8f80edc8f4942775551ca2f64acd7bd7 *DESCRIPTION
84dcc94da3adb52b53ae4fa38fe49e5d *LICENSE
c5889c4b1c6fa4f82f5f599935cacdb3 *NAMESPACE
ba729ca4901613d174923e68a4a81fda *R/are_clock_models.R
4304f2fad7a4d2f4b441f73f9ed8930f *R/are_equal_xml_files.R
cff8b8f1c0ed10bddf25431ded0300b7 *R/are_equal_xml_lines.R
1ed976e17050403eb23dfefdf162c511 *R/are_equivalent_xmls.R
05e34c6d07e238f6ba78e802e3c458aa *R/are_ids.R
210f2b742fb727a2ed1de8aa29d5e96a *R/are_init_clock_models.R
6e2ecd68d64ffb62343ef2d44f87c59d *R/are_init_mrca_priors.R
837cd152c5f807dc5e01d3ef6d921671 *R/are_init_site_models.R
fc6242b43740c5208205f39376d18b92 *R/are_init_tree_priors.R
f87946aa1969a5c2938d16233072051f *R/are_initial_phylogenies.R
13d8fae744d10964086042c0d28c0a4d *R/are_mrca_alignment_ids_in_fastas.R
aed36dc27a83847cb1289040eda9c654 *R/are_mrca_priors.R
40dfbbe77769b3dc567d712c985a19e7 *R/are_mrca_taxa_names_in_fastas.R
f18d3843c53042b6f6a155012ec2fb6f *R/are_mrca_taxa_non_intersecting.R
0d50fedd3bcc7098a34764377ba8b31d *R/are_rln_clock_models.R
101e2e56cc9212ce935068f2e23a9fed *R/are_site_models.R
7871b6213f841ab9836de0c27532d50a *R/are_tree_priors.R
5b44dd78bd3bc046496ae0623c4598cf *R/clock_model_to_xml_lh_distr.R
bb646f2ef2e960420a288c68dc1af415 *R/clock_model_to_xml_operators.R
7fc9e0736da7da660a78dcef25ac08e8 *R/clock_model_to_xml_prior_distr.R
50c88b5eae5c8a0b13130412b287cb32 *R/clock_model_to_xml_state.R
7f96036011332e81cb2c2d98dabf1835 *R/clock_model_to_xml_tracelog.R
d75fdf3015aada5a82fed3f343680f98 *R/clock_model_to_xml_treelogger.R
d9139ac8c0f4817413587ef5e6ea1209 *R/clock_models_to_xml_operators.R
6aa4045c4a406c87e0186f211444193c *R/clock_models_to_xml_prior_distr.R
f0665c659251bbccbdb9dfca57e47c03 *R/clock_models_to_xml_state.R
1d97420dc1c32e1833f7b40444951639 *R/clock_models_to_xml_tracelog.R
3f0c8aee2963e2eae5b0bd9b77bc3145 *R/compare_lines.R
4f792183d41d6b5967631ef254073f69 *R/count_trailing_spaces.R
eb4f75ac96e8d7ae2c4dab8658f860d5 *R/create_beast2_input.R
3fce671eaa10e0c1d7ebf8169b1581c6 *R/create_beast2_input_1_12.R
6f03dd776acd632bea1d998c54f22a9c *R/create_beast2_input_beast.R
466d3e99a91fc360ec55dd312ae3d021 *R/create_beast2_input_data.R
0e535bedcfa8c9fdc5b03eab1bab5c90 *R/create_beast2_input_data_sequences.R
b603529f8a7b84fe40866acd987f5ab1 *R/create_beast2_input_distr.R
2810040e8b4e46e7bd32d10a6f42a2e4 *R/create_beast2_input_file.R
f28f411e62b743ff675d91959913d8c4 *R/create_beast2_input_file_1_12.R
8d601392d305599ba925a9a395b521e5 *R/create_beast2_input_init.R
644b64795b5480e0706ae2054f8a7971 *R/create_beast2_input_loggers.R
0c65e5b83fa2e6764d8fb772ff266cac *R/create_beast2_input_map.R
851f6412151498968ad9ca4a37daf391 *R/create_beast2_input_operators.R
f3b7f99f5a20e3ac8d7bafb4cd7b8983 *R/create_beast2_input_run.R
46f8a33a791f539257ca14fa975895f2 *R/create_beast2_input_state.R
37b8e2b53a1058ea89bd5aaaa3550f91 *R/create_beast2_input_xml.R
45cac70f8b5df1fae4641412fbe1ace1 *R/create_clock_model.R
488b4ecb4c7b4d2a907db752ee31c112 *R/create_clock_models.R
39c64b6ce30a0c8ad202a2555aa0702a *R/create_distr.R
3ddebf703cfdb8185623feb6b38fffdd *R/create_gamma_site_model.R
4d560032c8e6f080290327abc1136bdc *R/create_mcmc.R
85cf20f862b34adae783d5727e889fb3 *R/create_misc_options.R
67e9ad3b1c0cb095207cae69b5561b35 *R/create_mrca_prior.R
6cb440d4ddf160846bada23c0948fa44 *R/create_param.R
d6dd0e692d7ab71f90760fec3ec63060 *R/create_random.R
73568dd8a00eb35e50691379813fc012 *R/create_random_name.R
237fe37cb87fb488508f24fea7f71590 *R/create_site_model.R
5431d2d5734177fb430db697d17602d2 *R/create_site_models.R
d0d543b3ea2fdccd3b58ed784dd3604e *R/create_tree_prior.R
b2c0c4e3d441af63e51a467e4b69a0a3 *R/create_tree_priors.R
b49d7e02a801b7b1f15f6d7a4750d414 *R/create_yule_tree_priors.R
6899efbf7d4aa31df644b93b739dcb9d *R/default_param_doc.R
624f22be4321e09a6144f0fc127efc5e *R/distr_to_xml.R
339457771cfa7ab80a347c8ad4cc8d08 *R/extract_xml_loggers_from_lines.R
5317dfec1285d278332f07a4350ad6e3 *R/extract_xml_operators_from_lines.R
559607c90d7fe4eb63027c32d59ff400 *R/extract_xml_section_from_lines.R
67c902e54c31e2abba949fec42d7a167 *R/fasta_to_phylo.R
1ae3acf33904f99d3b30feba7a0b0af6 *R/fasta_to_sequences.R
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aff7b8ba2f2f0f096b8c9f5a8cb98f4f *R/files_exist.R
31f64ad589647792d476c85bdb411ce7 *R/find_clock_model.R
5bbd112303803909c59b6ad2dda4dde6 *R/find_first_regex_line.R
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1d7a197da3da0654a1813b0e776fcc4f *R/freq_equilibrium_to_xml.R
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3e8b985257420e1ea983ab31b9f6c03a *R/get_alignment_id.R
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0cb7eaa68e6f4853706bc7d4af2fd521 *R/get_beautier_path.R
97f32c48f5e6a4b9fcfe924fa2db938c *R/get_beautier_paths.R
ae27fc8fc2a513307a3f0eae44da5ae0 *R/get_clock_model_name.R
d52a63bd3ce083cd35fbef1cda6d8eb6 *R/get_clock_model_names.R
20ac33b59be6cf09463d492919a171c7 *R/get_clock_models_ids.R
c97345551c6c86b0edb115c8c5e31128 *R/get_distr_n_params.R
1cede01b75ff99dc24c4650af38a0871 *R/get_distr_names.R
fc71498ae412bee6309702acd4001ea5 *R/get_file_base_sans_ext.R
012175f2bc491f052f03b64248fa6a19 *R/get_first_clock_model_index.R
7c46ceb787cfb547301358157f9c8897 *R/get_freq_equilibrium_names.R
0b5ca3bdd3343c09a384ff33a7b32f83 *R/get_has_non_strict_clock_model.R
5446d2f8615253f8a41340380944398d *R/get_id.R
943446aec0e99a972135404a791b7c7d *R/get_ids.R
3de41c9ae00e2eab9cfb5902f059cbd3 *R/get_n_taxa.R
3f4986484ad0e616b73cc4fff88ee1e7 *R/get_operator_id_pre.R
abd4adbc6c1040bdfcdae58f07f41074 *R/get_param_names.R
5d23bbc29ccbed2eded94aaec1ac10dc *R/get_phylo_crown_age.R
5d45cb8f7e37bd0bc99104bb0a1d9d63 *R/get_site_model_n_distrs.R
5acd1a30f3e1936a9849e20f790f6386 *R/get_site_model_n_params.R
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170f0ac555d326f9888be67f0d99b6b0 *R/get_site_models_n_params.R
986fa000c4a5b5f7427edc7f8038dec7 *R/get_taxa_names.R
97bb08753768f4f81c51ec32fddcd281 *R/get_test_filenames.R
a174d6771c1c2d4ae80ce5af70f64d6f *R/get_tree_prior_n_distrs.R
4a917a9c4c172588eeda1ce56b18e751 *R/get_tree_prior_n_params.R
785177dc441d9c418107b94de9341cc5 *R/get_tree_prior_names.R
0373da92b8dbfdf0b00484e2217c9b3e *R/get_tree_priors_n_distrs.R
1c40855b2fd22437ce23dfa56ee1d8ea *R/get_tree_priors_n_params.R
a70612bf92860ee91fe06d5b5f6c7e80 *R/get_unlinked_clock_models.R
6d696d32f76dbd1332d9425f26599594 *R/get_unlinked_site_models.R
edb844f884b24ba9787f0ee01f0c9c68 *R/get_unlinked_tree_priors.R
38692f1fbfff9fec56d5e6fddf9b8a0a *R/get_xml_closing_tag.R
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81bc77435b2cc985cd4de88311db03cb *R/has_shared_rln_clock_models.R
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3676c000ac753da36eb77930767cbbf2 *R/indent.R
3972d517ec7d5da31570c5153bd6a692 *R/init_clock_models.R
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14246534a0fac76f3bfd470a3af3c1d4 *R/init_gamma_site_model.R
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dd1c78656b65b496721d691139f96509 *R/init_tree_priors.R
b7d4e77258d097052e0af66329af717c *R/interspace.R
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be6333aaabb9b84f6b410feb66afbfce *R/is_beta_distr.R
bb70e0d84772908735cea44081285dd9 *R/is_beta_param.R
0a89ac9a0df1c17bee0c25cc7af3cf17 *R/is_cbs_tree_prior.R
92a9efc79dc5fc1c78742f52b014a454 *R/is_ccp_tree_prior.R
a4fa4f0cc59fc402aff7ab38676869d1 *R/is_cep_tree_prior.R
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33f2cf8b9f15c941076851ef599539d8 *R/is_clock_rate_param.R
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1a6077c8b963f916415241be1938a8a7 *R/is_init_mrca_prior.R
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5ddaa66380bea7c097e474fa45e18424 *README.md
7b1dae26b769eba92539c942da9de757 *build/vignette.rds
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c65d59f2da055eac6a8e375a1e5d76ee *vignettes/demo.Rmd
6d95a1ed38b4e1fec37029b2efbcede3 *vignettes/examples.Rmd
d00b8e97fba6638472daf48c3d18ff19 *vignettes/from_1_12_0_to_1_12_1.Rmd
