3aaf56c3c0910038554fa222f208f40e *DESCRIPTION
742433d7c9489a5a86fe5845179a8758 *NAMESPACE
d95b2a5cab464920de20a24a16bdf168 *R/alpha_parameter_to_xml.R
7c3fd6d56d84d9f279357624c91f7507 *R/are_clock_models.R
a3f971be2b6bb517e3ced24d002af4e8 *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
1014717e256a8b4472453da21cafa3c8 *R/are_equal_xml_lines.R
485b62d948f4da41e695abeb10287029 *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
bd25d2aafe459d9a095aefbc208dc3d0 *R/b_pop_sizes_param_to_xml.R
ccb6f288dc10697b0aab67db27d5a58b *R/b_pop_sizes_parameter_to_xml.R
564d5de8517d0a57239c2ebd25b70c90 *R/beautier-package.R
179195cc9885da2b258c05e93d2ca77e *R/beta_parameter_to_xml.R
1f1aee44ba8b69f065ff7baa227efbec *R/ccp_tree_prior_to_xml_state.R
bdac4d78961010fec64bbee1567e6c31 *R/check_alignment_id.R
7a68279ba31f419668245a1245182b4b *R/check_beauti_options.R
d98c3da3cbd054f10f8e7dd6f1a5a632 *R/check_clock_model.R
cec68b440908c75540dd0093ad32d8cc *R/check_clock_models.R
355a53a12de79c199e216cc4769e43f8 *R/check_empty_beautier_folder.R
4d75b4b88be8217f7088d61f904c0f5c *R/check_file_and_model_agree.R
34385811822e2b0dcf1afa266db6eb41 *R/check_file_exists.R
5fd7e6a44fbb81ba9fc46fbf2931e7d8 *R/check_filename.R
c34549cd73f4e87630c643363cd57d53 *R/check_gamma_site_model.R
93371bd54b538e27d68790a096abef1f *R/check_gtr_site_model.R
c6174a64b86639103356d8a128517c17 *R/check_inference_model.R
65af5733972dda574a9d23ea8cd0e8e8 *R/check_inference_models.R
b9fa27545f0c455a6eaa5bae56f4f3e7 *R/check_is_monophyletic.R
bab02aa724fc6143d6006bc73c4918bc *R/check_log_mode.R
a314474a7150a069bb77ad5153dd7429 *R/check_log_sort.R
becc610a9c077a06cbe1774b101cfbbc *R/check_mcmc.R
e1952eb853c256fabeecb7baeab37be9 *R/check_mcmc_nested_sampling.R
b6141cec1de51158bf084b1dd3ee5c83 *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
1ff857f6feb618457cfd17b77f627a63 *R/clock_model_to_xml_operators.R
747ca4eb9704c0b5f223a5103ded2ba7 *R/clock_model_to_xml_prior_distr.R
20ba8ace82c41f7a5f028815a4483185 *R/clock_model_to_xml_state.R
17ee2da1c32474d6c0fbdb026797a5bc *R/clock_model_to_xml_tracelog.R
49b4d830f498b0c49a8dcfaf8b0db0a9 *R/clock_model_to_xml_treelogger.R
d8ec9303bc28a18eeed32e5428c05151 *R/clock_rate_param_to_xml.R
307905f41e7826fa14725cfc29989e27 *R/compare_lines.R
10106f096358dda115347d5628038b82 *R/count_trailing_spaces.R
4180bc1a5627f121addf031e93f74c00 *R/create_beast2_beast_xml.R
7e86ad32d6a47cb910ce07d90aaa6f36 *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
bc0022579814901fce4a0151bf8e0915 *R/create_beast2_input_distr.R
6e610fdb87a13cae416d7ef92683749b *R/create_beast2_input_file.R
23659fad667a291fb857606dbdab0a06 *R/create_beast2_input_file_from_model.R
ea4dc51841d2e550060aa16a365c11f4 *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
12ac5c38b56646aee299c361bec6d0ec *R/create_beast2_input_state.R
f2d7b26cd60487a15cc687ba449e8400 *R/create_beast2_input_xml.R
984c258e3f45b014e20005cf9fb0bda1 *R/create_beauti_options.R
857633b42c8db469b853f07e1342b3e9 *R/create_beauti_options_v2_4.R
254b7d2998ca93e88c1e54d9d05991db *R/create_beauti_options_v2_6.R
3e9f83933183dfe7235a4ba6c7253220 *R/create_beautier_tempfolder.R
d41d8cd98f00b204e9800998ecf8427e *R/create_branch_rate_model_stuff_xml.R
53bba5b1423e07281378a33ec890ea1c *R/create_branch_rate_model_xml.R
6253dcf1be2704b8b80c6cb47ca09cf6 *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
dfe4e208646c56bb2bae8252cbf8f536 *R/create_clock_rate_state_node_parameter_xml.R
db9cfea9d5639809bfecd1147581c4b7 *R/create_data_xml.R
b4695b17cbf30e020e8707942b8fc938 *R/create_distr.R
0658ef77a6307f1e763fc24bd6aa01ad *R/create_gamma_site_model.R
9cbf8dcf3f38633f7e83d0d6932a85bd *R/create_inference_model.R
b69bfc7c1cd5c28a1a0a7e08609d78d6 *R/create_loggers_xml.R
304bf74161a83f0ce2b43c1fd57676a8 *R/create_mcmc.R
fd3c45d8043383e8e955e4b9e7a28b7b *R/create_mcmc_nested_sampling.R
35b6dcca28bf86799f3432fa6375ce2c *R/create_mrca_prior.R
03d07414e862ec54cf32ace50539190f *R/create_ns_inference_model.R
918c5e1875f0e4a0b71eb1374f6009d6 *R/create_param.R
161f4818fd57067b9f6b2345cd981026 *R/create_rate_categories_state_node_xml.R
c3210f8b572ba59a1d7704fa41bd316d *R/create_rln_clock_branch_rate_model_xml.R
b5270ad9a2a809903bccd2492ee1feee *R/create_screenlog.R
862a4988a5dce778a53f68e6e522aa01 *R/create_screenlog_xml.R
eba5cdcb1e06c76f283e2634dc849121 *R/create_site_model.R
a0e45bc129baa6b2ab6d2f6da63d8d34 *R/create_site_model_from_name.R
ae7fd84474cf0acc50f2542021be3614 *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
d71c7aaf0cb70dbe5874c00d5496aa00 *R/create_strict_clock_branch_rate_model_xml.R
11a94ff820d7cc0deb1815e11ade1f6c *R/create_strict_clock_rate_scaler_operator_xml.R
5c57d620a8565195733eb4bc2658d753 *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
4b2a7b66c2973ecf3d1548350bf4fa5e *R/create_test_inference_model.R
bab3d7fa1ff47fa084add48c2e06a8eb *R/create_test_mcmc.R
d10a99392d2d430ebb18a7db9e52ac52 *R/create_test_ns_inference_model.R
5cf5be036509943cd4669afe0aa48400 *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
3bd4bbbe4cb362fcd390140dc2b0ad8b *R/create_tree_likelihood_distr_xml.R
57a1c15fc69c39b79934bd03b06a91cd *R/create_tree_prior.R
dc19ba52fbaf9cd6e17c3baf41797b78 *R/create_tree_priors.R
7423717add07523686febc4a97962e50 *R/create_treelog.R
d7dba78b3896cc9e54f297588910f1b6 *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
84eb49c5e554202cf9c0a77cf851de2a *R/default_params_doc.R
2c0ff2d3133c33dc845183d1d966b8b1 *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
1e4c3516bdec03327fbeb2818e13ea11 *R/freq_param_to_xml.R
bde7e3b3eef83985d3cab2fae6975529 *R/gamma_distr_to_xml.R
7e788706c4203b2c8234528b70db4cdd *R/gamma_site_model_to_xml_prior_distr.R
867a18379bf00a862718165a38b29121 *R/gamma_site_model_to_xml_state.R
32a3aedf3520765ef5c4006d572a0b44 *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
e1cac3bb98898ee406cfa24e7cff6971 *R/get_default_beast_namespace.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
c7399faa61abbe7faf7e1b1115cc9ddb *R/get_n_taxa.R
fc47b7f0acc4f3d0da918199acf5e470 *R/get_operator_id_pre.R
313a45600a4e4f558c1b6a25b0b8b774 *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
7cf261519543915598f16f9e85793be8 *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
fb82e8e0a1995f29c955a6dbf96c7462 *R/get_test_filenames.R
1042c2d88b65a69b4c950839a9f1bb23 *R/get_tree_prior_n_distrs.R
1c7f0a560fd0813a280e2c3e11e5b003 *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
1eb0ea736a420ed7cddaa2494350b284 *R/gtr_site_model_to_xml_prior.R
40d73b7319d4998187c9e8200b2105df *R/gtr_site_model_to_xml_state.R
c493222a5147a3509b620464bf711d49 *R/has_mrca_prior.R
81b766be27972fcbd0fd2f0116cef2fa *R/has_mrca_prior_with_distr.R
d9d386405f52cdc0ea9ac2ff1852e462 *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
62d79acb9139ae7560edf084516517da *R/has_xml_opening_tag.R
dfbf775fb06368dad5454a5d9916aae9 *R/has_xml_short_closing_tag.R
c5e60fb3d95c12b6c9808bc8abfa1739 *R/hky_site_model_to_xml_prior_distr.R
f375c25a5921fac9b8874b72ffa46a13 *R/hky_site_model_to_xml_state.R
8451733880a598a261ef6c6b6bfef73b *R/indent.R
c30fae5ee835eaa40ccfa9932ea8917e *R/init_clock_models.R
c8b3818a4ad0a7a9486787b33eb174d9 *R/init_distr.R
171effcd5026ae50b5195168043d6cb7 *R/init_gamma_site_model.R
01bbbddf0e209bce863e8670e24d44a5 *R/init_inference_model.R
f0f63147545f1ea44e86fc97de79c2ea *R/init_mrca_prior.R
e1cd3a058d35e80c5ec460069898cc44 *R/init_mrca_priors.R
d77d0efe19e22be40feb5343ea9de446 *R/init_param.R
4b0b371437a76fee25650f9e468d6635 *R/init_site_models.R
318280a18f1dccbbdaf51f5579020f94 *R/init_tree_priors.R
4086f1819a76b2ab91fab2466a988f76 *R/interspace.R
c8e6feab1af63c726826bb0053b7b92f *R/is_beauti_options.R
217a65a360b293a6642da39af2b30ee1 *R/is_clock_model.R
fb354be76e04542adf3af01b7ef84a36 *R/is_clock_model_name.R
ba81e4afae07f4e003479d626ff666ab *R/is_default_mcmc.R
a805a7ca1a344fd0e2ea46965fff70e2 *R/is_distr.R
d0703b986c223c63072c128add56b8db *R/is_distr_name.R
667a3f0811ee953fe566b160139dc3cc *R/is_freq_equilibrium_name.R
c8be8c3e44313098f6908a05405bba48 *R/is_gamma_site_model.R
0440175c05907ff95a17ee5b94a37e30 *R/is_id.R
9c11427478ea590b2a26865c314f71b7 *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
2d4377e7d5bb99f6d03598308db44df4 *R/is_init_tree_prior.R
fc36d294f9841a1bcc587a66c7e6e11b *R/is_m_param.R
83b2f3a7565eb9cb77783ea0a372dc57 *R/is_mcmc.R
47d11aa0506556f2ac0e2be14cf81310 *R/is_mrca_align_id_in_fasta.R
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