b1aa60c1a5d499dd435ae9930c6470c5 *DESCRIPTION
7ce78896eda1ee9995847f25642489cd *NAMESPACE
16721e68430b4c8de01f2d2cd25ebf3a *R/alpha_parameter_to_xml.R
88668dd63778645cf467c2d300822b51 *R/are_clock_models.R
2fc441212e36d4e5d8f5d931a1c79e59 *R/are_equal_mcmcs.R
9aedd81d7fc1bf1cb33970384a148203 *R/are_equal_screenlogs.R
b6b1705783d6a0ad103ec8c2360d2fde *R/are_equal_tracelogs.R
aade4990c14cfcb8eb91816494e9fb5b *R/are_equal_treelogs.R
f2251dd5f6cd6e4408865dac3f1de8b8 *R/are_equal_xml_files.R
cc7d3ff603b01c4420eb5cd9edb8fd11 *R/are_equal_xml_lines.R
c0dede2b991f6dafc0825b3d540c8f2a *R/are_equivalent_xmls.R
e14ad423b8de52bcafdffe1451ff79aa *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
ae14e16b335b653c8a0638e8198f36d9 *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
722cc40490fc96bbceb3e554f8316f00 *R/are_tree_priors.R
fac5760c69f0311fbd0a60e09f0a5a06 *R/beautier.R
179195cc9885da2b258c05e93d2ca77e *R/beta_parameter_to_xml.R
1a106116c464783171af3f18fb86daa2 *R/ccp_tree_prior_to_xml_state.R
a2654c6ec184754969aaf8bbfe43bf32 *R/check_alignment_id.R
307d59db449d53a16f6a6ec0ecd9e7fb *R/check_beauti_options.R
e085e9b5aa0a5eff3a505c50edf43cf6 *R/check_clock_model.R
f470e5f82e9525ebb338c884c1f55738 *R/check_clock_models.R
4b939aa14954ea18a57230b96642f7d3 *R/check_empty_beautier_folder.R
91f69cb70c2db7e2d1ad814f501423e1 *R/check_file_and_model_agree.R
c194d57c96df96b8cfcb9f57324389da *R/check_file_exists.R
0edfd5472a66753c701a6505008b2926 *R/check_gamma_site_model.R
118aef0e95ddb92b85987f4df9c7c55d *R/check_gtr_site_model.R
8071b7067f855828a959817978a7621b *R/check_inference_model.R
5ff02c1048011de2655d1a31309c5f8c *R/check_inference_models.R
b9fa27545f0c455a6eaa5bae56f4f3e7 *R/check_is_monophyletic.R
bab02aa724fc6143d6006bc73c4918bc *R/check_log_mode.R
3f3bd9c6fb082434e6f2e3d0625d2ba6 *R/check_log_sort.R
cc56ade36b20e114b1b659448025d10f *R/check_mcmc.R
3c351b512650086eb5dbe91e61127965 *R/check_mcmc_nested_sampling.R
3eeac31797ef069c8813995bd33a4184 *R/check_mrca_prior.R
d6d9f37f256c854bac30fd6670861a8f *R/check_mrca_prior_name.R
bbfb7341275ed25396548930a66d29fa *R/check_mrca_prior_taxa_names.R
53452935bf7a7e9198062fa577f216a7 *R/check_param.R
0770655ba971eced8f7955adcb0f79ce *R/check_phylogeny.R
77d151242deaa7d4f60171c15e65b2c0 *R/check_rename_fun.R
9fa0fd926d57ef87b080a90e67308bd1 *R/check_screenlog.R
71e8991633cf9bc978eef24784391992 *R/check_site_model.R
99cb4c1cc973f071d7f8f3f517b64c58 *R/check_site_models.R
fc106e5cfd81d01a7f8f96cb023849ee *R/check_store_every.R
ed3a5b731a6aa2bebb1ea2992b0af4fd *R/check_tn93_site_model.R
dac3060af68f60aebb56aa1815d150ec *R/check_tracelog.R
9f9cb46913b6b8111b7592ef9f0cdf30 *R/check_tree_prior.R
baea3d3c173da34d5d10948713276379 *R/check_tree_priors.R
b5b35d9753cbaade41d2097c6f095302 *R/check_treelog.R
b2ea3ad03cdd1e1c62b22a2a9a47ff6c *R/clock_model_to_xml_operators.R
89240d8086a1a8382b3e1450c2ac0d7e *R/clock_model_to_xml_prior_distr.R
0ae50a60d5e5f8ece3860fa09931b17e *R/clock_model_to_xml_state.R
012f5ba52d51c88f01204d9fec5e233b *R/clock_model_to_xml_tracelog.R
49b4d830f498b0c49a8dcfaf8b0db0a9 *R/clock_model_to_xml_treelogger.R
3dcac0c2ce407f558b3b0f42f2051e90 *R/clock_models_to_xml_operators.R
3479e80dcf8323db6ade65b498a8c225 *R/clock_models_to_xml_prior_distr.R
dc6e8b047c4098d648e48899342607e6 *R/clock_models_to_xml_state.R
8f40aaa0c69572b3d6c0e5fd567ad46b *R/clock_models_to_xml_tracelog.R
57306768b15fb97f2c9aacc77e7d2b18 *R/clock_rate_param_to_xml.R
c69dc962ed8d7720fdd0ba2e5f46d702 *R/compare_lines.R
1c0173b5e7089944d1ebb6b44fa8fa60 *R/count_trailing_spaces.R
cd2845431ae6d9040e81e302e3c0fdf9 *R/create_beast2_beast_xml.R
f7780ceed7bd014d9f58fe18e77a2dcb *R/create_beast2_input.R
ec3a229c0ff23f44f59fe7b601933777 *R/create_beast2_input_beast.R
3e8ff948fef532c460a954dc419de35d *R/create_beast2_input_data.R
2fb0535df995c96fa146a9a5c045db68 *R/create_beast2_input_data_sequences.R
32c3d6b1ec2b7d8dd04c0a3003ee22e5 *R/create_beast2_input_distr.R
71875da2187acccfe030b2cdb128652d *R/create_beast2_input_file.R
61de490a3d5752f04864a292ea9208b9 *R/create_beast2_input_file_from_model.R
1a92e2498f9f783c5cea28916ab53f63 *R/create_beast2_input_from_model.R
6534680cd319246b88f17432ad9a25b9 *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
d0a5047a53ab19af7d6275590340e832 *R/create_beast2_input_xml.R
a14802d29e0fa3b858b30522b4a67c10 *R/create_beauti_options.R
15acc55d54fd1a54f5f8647eba356283 *R/create_beauti_options_v2_4.R
c986937c90dbf38e0b21add2a449b20b *R/create_beauti_options_v2_6.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
618de86992b3d1980905b96a3bcbc767 *R/create_clock_model.R
20bea18ac3680fddfeff279524688c74 *R/create_clock_model_from_name.R
5fa53b28d5d1d118b8f12870651c6c32 *R/create_clock_models.R
7b961de1deb8211d0836be20839cd995 *R/create_clock_models_from_names.R
f678da1b136c6c8f98ebb1de12a08c49 *R/create_clock_rate_state_node_parameter_xml.R
db9cfea9d5639809bfecd1147581c4b7 *R/create_data_xml.R
8bc5138574e443dd09355eee851d71e6 *R/create_distr.R
bd222df88066862c04f8c2469a4b4ecf *R/create_gamma_site_model.R
4972353bde5a170f4c8980e98afd4aae *R/create_inference_model.R
b69bfc7c1cd5c28a1a0a7e08609d78d6 *R/create_loggers_xml.R
7a6b36c45a37419bb396987dad185500 *R/create_mcmc.R
58d298e76876d85fa6025d12a4525dc9 *R/create_mcmc_nested_sampling.R
fc14b80e5560528b0ba9a71cff5ad7a8 *R/create_mrca_prior.R
80c8b2a3f0ee67f4ea1922d0406dd045 *R/create_ns_inference_model.R
931d487d84e5843f8908ca720856e04e *R/create_param.R
db0deb02867c33f035ad2460a7722e1e *R/create_rate_categories_state_node_xml.R
79ebe966cbc8f24ec9258d9e3d190d28 *R/create_screenlog.R
862a4988a5dce778a53f68e6e522aa01 *R/create_screenlog_xml.R
83e974cbc54fc2f8ac30bae4b8cd237b *R/create_site_model.R
22558133716e94d719311d338739ed64 *R/create_site_model_from_name.R
64d7dd38df6e07838373a396ff5552de *R/create_site_model_parameters_xml.R
a8cfec312b7caa40d92d8b9c676d3c39 *R/create_site_model_xml.R
5c105648420ca7256a8bd7bafdac31db *R/create_site_models.R
ef8a319a8a4f715ee9c71548d9f4727a *R/create_site_models_from_names.R
d2db6221d0b9101ca180672b40aec7e3 *R/create_strict_clock_rate_scaler_operator_xml.R
67d39b3f8926fa9fffb289c2903a0eda *R/create_subst_model_xml.R
f3e0055c91d4c490ca528e37b910a767 *R/create_temp_screenlog_filename.R
944094a35e5d013c67b9db89b58ac86a *R/create_temp_tracelog_filename.R
c9885a10eb1453088fa46cdec766c6cd *R/create_temp_treelog_filename.R
2d13c3b0959bb6be5ba817f65aa2f842 *R/create_test_inference_model.R
2f607a682edc6e883053c2cb6ec6f8d4 *R/create_test_mcmc.R
0ddc2c165fff158d248c46d7affd0f08 *R/create_test_ns_inference_model.R
6d71270e241331891962ba710e2cab84 *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
c1aed6581b923c8641406aad2f1c362e *R/create_tree_prior.R
d82ce8587b34531c48c025246a1a6f28 *R/create_tree_priors.R
090f43e58863974f3cd38b624b8122c4 *R/create_treelog.R
9aa56d7e93b7ab10e0e08db76dd86b29 *R/create_treelog_xml.R
2c9416576433e9c35ed26a625c0254cb *R/create_ucld_mean_state_node_param_xml.R
f2e73549657e07551b4ea36c2ba324bc *R/create_ucld_stdev_state_node_param_xml.R
85a305e9edcaf5c4af59b5d2bda08482 *R/default_params_doc.R
7ea7f4eb26631713960bf19c3ad1986f *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
376f1102d25aacf7adc8a4f8032daec9 *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
1fdf9a276b2e4bd03c8caee8ac15538b *R/get_alignment_id.R
9e359846f3d480b55a3fe57ecd2f4df7 *R/get_alignment_ids.R
23342a7fde3ba8bedf7a882d8720a406 *R/get_beautier_folder.R
70c4a11905440c2632b4fef56fa2f1d7 *R/get_beautier_path.R
c874793e8bcfac4cdebfae88c0007a9c *R/get_beautier_paths.R
bd8b00215c5f4cb7362a75eee618246e *R/get_beautier_tempfilename.R
c09a213e7eaa2d650870465971ae7e30 *R/get_clock_model_name.R
3a037ce3bef0436392dc41550ccdf04a *R/get_clock_model_names.R
e3d3872169f9dd5cc44eb7069b43eea8 *R/get_clock_models_ids.R
4f25dbc47d3b7cd5b686221395b6e373 *R/get_crown_age.R
c90cee2ae90c2d1199be40d25bfbf10e *R/get_distr_n_params.R
ba0316b32e80db9cbc0048375c118f8e *R/get_distr_names.R
274d5d3cba7067bcc9a6fad1a2ca0be7 *R/get_file_base_sans_ext.R
2e91ba35d10a637285a5b60b6a6e2ae3 *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
5519e76dc8462124a6aa9fa5d43fd494 *R/get_inference_model_filenames.R
2bda5bd98b81e56e0915943673d2c299 *R/get_log_modes.R
1d553e38e9acb80ca60cac2c3d16843c *R/get_log_sorts.R
b49df880eb5140342061e246514e1307 *R/get_mcmc_filenames.R
6609b09d604d17cb839200f813592fe1 *R/get_n_taxa.R
1cd70d94b39537c3a0f82ba6c3969d54 *R/get_operator_id_pre.R
e4fbe9cc9a24843c2dbe095a492b33f2 *R/get_param_names.R
0bb23423aa289d6dadcf9b379e72319e *R/get_remove_dir_fun.R
e669058cae43cef9e924b0d3b8af2856 *R/get_remove_hex_fun.R
dc1d3ec58b6510e2311e1cf8574d41bd *R/get_replace_dir_fun.R
870b4cf9539fc1e1a53d143f6ff61830 *R/get_site_model_n_distrs.R
a61233fe78a48bc348b33931cd31503d *R/get_site_model_n_params.R
f6ff8bb2c71aaaddfa4aa2f9dd0b8ec4 *R/get_site_model_names.R
073e736520bbc15f98577966a22e333b *R/get_site_models_n_distrs.R
2760df075b864be5fe70b3c12bb9bc39 *R/get_site_models_n_params.R
f16cbe315c194fb2474ebc2cbd348e7b *R/get_taxa_names.R
b5c6cbb1e13fd1d76b972d3899525b35 *R/get_test_filenames.R
45b1248b0fbec4c3c8bd96da99268135 *R/get_tree_prior_n_distrs.R
cc018b92f42741e503cf1acc8316f84d *R/get_tree_prior_n_params.R
afaa65fe2bb4d87bbf30a1510238db45 *R/get_tree_prior_names.R
61a374cccdede0aaa674527c9b947fc4 *R/get_tree_priors_n_distrs.R
2fe07f911c57afe44127332ba0c3cc1f *R/get_tree_priors_n_params.R
0727c2e2607627dda492c54ecd9621be *R/get_xml_closing_tag.R
a6707b50422fd3a2474d1d1ff2fbb707 *R/get_xml_opening_tag.R
c74c8160f0ecff97a1c87a7e6da30788 *R/has_mrca_prior.R
81b766be27972fcbd0fd2f0116cef2fa *R/has_mrca_prior_with_distr.R
9da89bb9e6f4e69073de18694429e5e1 *R/has_rln_clock_model.R
0ffe3edf515018da392e21378771466e *R/has_strict_clock_model.R
94312aa00820daef91c83b808d368019 *R/has_tip_dating.R
48739773a67b2e8fc134fa5f53eb1576 *R/has_xml_closing_tag.R
9ea6b431e6a2550543ae2d46376228f6 *R/has_xml_opening_tag.R
dd578ff73740392539608f546d535bd1 *R/has_xml_short_closing_tag.R
8451733880a598a261ef6c6b6bfef73b *R/indent.R
77f5811d0980d52bfed11aa3b6696401 *R/init_clock_models.R
c8b3818a4ad0a7a9486787b33eb174d9 *R/init_distr.R
92cbc80214d8971bca6f5e4713da4fb2 *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
4b3027c31e39e7010e35c4fceea51ca7 *R/init_site_models.R
318280a18f1dccbbdaf51f5579020f94 *R/init_tree_priors.R
4086f1819a76b2ab91fab2466a988f76 *R/interspace.R
86ae1a7f592fa7c756bebbe6398e3ddd *R/is_beauti_options.R
66984aa52f794ba2a4c042bdb48be6d0 *R/is_clock_model.R
b917edc9b0872a40faeb4c9ea28b56e8 *R/is_clock_model_name.R
0daa0c9a1549dc5bbb431c2ac264ecf5 *R/is_default_mcmc.R
87950672431c5dbf35d31f8d66d848f5 *R/is_distr.R
756da60020f3accdd1c8143388ae7fef *R/is_distr_name.R
89a52d7be75f9497024dfe13ce259ab4 *R/is_freq_equilibrium_name.R
eaa6905c265850589454bab1f0ab832a *R/is_gamma_site_model.R
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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
072f3eca90a7678323aae231aceeeecf *R/is_init_site_model.R
dc73d7fa9da32cc76f3629330df84c09 *R/is_init_tree_prior.R
b3290949147bcb8933dddaf6673b5ec1 *R/is_m_param.R
8901f60441a914294d7834e925bcd1c5 *R/is_mcmc.R
47d11aa0506556f2ac0e2be14cf81310 *R/is_mrca_align_id_in_fasta.R
0d486106bb30334f5458a623512db7f0 *R/is_mrca_align_ids_in_fastas.R
03dfec4c94394617b4a727c4b10b9323 *R/is_mrca_prior.R
158b4ebdb305d966ac422f7b141bf386 *R/is_mrca_prior_with_distr.R
864a4dd4ff9416044cafe579972b4453 *R/is_one_bool.R
c415fcebaa79880418f4e6941f7a22fd *R/is_one_double.R
70171423ee4524109fcb43f971d6ac13 *R/is_one_int.R
6dadf5534cc39288b7f225ed6bbf8070 *R/is_one_na.R
ea6ed1ed3f6ac16fffbf25685226aec7 *R/is_param.R
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