff275434c8a4706b6be4fc073808 *R/create_beast2_input_file_from_model.R
c31f6a296ddf52e443117c25072b6e89 *R/create_beast2_input_from_model.R
3cb98f7f07a0ade3a6c00f4b1e32b8ab *R/create_beast2_input_init.R
1b91bc979b9d7cf749a1725c97d8d256 *R/create_beast2_input_map.R
7c4f3bdcaebba046c9c424dde45939ff *R/create_beast2_input_operators.R
0b09abb3d5bf6354cf481c5e7f531cd0 *R/create_beast2_input_run.R
1dc4bed099aedc9bb5cc6e657e5154f4 *R/create_beast2_input_state.R
f2d7b26cd60487a15cc687ba449e8400 *R/create_beast2_input_xml.R
e7348ac9aa5e74d5494d93190d089beb *R/create_beauti_options.R
01fef58e2a1ae4dedbf92a6955061315 *R/create_beauti_options_v2_4.R
660113187b69be5329a63b1cf9e4b751 *R/create_beauti_options_v2_6.R
3e9f83933183dfe7235a4ba6c7253220 *R/create_beautier_tempfolder.R
5ab44f4779f8309b7a64679ce2ba1616 *R/create_branch_rate_model_rln_xml.R
78890b6a2bd34a4e7be68aff16bf860f *R/create_branch_rate_model_stuff_xml.R
68b013cf204249d71144570f098218b0 *R/create_branch_rate_model_xml.R
3a5c06ba4d26213f8d362f40cea45895 *R/create_clock_model.R
62db2f2b55b71573352e85fda3576d4e *R/create_clock_model_from_name.R
45bf62a8c895cb5a5c3a705766c26027 *R/create_clock_models.R
89ab20d2e9bee12c232007a6fbd2cdb5 *R/create_clock_models_from_names.R
0c2d8e10b8b696cb351dcbcb24be7fea *R/create_clock_rate_state_node_parameter_xml.R
db9cfea9d5639809bfecd1147581c4b7 *R/create_data_xml.R
8d979155755c88c648a75b8fef4f0632 *R/create_distr.R
06f31802fd6a18a3b7c419d0e1788a51 *R/create_gamma_site_model.R
ddb4dbc4a1b35b63a5cd3d638670865d *R/create_inference_model.R
b69bfc7c1cd5c28a1a0a7e08609d78d6 *R/create_loggers_xml.R
3dca7c748dac47c898190aa1ca3a9acb *R/create_mcmc.R
0d948f53c0e103d870d1b2c9e2761cc0 *R/create_mcmc_nested_sampling.R
35b6dcca28bf86799f3432fa6375ce2c *R/create_mrca_prior.R
03d07414e862ec54cf32ace50539190f *R/create_ns_inference_model.R
67472e73d34d8a90461e6643e035d67b *R/create_param.R
161f4818fd57067b9f6b2345cd981026 *R/create_rate_categories_state_node_xml.R
b5270ad9a2a809903bccd2492ee1feee *R/create_screenlog.R
862a4988a5dce778a53f68e6e522aa01 *R/create_screenlog_xml.R
a653ddee35bb045b9cafabf66442b68b *R/create_site_model.R
a0e45bc129baa6b2ab6d2f6da63d8d34 *R/create_site_model_from_name.R
44936cda6f582d57e2c269f40b8937d8 *R/create_site_model_parameters_xml.R
7396ae4e66a268a3961aacb161ba188d *R/create_site_model_xml.R
915894b5d996e01e6a8895a43c62b362 *R/create_site_models.R
87b9832e8b2c7200e347511cceb1be68 *R/create_site_models_from_names.R
89e067347028cea3c8642cb7c72ac68a *R/create_strict_clock_rate_scaler_operator_xml.R
2f7af609e03e0888ec8a8ec11ff69354 *R/create_subst_model_xml.R
c58f7b4c6d7945b95f26275647d8ef8f *R/create_temp_screenlog_filename.R
68047df266018180dc78ecd9ec545be8 *R/create_temp_tracelog_filename.R
5a7ef52d851c03e50821801fcec26959 *R/create_temp_treelog_filename.R
43534d4b1c12b1eebe83a1ba68309b66 *R/create_test_inference_model.R
8054c6d6572bff0edec72bbc6227b45c *R/create_test_mcmc.R
d10a99392d2d430ebb18a7db9e52ac52 *R/create_test_ns_inference_model.R
7d987e10df1afaf6dee6abf31d3d2308 *R/create_test_ns_mcmc.R
15e42e7135687db8d4228650f9cb3fdf *R/create_test_screenlog.R
2cdff2ee92bb4df3dd4952402e080143 *R/create_test_tracelog.R
e0feca4f42276f1fbf4e51dce6069535 *R/create_test_treelog.R
d644a5872ab472d1a5bd74b02caa6263 *R/create_tracelog.R
0d8db3529b202ad98f24dc01e04679c9 *R/create_tracelog_xml.R
778581086ae1c4485aec98798bcc8460 *R/create_trait_set_string.R
9e310d896b802d1f75337e6ba1f4f777 *R/create_tree_likelihood_distr_xml.R
234be9a8a5032fc8aaaae4dcca75e506 *R/create_tree_prior.R
dc19ba52fbaf9cd6e17c3baf41797b78 *R/create_tree_priors.R
7423717add07523686febc4a97962e50 *R/create_treelog.R
9aa56d7e93b7ab10e0e08db76dd86b29 *R/create_treelog_xml.R
2c3e58b068d86361fa6f44e9d5aaa9d4 *R/create_ucld_mean_state_node_param_xml.R
7bb994228e8537f57f394d36ebc9fc6a *R/create_ucld_stdev_state_node_param_xml.R
34a7931d66c01eebd20cab9c609dc1e5 *R/default_params_doc.R
9ec41418ebbb49b90011b8488c135a04 *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
9cceeeeafbeb8ba939bf448414a73bbf *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
7da9bdc1cd3a0712d8e1ebe0a0937d30 *R/freq_equilibrium_to_xml.R
dc29f0335a9ad8cb7c4d76779cad2f9c *R/gamma_distr_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
4234d5ff185f5d67176cac5de24023a0 *R/get_alignment_id.R
a5932c35dba396cdf656df2f190f5d53 *R/get_alignment_ids.R
d6fb49bb0dd96ec73a4a3aa7fb1fa876 *R/get_beautier_folder.R
4622dd8b13b59c18db1f64157bc61d54 *R/get_beautier_path.R
cdfc706c05d7ac78d8e7d348eb93b87f *R/get_beautier_paths.R
bd8b00215c5f4cb7362a75eee618246e *R/get_beautier_tempfilename.R
288e08e49f7e14f30ffdb882b8887dd7 *R/get_clock_model_name.R
1e598de48517eefa81008b74aded3ac1 *R/get_clock_model_names.R
e3d3872169f9dd5cc44eb7069b43eea8 *R/get_clock_models_ids.R
7546a8b1072c63f281ebadf5c1e34b8a *R/get_crown_age.R
35a34779f6c3d452e4d71376372c197e *R/get_distr_n_params.R
50462853900c3997c70d5767a4c910e8 *R/get_distr_names.R
6e50bacf4e53fabd8e1416c0e3ed0ec5 *R/get_file_base_sans_ext.R
556bc71e5e4b682032206f9a012eae9e *R/get_freq_equilibrium_names.R
d00086c87e38b0064a58e32275e5add1 *R/get_gamma_site_model_n_distrs.R
917917cf58b89c73930aef60919c9052 *R/get_gamma_site_model_n_params.R
325163c41ab281979ea122a0ed157e45 *R/get_has_non_strict_clock_model.R
8e26688d4cbe5cda98a479a516f60a66 *R/get_inference_model_filenames.R
2bda5bd98b81e56e0915943673d2c299 *R/get_log_modes.R
1d553e38e9acb80ca60cac2c3d16843c *R/get_log_sorts.R
ee2a3df07711cc07b538dbbe63e091e4 *R/get_mcmc_filenames.R
57343db3139330b9e65bae09eace4310 *R/get_n_taxa.R
fc47b7f0acc4f3d0da918199acf5e470 *R/get_operator_id_pre.R
b190e7c05032b481b8926440a57330d7 *R/get_param_names.R
0bb23423aa289d6dadcf9b379e72319e *R/get_remove_dir_fun.R
aa8dcdc147db291df0793712ab5062fc *R/get_remove_hex_fun.R
dc1d3ec58b6510e2311e1cf8574d41bd *R/get_replace_dir_fun.R
2038f043422341b475a7348d51f0165f *R/get_site_model_n_distrs.R
8c645d969c23ba34cc3d7a855101e6cb *R/get_site_model_n_params.R
108f33219fc222c4efbadac0fb1910ba *R/get_site_model_names.R
38cffab11aed48f52346b9b8b464f128 *R/get_site_models_n_distrs.R
0fecaae1b8983fb749d58abbf689cfef *R/get_site_models_n_params.R
226ff7c2b98786370d3103f8375baa8a *R/get_taxa_names.R
562a6e36894b1d72f9a06283344bbe67 *R/get_test_filenames.R
1042c2d88b65a69b4c950839a9f1bb23 *R/get_tree_prior_n_distrs.R
ad27354664fccb1956e3b137c677ed2d *R/get_tree_prior_n_params.R
ee8f77fe64e48cc4536d0f9fb2770c7f *R/get_tree_prior_names.R
ec2da9f0b9a694ab0a6e915cc015d7e1 *R/get_tree_priors_n_distrs.R
2e049f9cc3af370824c3756427cd12c9 *R/get_tree_priors_n_params.R
be76553477cff5c0f9f2c8395e532fda *R/get_xml_closing_tag.R
a6e6f339dc0408eca2e40fe18221c4b2 *R/get_xml_opening_tag.R
c493222a5147a3509b620464bf711d49 *R/has_mrca_prior.R
81b766be27972fcbd0fd2f0116cef2fa *R/has_mrca_prior_with_distr.R
c9d6b7e16a8c00a594214b922e75a4de *R/has_rln_clock_model.R
2c4a4cbd69d57dbc55e154cfa80f74bd *R/has_strict_clock_model.R
6712d39c0070d5ee1c08bdface2a39b7 *R/has_tip_dating.R
48739773a67b2e8fc134fa5f53eb1576 *R/has_xml_closing_tag.R
9ea6b431e6a2550543ae2d46376228f6 *R/has_xml_opening_tag.R
dfbf775fb06368dad5454a5d9916aae9 *R/has_xml_short_closing_tag.R
8451733880a598a261ef6c6b6bfef73b *R/indent.R
d343c610e18121e2a53b345e4e00a53c *R/init_clock_models.R
c8b3818a4ad0a7a9486787b33eb174d9 *R/init_distr.R
171effcd5026ae50b5195168043d6cb7 *R/init_gamma_site_model.R
094a2a4f1e9ff8905305db6719e3578b *R/init_inference_model.R
f0f63147545f1ea44e86fc97de79c2ea *R/init_mrca_prior.R
ae8cb2882b6ebc605397736925ee4dd8 *R/init_mrca_priors.R
d77d0efe19e22be40feb5343ea9de446 *R/init_param.R
8eff4cba22c5d34e9c72c931b404bc1f *R/init_site_models.R
318280a18f1dccbbdaf51f5579020f94 *R/init_tree_priors.R
4086f1819a76b2ab91fab2466a988f76 *R/interspace.R
c8e6feab1af63c726826bb0053b7b92f *R/is_beauti_options.R
f828a9a16b1e3b4ee2ee5aee42ee99d7 *R/is_clock_model.R
fb354be76e04542adf3af01b7ef84a36 *R/is_clock_model_name.R
9bf72e728deb8f916fa2f0628027bde0 *R/is_default_mcmc.R
6ecf542830b868e7e24626c7eec85d1a *R/is_distr.R
d0703b986c223c63072c128add56b8db *R/is_distr_name.R
667a3f0811ee953fe566b160139dc3cc *R/is_freq_equilibrium_name.R
36febe7f86ab74862ea2b478e4edb6f8 *R/is_gamma_site_model.R
0440175c05907ff95a17ee5b94a37e30 *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
20f684679aac053277456e39def68622 *R/is_init_site_model.R
dc73d7fa9da32cc76f3629330df84c09 *R/is_init_tree_prior.R
fc36d294f9841a1bcc587a66c7e6e11b *R/is_m_param.R
fa0dc8c7280ccb2961119c57cdee5029 *R/is_mcmc.R
47d11aa0506556f2ac0e2be14cf81310 *R/is_mrca_align_id_in_fasta.R
0d486106bb30334f5458a623512db7f0 *R/is_mrca_align_ids_in_fastas.R
072e2c836b5d7375f465ac84958c225f *R/is_mrca_prior.R
158b4ebdb305d966ac422f7b141bf386 *R/is_mrca_prior_with_distr.R
6313e6cdd683256fa9e9848da4696519 *R/is_one_bool.R
a4674ec9cc9424d0ff8947512acb34d3 *R/is_one_double.R
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