48c7e4f5659722221a1b5af68b04b528 *DESCRIPTION
7b61f86da6bdf81b963518901e9b009d *NAMESPACE
27dc2505b3a49d93bd81e94d40a28ecb *R/alpha_parameter_to_xml.R
ca356afb3d674d0bae24824fb53d2028 *R/are_clock_models.R
f44a23438c3e3c5d146efcfb94dfa3da *R/are_equal_mcmcs.R
cb419a3e889f4a232bb11b2efe1868b3 *R/are_equal_screenlogs.R
e941b41f3afb765785cf983245c34a6c *R/are_equal_tracelogs.R
3526d507081d6339c45ecfd23bb980c1 *R/are_equal_treelogs.R
978a2516432141dcff6bc4491462666d *R/are_equal_xml_files.R
d19d0b30229c95732503645303ec7d02 *R/are_equal_xml_lines.R
da8014e52f64f1479957ba3dad27f837 *R/are_equivalent_xmls.R
d22ede24f72fc2c8468695bde9e425d5 *R/are_fasta_filenames.R
d88f864b65fabf1fd43a798b80c5194a *R/are_ids.R
cc8b1e4842ffef836a944208e53d065c *R/are_init_clock_models.R
d8c1679196e66c078ee5a10db4130e1c *R/are_init_mrca_priors.R
312eb1e597a1b7b4a6c3e92e3be4e62c *R/are_init_site_models.R
5dcc49d9561946a6c2c3ec3845de6332 *R/are_init_tree_priors.R
225e402dd5117749d03e88a8dd999440 *R/are_mrca_align_ids_in_fasta.R
1e7e684e8a4fcf6bfd4b2d347127cdbb *R/are_mrca_priors.R
9027fa792ce5a4b1164fa23e58cf62e4 *R/are_mrca_taxon_names_in_fasta.R
cb4b248dd09318b09ab42a27343089f4 *R/are_site_models.R
9e5414fd537b6e87c7f39bf289649c31 *R/are_tree_priors.R
08c3cac49202c250537f6281c83a6be7 *R/b_pop_sizes_param_to_xml.R
6533aa9d0f5783d153886a30224262cb *R/b_pop_sizes_parameter_to_xml.R
a20fba207ab6c814d5924cb6b4890808 *R/beautier-package.R
43bf7e058c20a6747e5a18921501740a *R/beta_parameter_to_xml.R
4390fec2ff0ae07ab5d0d7377123d839 *R/ccp_tree_prior_to_xml_state.R
bb2a9c3fda48346ad6d8e3c89c58f216 *R/check_alignment_id.R
4750410f849531a84695605b9d4572af *R/check_beauti_options.R
8137a4e6831078cf78c476cdb5adfd21 *R/check_clock_model.R
2ddabf6cb74379791e5e2582250a1972 *R/check_clock_models.R
29010171dd755a001cd94f2ff5b787df *R/check_empty_beautier_folder.R
745f2366b1181498b7bf617b9b0ae045 *R/check_file_and_model_agree.R
5b79abfba0bb65a2b3d4f8a21f7e7ec5 *R/check_file_exists.R
cc3352334391d4bc3f92266ece2a8519 *R/check_filename.R
5fa7232bf8d3484730d04bbbdcfd451e *R/check_gamma_site_model.R
7809cedbdfb4ad0a1aa32bd07ab1f39f *R/check_gtr_site_model.R
b45c78dad9c3c674c2ae57977c3a3bee *R/check_inference_model.R
d99c98da851970c35f34d907bf08885d *R/check_inference_models.R
c51559b7020495cf4df91aefcf2d71ce *R/check_is_monophyletic.R
6611d22f0150adf1d96409be4da101cf *R/check_log_mode.R
ef7b6b3b43495c4f7bb62434e8926ae7 *R/check_log_sort.R
827f5e10fda93403a2dad3048e14324a *R/check_mcmc.R
794338b7a1f79586d8660bf8906997a9 *R/check_mcmc_nested_sampling.R
0edb5f0b96b056dc6b1a9c3ff6e6f406 *R/check_mrca_prior.R
6d0ff8b66084a855e9cdb2fb6ee449b8 *R/check_mrca_prior_name.R
2e6889303c15d4c91675bc8abf06e79e *R/check_mrca_prior_taxa_names.R
c7ee2d71b4976f3ffd991052a3f5c8b6 *R/check_param.R
86d49cb9c2ed667117d5f2fee65055e6 *R/check_phylogeny.R
c474024da9410f62282752ed875c59ae *R/check_rename_fun.R
b45e23e77d737325e05e09f1182b4051 *R/check_screenlog.R
37b6307b40b2104ab13b9cbde1596629 *R/check_site_model.R
d7773994f43de3ac3a0b11dba65eadb4 *R/check_site_models.R
224f05cca225669341d9aba89d2c613a *R/check_store_every.R
73736e6036e12f8747447da915262529 *R/check_tn93_site_model.R
911d71bff7bb481aeedf2450a872a863 *R/check_tracelog.R
f63cdb20d4c5fd04b31631e4f636f19b *R/check_tree_prior.R
8aec49cc93848a4f0591f91cae13202e *R/check_tree_priors.R
1be7711d273cff0c856d783cc964648e *R/check_treelog.R
9b7b39c120e9d6ea1b988460536314b4 *R/check_true_false.R
d882a06d925f91b1042b06a01bbc6750 *R/clock_model_to_xml_operators.R
c1cf71affccd575b81f5dff8ba1120aa *R/clock_model_to_xml_prior_distr.R
af1b5d2e7584e47d5e5f7bac85b116af *R/clock_model_to_xml_state.R
fdecb8c6a3fb0140ba273482abcae963 *R/clock_model_to_xml_tracelog.R
447e73a932f8059f60c009fd2edc9406 *R/clock_model_to_xml_treelogger.R
81b62e62a629c824ed83411629545c5a *R/clock_rate_param_to_xml.R
f16f2b35f3a5880ae74b99e58b6edc6a *R/compare_lines.R
10106f096358dda115347d5628038b82 *R/count_trailing_spaces.R
4180bc1a5627f121addf031e93f74c00 *R/create_beast2_beast_xml.R
c79c1a5be07308d28d168ede4ad7da90 *R/create_beast2_input.R
def8704aeaa6fa7eedfd69fa3c4d9f16 *R/create_beast2_input_beast.R
305ac5bed230d9072c55878933015863 *R/create_beast2_input_data.R
669de60a7d6d67fc7740cf6f9199fc4d *R/create_beast2_input_data_sequences.R
070eed24eefcd5061e9919d8f0ecae57 *R/create_beast2_input_distr.R
45535b09bb68e9953b58072d9eb2f7e6 *R/create_beast2_input_file.R
eacedd31e999ac16ae113db7642160f5 *R/create_beast2_input_file_from_model.R
4429ebb704293da1a8419804dde6c82e *R/create_beast2_input_from_model.R
6ec4de3a559085e0e20f431fb77024d5 *R/create_beast2_input_init.R
d2d41e41ab4697de913e63a1a73111d3 *R/create_beast2_input_map.R
e1224cbeaa45fe071db84532b2ef8d8c *R/create_beast2_input_operators.R
5bfc2cc2bf953079b3b21970c01a5ed2 *R/create_beast2_input_run.R
08efc273a57fcebc9e1d984bb65b8f34 *R/create_beast2_input_state.R
f2d7b26cd60487a15cc687ba449e8400 *R/create_beast2_input_xml.R
98d3540e9d96c2093d66e8c9c57fa2ce *R/create_beauti_options.R
7c7c43d3e7b1f658828717c728968644 *R/create_beauti_options_v2_4.R
1bb8e43b5bbf79662671db4a424eaf95 *R/create_beauti_options_v2_6.R
a2576658a63a183dad92750edf38752d *R/create_beautier_tempfolder.R
d41d8cd98f00b204e9800998ecf8427e *R/create_branch_rate_model_stuff_xml.R
5552e02b1071fce421ca84dee13d1d47 *R/create_branch_rate_model_xml.R
32f4e588a1ae4e5d534a5b44b9b48124 *R/create_clock_model.R
b84bdf79aec90e39687670127a59cb89 *R/create_clock_model_from_name.R
c901b51859317af818f7d7a4fdda4b5e *R/create_clock_models.R
2dd0ddbd8f7a54618b2729f517afd6e8 *R/create_clock_models_from_names.R
471183111e8325cb5b7a973b9f98e516 *R/create_clock_rate_state_node_parameter_xml.R
db9cfea9d5639809bfecd1147581c4b7 *R/create_data_xml.R
9d22479e03b8b413d55eb853400ec7a4 *R/create_distr.R
80026a88715e65d883959a01900a251d *R/create_gamma_site_model.R
5c64d803503c2c42fcdb173289c255b4 *R/create_inference_model.R
3ac3fdec4758be17f6ff1f50fe831e17 *R/create_loggers_xml.R
7e0fc2cb8afa997917047cb92b09672c *R/create_mcmc.R
d19017706e2dda9764d15ee43b3f6985 *R/create_mcmc_nested_sampling.R
3b98cda7390b3cb4b79cbfa61929a1ee *R/create_mrca_prior.R
855f70a63a0524fd65303f2f346acc02 *R/create_ns_inference_model.R
011928936ecbcee7d1ee698657e52128 *R/create_param.R
7f198b0a9bebdc77783bff924bdd0f6b *R/create_rate_categories_state_node_xml.R
5d2b61ea603f2037f0423b59b088abe6 *R/create_rln_clock_branch_rate_model_xml.R
3a3c2ead84e7918572d996e5abc96312 *R/create_screenlog.R
2e2dce4d04f2a547fa8954c91490fb6f *R/create_screenlog_xml.R
ece0bd0890bf8e5b44a54a2e8d379d5f *R/create_site_model.R
936be215dd46a87ac0b5aa460603d311 *R/create_site_model_from_name.R
628197c9df70fbe2e412de3843fc7a95 *R/create_site_model_parameters_xml.R
991ae9ed6f83a2f726b41908dcbb5f42 *R/create_site_model_xml.R
56c7ac0a9dad630035480bbf0ed75842 *R/create_site_models.R
ae02cc0881fcb88fb04e47a5d45aca22 *R/create_site_models_from_names.R
717734e0d10d6f078ec49e98e790e592 *R/create_strict_clock_branch_rate_model_xml.R
2a444af6a4be871f4de5507ab98878ce *R/create_strict_clock_rate_scaler_operator_xml.R
61a8753db11d1546def928a02aedd96b *R/create_subst_model_xml.R
310d441ed52c08bc99e9964d44f57954 *R/create_temp_screenlog_filename.R
0d7741166081bcec9d589c719eb9658d *R/create_temp_tracelog_filename.R
725f589c078f62515d4fdaef523681b7 *R/create_temp_treelog_filename.R
8a01f503026dcb644a9f4769b287e4bd *R/create_test_inference_model.R
ac4d6155ac305f63a1255c1614c0116a *R/create_test_mcmc.R
6179ffbf7f7b77e76dc87bd0ab34bd52 *R/create_test_ns_inference_model.R
aaaafac161cbe3170f7c3938268eb8c4 *R/create_test_ns_mcmc.R
f3b19be3ed3fba10a373eab17722a44e *R/create_test_screenlog.R
3391f86eb6859d64a53b86d3773a6ee9 *R/create_test_tracelog.R
2c355a4ed9daf801ac75d73d97d6c4ff *R/create_test_treelog.R
0c8403b2fa1c7d87e1e3b8f5959ee116 *R/create_tracelog.R
a154a6c4170d56595156298d5de740cd *R/create_tracelog_xml.R
d7ab57158eac44e269affc89ed2611fc *R/create_trait_set_string.R
c7bd654ee3b5a522cf416b564d323303 *R/create_tree_likelihood_distr_xml.R
eef635b50d4b24a631e618d2d2bc49f9 *R/create_tree_prior.R
778a7097c74950cac7f68a9e1fe96dd4 *R/create_tree_priors.R
09ec0be8e34074c9c6c47ccc9d9e3820 *R/create_treelog.R
295f6c42b770c5b0d955be9afb05661c *R/create_treelog_xml.R
8d907db088444e7766ec411b1de55e16 *R/create_ucld_mean_state_node_param_xml.R
546adb2fef9a03dae564f3053cdebd65 *R/create_ucld_stdev_state_node_param_xml.R
2c1cfb4382ef8b423b0ce440ccdf468f *R/default_params_doc.R
4df0ef7acb9287062ce1b23dc2c71d0e *R/distr_to_xml.R
98f471c9291fe87a67139171c9c8aedb *R/extract_xml_loggers_from_lines.R
f0eee4689d0daeff78fda63dbab74ce7 *R/extract_xml_operators_from_lines.R
b9da9b92396a1912a5507569757e3ba5 *R/extract_xml_section_from_lines.R
9766d4958ac2fb0f9ac6b7f8776a155b *R/fasta_to_sequences.R
a47bd397185436e4897431902b4d1128 *R/find_clock_model.R
e689752865a1d6a6acc1a4868b0e1392 *R/find_first_regex_line.R
48e61248a5bedc3c30bb9643fef02f83 *R/find_first_xml_opening_tag_line.R
12b165edf84b5816831f43af911efd75 *R/find_last_regex_line.R
2c59ed146fad84cb041b2deaf8c8453a *R/find_last_xml_closing_tag_line.R
c7c12353c012694c39b15baae2aad8a9 *R/freq_equilibrium_to_xml.R
5436c2f22441234d8d976ed2e351744a *R/freq_param_to_xml.R
382b5ef516c31a9c8d296ad799aafa5d *R/gamma_distr_to_xml.R
f25e3eff22fae17452f0ffa8eb7e691a *R/gamma_site_model_to_xml_prior_distr.R
c3e845d659f820df8a8409ce31562d36 *R/gamma_site_model_to_xml_state.R
32a3aedf3520765ef5c4006d572a0b44 *R/gamma_site_models_to_xml_prior_distr.R
a67617f0d8ae1d3ef6b0709d85f38a0b *R/get_alignment_id.R
e9e1b98c8fb9ffe3397eea02f0f068d2 *R/get_alignment_ids.R
d6fb49bb0dd96ec73a4a3aa7fb1fa876 *R/get_beautier_folder.R
4622dd8b13b59c18db1f64157bc61d54 *R/get_beautier_path.R
4749103849b2fce232fbaa2e35ac07c0 *R/get_beautier_paths.R
bd8b00215c5f4cb7362a75eee618246e *R/get_beautier_tempfilename.R
90464cf12178759927bf476bcfadfd0e *R/get_clock_model_name.R
1e598de48517eefa81008b74aded3ac1 *R/get_clock_model_names.R
1c0994f528e4f3e80a2e91d25a64d8f4 *R/get_clock_models_ids.R
3a8ff92ef76c54dd045b80d0a6f2e641 *R/get_crown_age.R
e1cac3bb98898ee406cfa24e7cff6971 *R/get_default_beast_namespace.R
4a0bf14cbbb780416899819d96e74789 *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
a0223d511e91db1aef3b43498f44acb3 *R/get_gamma_site_model_n_distrs.R
26d1b7ecafdf119c4e7e3f4dd26094f0 *R/get_gamma_site_model_n_params.R
987fe2d0e62f4f5dc32c77af32d14937 *R/get_has_non_strict_clock_model.R
8b8486b80672e410ce973bf747b8bc5c *R/get_inference_model_filenames.R
21ecdb5eaf81295bb2c11b4581e7f4f7 *R/get_log_modes.R
5151a94757058708ae436249520946cf *R/get_log_sorts.R
c220e0091eca5b8ba06f5fa0501516f0 *R/get_mcmc_filenames.R
632563d583876af32c758e7e6960d0dd *R/get_n_taxa.R
bf668423c3beda5b4921b80cf3885e8f *R/get_operator_id_pre.R
313a45600a4e4f558c1b6a25b0b8b774 *R/get_param_names.R
16d650900abf7ee30796506e5b0a5056 *R/get_remove_dir_fun.R
a397fadaba5ec4f2e6ae2ed4098cd7cd *R/get_remove_hex_fun.R
82d376c4dbbe49f1bdde8823d1964de3 *R/get_replace_dir_fun.R
21f747c54b083819ae2bd991809ee0a3 *R/get_site_model_n_distrs.R
ededc4f54ab4e3e87682526e18d6bf09 *R/get_site_model_n_params.R
108f33219fc222c4efbadac0fb1910ba *R/get_site_model_names.R
f074c1533753213f06b802e2a66cd4cf *R/get_site_models_n_distrs.R
a62cabdd50c6c2d36f47ba4e547c4426 *R/get_site_models_n_params.R
713096ddd17b5d8233c18afac2b0cfa5 *R/get_taxa_names.R
d33356fee65d3a34b7985c915f77c166 *R/get_test_filenames.R
ae0bff83dd1efcc2dbb278e7a62d55ec *R/get_tree_prior_n_distrs.R
27018e5745104665aedca9d95e08ee51 *R/get_tree_prior_n_params.R
ee8f77fe64e48cc4536d0f9fb2770c7f *R/get_tree_prior_names.R
9b320b1d7892b90dc2b3f948f11072ab *R/get_tree_priors_n_distrs.R
076c5fb5dce8f98f846f9a063b8b0a0d *R/get_tree_priors_n_params.R
be76553477cff5c0f9f2c8395e532fda *R/get_xml_closing_tag.R
a6e6f339dc0408eca2e40fe18221c4b2 *R/get_xml_opening_tag.R
3d9825776eaf4bd65b831ef9e4e5d6f2 *R/gtr_site_model_to_xml_prior.R
3988d6860704c9132b87200c339ed864 *R/gtr_site_model_to_xml_state.R
dbcf7794ef0e3d337bdd803bb1b721f8 *R/has_mrca_prior.R
96b89f315a8c9de3b36dbee9aa0741f2 *R/has_mrca_prior_with_distr.R
6350717d83fbc61c05aed5404491f727 *R/has_rln_clock_model.R
649e99bfa66d63cb002fea8cee108990 *R/has_strict_clock_model.R
f018b9d1a9a8bd53a6c4479e8e5d7f4a *R/has_tip_dating.R
f6a8fb8f9921bd8b6a1d9a275cb5ac39 *R/has_xml_closing_tag.R
d0a02a4c6c0b38cf37017e23e4ff25a1 *R/has_xml_opening_tag.R
fdfea87627c1a3305a26f09559385384 *R/has_xml_short_closing_tag.R
8c427f5cdf893858e1920dfd9afd3c86 *R/hky_site_model_to_xml_prior_distr.R
6c2ce583fbf37091ef03b2e1c70a2b4e *R/hky_site_model_to_xml_state.R
c80a9eb1427c585807cecf618b6f3870 *R/import-standalone-obj-type.R
c40f882046a958444c6058a9e2cb9a3b *R/import-standalone-types-check.R
d60887db5e8bdd75891f19266e46efc0 *R/indent.R
3cfd83d46b8ff9152c49e24d3fc72738 *R/init_clock_models.R
1e4673d1adce9336fed3d4a0ee0e5f53 *R/init_distr.R
742ba1ee807ba223bacb56b31da340cb *R/init_gamma_site_model.R
0da34735ad7aa7d962c4e19466dabe53 *R/init_inference_model.R
5e692c4c1fd48da4f9689f9bbc643a08 *R/init_mrca_prior.R
91688d03b2030563db21a8f167b7ee4a *R/init_mrca_priors.R
b61583b9f7df62bddc83be6dee78b220 *R/init_param.R
bde8862977d4ce9fad808a7922324611 *R/init_site_models.R
a08b5188b75f2a98a66df716f05aa448 *R/init_tree_priors.R
512102b96acce97ee891577d21e9d9d0 *R/interspace.R
c8e6feab1af63c726826bb0053b7b92f *R/is_beauti_options.R
749791ca7a957d6002392a153d10fb2a *R/is_clock_model.R
d67335139ede24afabef37f40d7f1f31 *R/is_clock_model_name.R
95ccb249bcc99a00bb51e34bbb95ea24 *R/is_default_mcmc.R
6d6f29c8f2c28e75f520646c2d9bd772 *R/is_distr.R
4796d8092f7429f7e54d82fdeb35f69a *R/is_distr_name.R
2c653f1832f97deae344e46fb98a0718 *R/is_freq_equilibrium_name.R
992d7d24a90a502c27dc6a2c76060abe *R/is_gamma_site_model.R
cd04f21e000c1e50842125c6a827e91d *R/is_id.R
65e0c7f9a9c37ff39abf8927140dadb5 *R/is_in_patterns.R
93ee351921181505aa6e4804819f515a *R/is_inference_model.R
cb9aad92b6806d08967d14811d2d8975 *R/is_init_clock_model.R
377f9ea55e61dcc59756d16002cb612c *R/is_init_distr.R
9b1db74a7b0f2f843e3bb8dc9d087998 *R/is_init_gamma_site_model.R
1bf9f24bd0e36f5a9eb04f7d5f14682f *R/is_init_mrca_prior.R
b41e4b42f151c0ebfe5ae80cb5328a16 *R/is_init_param.R
81a860a9068b5b9aca3712aeb23a370e *R/is_init_site_model.R
ad547523ffddfb8353f1d1d31d8571c6 *R/is_init_tree_prior.R
036466056609a81d3deb3f3d7f53e9f3 *R/is_m_param.R
a117e240b4188f6652262addabe90329 *R/is_mcmc.R
c7a0a2dab53c2f4cbb56857c62a99066 *R/is_mrca_align_id_in_fasta.R
d5772bbe16774cfa71892569d9858812 *R/is_mrca_align_ids_in_fastas.R
b898f2c917958694db370b697e1707ed *R/is_mrca_prior.R
26899916a9efc0bb266029f9728f31f6 *R/is_mrca_prior_with_distr.R
4940192e7b318bc64764952e3257a85d *R/is_on_ci.R
6bc7f2004180f1980a55210c166fd78b *R/is_one_bool.R
d2ea8c0b7ada58b7dc03abd7a5220fed *R/is_one_double.R
8b5a532ba591423e8a433565fbe8ce5a *R/is_one_empty_string.R
5f44cdf4fef9310b98b59d60ddb602d8 *R/is_one_int.R
f35a6791c6e8727b5b4da3ea1d506943 *R/is_one_na.R
19866b09b57c8770f85850acd015315d *R/is_one_string.R
2b170f68ade69046d167e562955c2717 *R/is_one_string_that_is_a_number.R
6dfb815fd25871102e13186452f0ce65 *R/is_param.R
704e27b4152d54c6769717e62a47f3b4 *R/is_param_name.R
658fa5536bd27cf343d0cdd3d3edaeda *R/is_phylo.R
c78afbd005d9135241a4563fc9a7dcf6 *R/is_site_model.R
249af1ee5364b24ff9f928f55b10777c *R/is_site_model_name.R
6a94db605ed82b742fd8b0b5ae10d0d8 *R/is_tree_prior.R
4aa965a3d7884265ea1105b3b08356a6 *R/is_tree_prior_name.R
7efc76e57c67edb7e353ada391ea8a9b *R/is_xml.R
01d231f9784a4bbb04333d5bad6e07b9 *R/jc69_site_model_to_xml_state.R
714a977d33bb99c2275ee2e120c72948 *R/kappa_param_to_xml.R
f7dfa6b0ededd6a122f6dd0bc912ca92 *R/m_param_to_xml.R
c5ba37b0b9fd04075c3655e1943b1d5d *R/mcmc_to_xml_run.R
d5197ff975a08aea530c2ea3df371018 *R/mrca_prior_to_xml_prior_distr.R
390ec1953f536438b432c2e3c500daf9 *R/mrca_prior_to_xml_state.R
1c26b7c5b2ed6c5e0a67e1ccab4df0ef *R/mrca_prior_to_xml_taxonset.R
3b7135c5451017a3ae3ff6a65934cb12 *R/mrca_prior_to_xml_tracelog.R
578ef2ffe63e88495c79e64574b715af *R/mrca_priors_to_xml_distr.R
51551667289ea0b9213d7d19c24a7bd1 *R/parameter_to_xml.R
819d93c75abc48a558b3d7746c2e4a92 *R/remove_beautier_folder.R
b81b2d3ed7c23e4a49a9a21e3cc979cf *R/remove_empty_lines.R
b617fc9254b897ac6dd36d08c669b55e *R/remove_multiline.R
d607f2afc49484524831535cec14c657 *R/rename_inference_model_filenames.R
37945ed028c1a7ce7d836e9fbd83bc99 *R/rename_mcmc_filenames.R
aebd43a7710ecd9f14b7807dc68b6a8f *R/rln_clock_model_to_xml_mean_rate_prior.R
41383e4e26bd3d4a916d62d79439f07f *R/rln_clock_model_to_xml_operators.R
9709b54e181fb568901a980377a1e1b5 *R/rln_clock_model_to_xml_prior_distr.R
b595a2d0071506ea8fd931960b0195fc *R/rln_clock_model_to_xml_state.R
ae5b2c77fc3814b857edae772a546772 *R/rln_clock_model_to_xml_tracelog.R
7f33f8aa67716e0defc77b7b8d78f0f7 *R/rnd_phylo_xml_init.R
a982e7f895c3babdfd64603144f1992e *R/s_parameter_to_xml.R
d212ad39600dd9b87cc12328545e901e *R/site_model_to_xml_operators.R
1827d19fafa0b3aa40f3627764cdef07 *R/site_model_to_xml_prior.R
fdf644598b522b35bdf5da7f56292df7 *R/site_model_to_xml_state.R
a0f8fe3bf6702ee10669d8b37c83049a *R/site_model_to_xml_tracelog.R
12c95b671896fc1b2a147ed6c40f9995 *R/site_models_to_xml_operators.R
bca394aaa8029febd15b04425cd0bc61 *R/site_models_to_xml_prior_distr.R
530dc50f269ba4b482009b025eec4e7f *R/site_models_to_xml_tracelog.R
f3e24c004172d16e908b7605aadf75f0 *R/strict_clock_model_to_xml_operators.R
d2b5fbbf40e741f10f63427139ba89d8 *R/strict_clock_model_to_xml_prior_distr.R
0b7358b189729424b22a83ab06921329 *R/strict_clock_model_to_xml_state.R
a510713116ef0fe41bc4adaae4cb0d40 *R/strict_clock_model_to_xml_tracelog.R
24efc16f8bd1064529344f8476692a19 *R/taxa_to_xml_tree.R
be4221c4c5c4201407dd6659f3d51fa5 *R/tipdate_taxa_to_xml_trait.R
2e61ec99db246d39e3d14b001bf7b6c1 *R/tn93_site_model_to_xml_prior_distr.R
62e83fc3437c22b58009407a83af5856 *R/tn93_site_model_to_xml_state.R
50b375d6d09abef44a9238717252bcc9 *R/tree_model_to_tracelog_xml.R
bb54cb6d8bc4ea9a8326e4374cad0be9 *R/tree_prior_to_xml_operators.R
23e9023d7a9a5607ea3bf5c43bc6c723 *R/tree_prior_to_xml_prior_distr.R
db7736d767298448f25a81e52c7834af *R/tree_prior_to_xml_state.R
e0b7741ab83aa9b2c98caf5408cc36f1 *R/tree_prior_to_xml_tracelog.R
d4ab1e1a1a06e3e60b600063d9d64b8c *R/tree_priors_to_xml_distr.R
7146289a5507dc01f390227213ce75ec *R/tree_priors_to_xml_tracelog.R
7070e51273a22343df15d3631d772628 *R/unindent.R
6659fe837946fe4afbab1b2e864cd13b *R/yule_tree_prior_to_xml_operators.R
cdba3b212ae69c0a7bca1e06fc493b60 *build/vignette.rds
193ba2b3275450fe3c2f513549665b88 *inst/CITATION
48ceb4b9a448e23255f32e169a67c64c *inst/WORDLIST
74a9f6cbf17526f647f3a73886327101 *inst/doc/demo.R
2c9503f5c6de0bedc889ddf6d68cdadf *inst/doc/demo.Rmd
447e8af4273e79825784f55948324a93 *inst/doc/demo.html
a84a85c2b8b5ed41b70220dd39e4d052 *inst/doc/examples.R
c73a2f81d34a803062d0a2886b5b76fc *inst/doc/examples.Rmd
7335ca7a119c48744bb809058e39addd *inst/doc/examples.html
a127842886136a967f072bd1d2d50df7 *inst/doc/inference_models.R
b25ff646358933ce64e49a50b6680fcb *inst/doc/inference_models.Rmd
6bef23dcaf0320c4611133b889e79e39 *inst/doc/inference_models.html
ab8a5a5c4df00592d083429ac59b400e *inst/extdata/2_4.xml
4518fad1510f98fa3c2956a177675e13 *inst/extdata/2_6_0.xml
f571a0f8e7ffbac2241ad766c899dd5a *inst/extdata/2_6_2.xml
a984eaa183aa9c5f8071a26ba26a3356 *inst/extdata/Felinecoronavirus_Envelope_1.fas
9379437996332fa0c4c21031b24b4ef5 *inst/extdata/Felinecoronavirus_Envelope_1_no_quotes.txt
e67325fd7bfce7aff6687e6e7d0f1323 *inst/extdata/G_VII_pre2003.xml
ee9015ff9647397027e9d62f6fbbb246 *inst/extdata/G_VII_pre2003_dates_4.txt
8470c763001b91d030ecc8cfb5beb610 *inst/extdata/G_VII_pre2003_msa.fas
4c0cf2886802d77761fb19e3d343b1cb *inst/extdata/G_VII_pre2003_no_tip.xml
03bd5d9d8517f7f1c1e1f4ea499d4ddf *inst/extdata/Heleioporus_species_ND2_Pop1.fasta
0fddec382e48736adf331ee832e2f12f *inst/extdata/THAILAND_TEST.clust_1.dated.fa
df03cb297e86c50cd1e4f8ceb8245732 *inst/extdata/THAILAND_TEST.clust_1.dated.txt
4bff5c4a0197761802098d92904a1016 *inst/extdata/aco_hky_nd2.xml
5a4de5602198368b992c79962204b444 *inst/extdata/aco_mcmc_chainlength_10_store_every_1.xml
2ea273800f4116488eeb800b77913d4f *inst/extdata/anthus_15_15.xml
7ed16c2bf51623706d6d04d5aed06ee4 *inst/extdata/anthus_15_26.xml
4581fa3098cf89f533f1c147270dff91 *inst/extdata/anthus_15_na.xml
0eedfd95a1fff834d513246b4e4624e2 *inst/extdata/anthus_aco.fas
d37753c82288c23dda0c95c496f50ef9 *inst/extdata/anthus_aco_sub.fas
fe0858e495d81990631aa9d684f942d5 *inst/extdata/anthus_aco_sub.xml
26b58a6d7bc0f49d0638d9914bf58ba6 *inst/extdata/anthus_aco_sub_20181016.xml
2fdedcea03178ab851085954352a46c3 *inst/extdata/anthus_aco_sub_20181016_all.xml
0723559a4c2d7ff82277ee86a438c0c6 *inst/extdata/anthus_aco_sub_20181016_all_monophyletic.xml
635058fe650c9df7a4b1f5070514e3c6 *inst/extdata/anthus_aco_sub_20181016_all_one_div_x.xml
c38a508f0044f186775ca4d45cfc07ad *inst/extdata/anthus_aco_sub_20181016_all_one_div_x_monophyletic.xml
992cf9fd0caf2936d207fa37ea7a1d82 *inst/extdata/anthus_aco_sub_20181016_all_one_div_x_rln.xml
27618c7571bfba0da5e49cbddf8bf1ff *inst/extdata/anthus_aco_sub_2_5_1.xml
321966c7a7d9342442e0ecd37709eff9 *inst/extdata/anthus_aco_sub_2_6.xml
321966c7a7d9342442e0ecd37709eff9 *inst/extdata/anthus_aco_sub_2_6_again.xml
43d1b3ca7d4746dbac4422a5df5258f7 *inst/extdata/anthus_aco_sub_calibrated.xml
04616619e915312f562d7f7ba2f8adf5 *inst/extdata/anthus_aco_sub_calibrated_no_prior.xml
914e22a8f33194faccae17db350b6fca *inst/extdata/anthus_aco_sub_calibrated_rln.xml
3cc21807485f89b0db39aacab9f19828 *inst/extdata/anthus_aco_sub_calibrated_rln_monophyletic.xml
e97ddd3db9921d9399bea9d21b992b4f *inst/extdata/anthus_aco_sub_cbs_groupsize_4_dim.xml
58632bb9c46b2a79b5d19fe642413756 *inst/extdata/anthus_aco_sub_two_mrca_priors.xml
eb275854328e8fc88c7ef6adcfc96ad3 *inst/extdata/anthus_na_15.xml
4f47d3dda06c4ad6605b84cf43579113 *inst/extdata/anthus_na_na.xml
93d45a2f0c0145ebfebdedeb073025f1 *inst/extdata/anthus_nd2.fas
06d16968e24a50589d5143bd40c5dc01 *inst/extdata/anthus_nd2_sub.fas
8b235cf2f1e73dfa3694d2e32be45d4c *inst/extdata/anthus_nd3.fas
557ce9b9297b422a02e34239f0712fa9 *inst/extdata/anthus_nd4.fas
44adb9268a506091b4d45b9aeb8d5022 *inst/extdata/bd_2_4.xml
16bed6d043bf9ca15567b3d59319236e *inst/extdata/bd_6_taxa_2_4.xml
47008dd0b09a468b9f91ce66b703ee5e *inst/extdata/bd_birth_rate_normal_death_rate_gamma_2_4.xml
e119bccc8398614631aa43e2ec5d7b0f *inst/extdata/birth_rate_beta_2_4.xml
922686db0b9c63745e087c7d2adeebb2 *inst/extdata/birth_rate_exp_2_4.xml
061aa1bfe45432b70b346fa50ed0a0e3 *inst/extdata/birth_rate_gamma_2_4.xml
8eb627a88d8bbee08050b531eda648c4 *inst/extdata/birth_rate_inv_gamma_2_4.xml
04c38ae3c0b26f568ac8b7e5e673c45d *inst/extdata/birth_rate_laplace_2_4.xml
a008e7e6183d073307138212c0abddc7 *inst/extdata/birth_rate_log_normal_2_4.xml
66be5c37ac475bf0f8ed4df4c5c0abeb *inst/extdata/birth_rate_normal_2_4.xml
c5a60a83c1e1ecfb03920b7f8bdba789 *inst/extdata/birth_rate_one_div_x_2_4.xml
8d0a71aa162f4965ca1fc18fdd4b3d83 *inst/extdata/birth_rate_poisson_2_4.xml
ab8a5a5c4df00592d083429ac59b400e *inst/extdata/birth_rate_uniform_2_4.xml
83175e1969649d46fc559ddd3c519a24 *inst/extdata/cbs_2_4.xml
65237eca43bfa7fb918400c07436faa0 *inst/extdata/cbs_6_taxa_2_4.xml
39051f7dc27012bfa2ddda745a0ac856 *inst/extdata/ccp_2_4.xml
9df6cb5b1c316d9c6cf5ab653b366d47 *inst/extdata/ccp_6_taxa_2_4.xml
b4ba448f219d916b430e030966df9f09 *inst/extdata/ccp_pop_size_gamma_2_4.xml
4711d7922aa14d6cf0e1f37552ca8919 *inst/extdata/cep_2_4.xml
fb1216067317ebcf381f4db89a3a4dc3 *inst/extdata/cep_6_taxa_2_4.xml
f62ad967d7a6410ee3d0d97ab5880732 *inst/extdata/gtr_2_4.xml
cdbd9db897ef307f4e8a6e7807eacdd9 *inst/extdata/gtr_2_6.xml
842b2a51445d2852e91ebd7b9a8bf2f4 *inst/extdata/gtr_gcc_1_2_4.xml
b18cf933270115e6c63fe9f0bc328d09 *inst/extdata/gtr_gcc_2_2_4.xml
1638e99fe0d85b60a8bc5bf8feb69d5c *inst/extdata/gtr_gcc_2_shape_1_5_2_4.xml
a0ede49dff20b1777cb358bfdcee3265 *inst/extdata/gtr_gcc_2_shape_1_5_prop_invariant_0_5_2_4.xml
e86ff19c6f0600df95c20ff1f3690115 *inst/extdata/gtr_no_rate_estimation_2_4.xml
dc5c1bed1e7f4d8421d5cca71a70398c *inst/extdata/hky_2_4.xml
662095277971e20463c8a44c1a31e0a0 *inst/extdata/hky_2_6.xml
74bd7cf5cf778538cd4f007e026f4164 *inst/extdata/hky_gcc_1_2_4.xml
5e480a92dcb54846062106dd134c5da2 *inst/extdata/hky_gcc_2_2_4.xml
eba38f72e1007637fc483c60c58ffa58 *inst/extdata/hky_gcc_4_2_4.xml
56da253f367bb64bae70b57f4464848d *inst/extdata/hky_kappa_2_4.xml
d89d329cb1ebee6417de2f7fd6f97b8e *inst/extdata/hky_prop_invariant_0_5_2_4.xml
03527519a5af45160bb449fa2173799e *inst/extdata/issue_135_mrca_estimate_beauti.xml
810461bca47fd24343a5a24127b7cdb5 *inst/extdata/issue_135_mrca_estimate_beautier.xml
37c2611661760eb80ec5a2f77703ffb2 *inst/extdata/issue_135_mrca_no_estimate_beauti.xml
810461bca47fd24343a5a24127b7cdb5 *inst/extdata/issue_135_mrca_no_estimate_beautier.xml
00aa723c6c7a277d5a369d0d3a7bc96d *inst/extdata/issue_135_no_mrca_estimate_beauti.xml
68a4d04aa1e645f21b3c8a5607669f69 *inst/extdata/issue_135_no_mrca_estimate_beautier.xml
b0db4e11fa72209145ec30ae47d12c46 *inst/extdata/issue_135_no_mrca_no_estimate_beauti.xml
8d0f99b1d4cbcbf084f61979c6e1571d *inst/extdata/issue_135_no_mrca_no_estimate_beautier.xml
4b6cc23a9629285cece92770f41180e9 *inst/extdata/issue_137_lognormal_estimate_beauti.xml
163af492e7d7e0c70c098419e44832a4 *inst/extdata/issue_138_v2_6_7.xml
dd92d10dd3ff3cd24efc25992235b8e6 *inst/extdata/issue_138_v2_7.xml
ab8a5a5c4df00592d083429ac59b400e *inst/extdata/jc69_2_4.xml
f40dc625706ffda64e04b2e77660e8b5 *inst/extdata/jc69_gcc_2_2_4.xml
ca2ce3159952d4a37a18328f80884b83 *inst/extdata/jc69_gcc_2_shape_1_5_2_4.xml
a9efb6806a542a76e7bf23b37193caf7 *inst/extdata/jc69_gcc_2_shape_1_5_prop_invariant_0_5_2_4.xml
ec4b822379788832562a7f361ad3c704 *inst/extdata/rln_2_4.xml
e9e98c887c8b041dc58ba2ac588fa61c *inst/extdata/rln_2_6.xml
16c8ec7976acefc0aff158ea50b83cda *inst/extdata/rln_mrca_2_5.xml
4a05059ba5b019a70b037252adfbe455 *inst/extdata/rln_mrca_one_div_x_2_5.xml
a2890d3c957559edaa4cccf158c2057a *inst/extdata/rln_tipdates_2_6.xml
9e610c7d7780a6614d17d23e8ba0f404 *inst/extdata/rln_uclstdev_beta_2_4.xml
ab8a5a5c4df00592d083429ac59b400e *inst/extdata/strict_clock_2_4.xml
8129481386c11ce5aa8a5846dd721415 *inst/extdata/strict_clock_rate_0_5_2_4.xml
e3517e0e9266d590e79870f7d06976fc *inst/extdata/test_output_0.fas
5eedced14a925e900091e7fababf818b *inst/extdata/test_output_0_n_init_attempts.xml
a39f7a45f4e0329178cb0fb4c2cad1dc *inst/extdata/test_output_0_pre_burnin.xml
197476cd508359a9d682e67100fe9669 *inst/extdata/test_output_0_tipdates.tsv
a7ce1f2ed7f9b7bae358166c0528f30a *inst/extdata/test_output_2.fas
e3517e0e9266d590e79870f7d06976fc *inst/extdata/test_output_5.fas
ec083e238606229bcc5ad0a2ea17a456 *inst/extdata/test_output_6.fas
21597125741d41b743cd6cb805fd7805 *inst/extdata/tipdates_2_6.xml
d655b6f360f4e79595a82182cd50827d *inst/extdata/tn93_2_4.xml
17f5a5551eaca220a6723bdaefe3c94b *inst/extdata/tn93_2_6.xml
6bc2ab38544831cf1b1b539d773afd7b *inst/extdata/tn93_gcc_1_2_4.xml
f5bbf19d02a1f37e4a95ad083e9c6dd7 *inst/extdata/tn93_gcc_2_2_4.xml
a50f1bab306c3e948c066cf9bacb332d *inst/extdata/tn93_kappas_not_estimated.xml
ab8a5a5c4df00592d083429ac59b400e *inst/extdata/yule_2_4.xml
fbb13fb1685da603e8dcc9af509af424 *man/alpha_parameter_to_xml.Rd
e102ee0c592ab7314065ed97ccb202c2 *man/are_clock_models.Rd
737f9781f1d9f3bf4c04eb50857706d2 *man/are_equal_mcmcs.Rd
fd3466787518ee4ba125bd565503b50d *man/are_equal_screenlogs.Rd
2719558b3ac3b10bd3bb4eccffa118ef *man/are_equal_tracelogs.Rd
8bc3fded443344a90042da5a07b290d9 *man/are_equal_treelogs.Rd
88a3f810356ddffb355ebcfebaaf22fe *man/are_equal_xml_files.Rd
7cf70d2db30768c45ea607a2031e7fac *man/are_equal_xml_lines.Rd
07c5d92788e66a04fa823932aa826ebc *man/are_equivalent_xml_files.Rd
eaab3c48a643ab3a324503c95cda2780 *man/are_equivalent_xml_lines.Rd
687ca1ec02eec2670e5d3ee51df6d905 *man/are_equivalent_xml_lines_all.Rd
7d050ea92ab0c0c9be922695152f1767 *man/are_equivalent_xml_lines_loggers.Rd
50b6dca8f2309c4574624161e216a157 *man/are_equivalent_xml_lines_operators.Rd
b7a0dba4dfb08f2b8a5649f1c2270dcf *man/are_equivalent_xml_lines_section.Rd
4e09881b03b9e32359a6205e21913eda *man/are_fasta_filenames.Rd
45be6383b53ef09c248cd4f77778a739 *man/are_ids.Rd
b19dd7b4b530b7356bfbc8488de53d02 *man/are_init_clock_models.Rd
44f90d5c1a761e75cf9a6af17b369104 *man/are_init_mrca_priors.Rd
5a5c071cbe3cdff3e0b9fe0b7b4e8c64 *man/are_init_site_models.Rd
a0ea0d423e387a4fd88767843d1c4682 *man/are_init_tree_priors.Rd
63b2e886567ad58510a0f45135b4debf *man/are_mrca_align_ids_in_fasta.Rd
d6f6b28ab665b14091f3b3eb9fbfddac *man/are_mrca_priors.Rd
906b3e1ae0ca15e1b45167dd43b00dc7 *man/are_mrca_taxon_names_in_fasta.Rd
1962eacdaa13fc6786b55ee10ba8877d *man/are_rln_clock_models.Rd
39c3552f3468dbd32733e65613d28209 *man/are_site_models.Rd
9046f31cbc66b0bb85a0c63e8bf7e416 *man/are_tree_priors.Rd
95dd2f77292fde0e73c46ec0075cbfce *man/b_pop_sizes_param_to_xml.Rd
8b1ae5104e85b1968fb77755496553c8 *man/b_pop_sizes_parameter_to_xml.Rd
acb140f3f425228fa3ff181a755d191f *man/bd_tree_prior_to_xml_prior_distr.Rd
8d35c834369cdf1a791510ab59a01d59 *man/beautier-package.Rd
9a0670725d8a49b8f7c0563fd65a7237 *man/beta_parameter_to_xml.Rd
53961ed527d10134f0f3dd5322e2d768 *man/cbs_tree_prior_to_xml_prior_distr.Rd
deccf6f5ca8eeaf3f0594ecc59546354 *man/ccp_tree_prior_to_xml_prior_distr.Rd
46c17ebbe71514883e942eebce280059 *man/ccp_tree_prior_to_xml_state.Rd
11c9817af4684d7cbe13ce4b39efee74 *man/cep_tree_prior_to_xml_prior_distr.Rd
1d3202cdd1180e7f489a72080ec15c30 *man/check_alignment_id.Rd
dd20239109d67597082dd4e95a86d46d *man/check_beauti_options.Rd
74178e0894fb07ad10f2b6c6a8126c54 *man/check_clock_model.Rd
6bf5f0e5851c7ba592c976473932141e *man/check_clock_models.Rd
153d12c3acc03753ecfa519875ad7208 *man/check_empty_beautier_folder.Rd
fd2bd67641accef2b9d342f2fefed3ca *man/check_file_and_model_agree.Rd
13ce7f66ff8d109b2da5f2b5a3c6fe3e *man/check_file_exists.Rd
614b9e2a2d93a7970aa3ca691563c96c *man/check_filename.Rd
73826b0951107a87603f32af88e90064 *man/check_gamma_site_model.Rd
125052065385da87da3ba7b470c4da73 *man/check_gamma_site_model_names.Rd
159e2b4c10410c94e300d250a8bbbb4c *man/check_gtr_site_model.Rd
a827549bfe7cb12e203f24b3fb54a485 *man/check_gtr_site_model_names.Rd
30ca0c7470b140e5d6ca2e53ce34899f *man/check_inference_model.Rd
86aed0d59bf9ff67ce33ae5300e50557 *man/check_inference_models.Rd
ccfc1bde7eab41416e9643facb72ec52 *man/check_is_monophyletic.Rd
1f4cfb1ab3668fe830814b27ebed9427 *man/check_log_mode.Rd
a46f7c477bd269ed6d7283c75295b634 *man/check_log_sort.Rd
60b2eba649b14b8b51f95a8d43dccde3 *man/check_mcmc.Rd
d9ad6503d86d819359bdb20ae515378e *man/check_mcmc_list_element_names.Rd
cccb0082ec20f96a99b975586c00a9aa *man/check_mcmc_values.Rd
c88bab6e81cfc00470b807e3fe36c9d0 *man/check_mrca_prior.Rd
92cfa28f8949bf05c2d59c2885726a0a *man/check_mrca_prior_name.Rd
0eff433108c074681beb0c0bff16f19c *man/check_mrca_prior_names.Rd
03eb99f2b6d5d7f424dd99d072f04a23 *man/check_mrca_prior_taxa_names.Rd
dc17bd2133ca56bc76b2acfc619ab171 *man/check_ns_mcmc.Rd
3702d0bc0d77250857bfc287b215b73c *man/check_param.Rd
a0b732a85fdb1e4ac23b8d41aa5880f0 *man/check_param_names.Rd
b194b5ba3f24f1838d634bd1ce7735ea *man/check_param_types.Rd
bdf1ca3b6293f543a51acfc8debd4633 *man/check_phylogeny.Rd
05220c4e8898093bc9ea29351fe28f8e *man/check_rename_fun.Rd
5dfa6bde71dfcea603150d560835a9b9 *man/check_rln_clock_model.Rd
faf571a9b220dc97b9ff0780b70cf777 *man/check_screenlog.Rd
ba50f7229969080480845175ac39cd12 *man/check_screenlog_names.Rd
0691cae6e8330f0ad45675a4f49d4f77 *man/check_screenlog_values.Rd
7e281008378a3f36ae45eff4081ed44a *man/check_site_model.Rd
44e885905e5cd77639da8f0d1a4e5df4 *man/check_site_model_names.Rd
8ac44ba56494d611e031d4441a697c8f *man/check_site_model_types.Rd
88e4b49be0b7a49ea0022c5e55f3a470 *man/check_site_models.Rd
225d13e19be8c1fc2a6037ecd5c696eb *man/check_store_every.Rd
560ecbfa4e50f67010b12472d88cfac5 *man/check_strict_clock_model.Rd
0edab1bc0fc7accc4a94be6a0dee5226 *man/check_tn93_site_model.Rd
bd12fe573213e57666d72999d63662ed *man/check_tn93_site_model_names.Rd
85e0178e7a99344c6c6c9627248e2d22 *man/check_tracelog.Rd
41bd006ed42d546998163535ad4d243b *man/check_tracelog_names.Rd
9d3b9db55e553d70c74dfa9edbefd847 *man/check_tracelog_values.Rd
83b254e75b110f0bcb7f94587c1a2530 *man/check_tree_prior.Rd
ca7b66bfe182b2af2a2de363fb96d3cf *man/check_tree_priors.Rd
9647399e258ea2174662ec80d361a23b *man/check_treelog.Rd
734cee001bd4c238c3cd3da498a7a250 *man/check_treelog_names.Rd
15e790066333d7a1158fcbd8de0b0d10 *man/check_treelog_values.Rd
b05c573a7977aa87bd1fa434fa6a1871 *man/clock_model_to_xml_operators.Rd
3656a1e3d6c61d645fd8f3b18bb3093f *man/clock_model_to_xml_prior_distr.Rd
5f4ab11f0f5a6b06d9a6014d16f25bd9 *man/clock_model_to_xml_state.Rd
0f772bcfb4ae2780c2710dc7f3084515 *man/clock_model_to_xml_tracelog.Rd
3206686a00cf91b1265dfe87401b4158 *man/clock_model_to_xml_treelogger.Rd
ca021a196c360192eed8453089cf144f *man/clock_rate_param_to_xml.Rd
d5c962526ca99f063b5509a5a0b43e14 *man/compare_lines.Rd
ba42392decc081a2fac30d1edd0833e0 *man/count_trailing_spaces.Rd
38ab48725e6109b47ee9ecc0ed2de2a5 *man/create_alpha_param.Rd
54afa6465c2628c0c9ce7a7eb09b8b28 *man/create_b_pop_sizes_param.Rd
a59403b3f922891d0a500240b4688b2d *man/create_bd_tree_prior.Rd
f4c6aff0ce39c925bb4c3f8c0527d473 *man/create_beast2_beast_xml.Rd
e7dc88995398b7f74512b6271340f5e1 *man/create_beast2_input.Rd
e1cbad116b14b41c4791413d87e3e9a3 *man/create_beast2_input_beast.Rd
7ff4281e9eea2a437c5969b6bbed44eb *man/create_beast2_input_data.Rd
c66dc3dce0c50d9221ff3213698f66fe *man/create_beast2_input_data_sequences.Rd
a2f18bc28127e7946a0f3ac2c4b4f4f2 *man/create_beast2_input_distr.Rd
f310963bca7d4b839149a926b61b62dd *man/create_beast2_input_distr_lh.Rd
d5edb1d39e726d17ec89dabd481d88d2 *man/create_beast2_input_distr_prior.Rd
33fe8e198a6ae48a7578939976f7fd71 *man/create_beast2_input_file.Rd
abd40c535a52172c652952d86c07b031 *man/create_beast2_input_file_from_model.Rd
594ab9199d591571e2decea9379f5c4d *man/create_beast2_input_from_model.Rd
ee3245eb950da4952c34aac2ba8d445e *man/create_beast2_input_init.Rd
4e271f48c81140e80ad46f2eb4f6f7e7 *man/create_beast2_input_map.Rd
fed525bde76431f88c8b86d63f619837 *man/create_beast2_input_operators.Rd
70cb9e1648e23beab9e8266a883bcb94 *man/create_beast2_input_run.Rd
5d11c8d3529a4b8ba6b5209c838b32bb *man/create_beast2_input_state.Rd
89b0df02bb641f27fff280047ef2ecfe *man/create_beauti_options.Rd
4fe2a322f9ec6d75bd8cf6a95ee64130 *man/create_beauti_options_v2_4.Rd
14369450bf811d8685e7987c1e66cf75 *man/create_beauti_options_v2_6.Rd
b729433acdf0cfd9276030af26d08198 *man/create_beautier_tempfolder.Rd
3385465d948b166723f9c3dcab6c6ac1 *man/create_beta_distr.Rd
0c7cf26db34b86510da95b6819cbfc3a *man/create_beta_param.Rd
2c4f2451814840dfacba7be44cc02433 *man/create_branch_rate_model_xml.Rd
3991c0400214fa2543a90b4ea5358921 *man/create_cbs_tree_prior.Rd
b9ea32e1919e24c298de4ab3c7124575 *man/create_ccp_tree_prior.Rd
d70bc05cfe83e508b833ace770c36ef7 *man/create_cep_tree_prior.Rd
bf2a04688063c1332b8adcc2ef701aa5 *man/create_clock_model.Rd
ec6171a10d942b545dbf13465f8b03b9 *man/create_clock_model_from_name.Rd
f40c5b7c96ad573911a060cf0eafd52d *man/create_clock_models.Rd
9cebc63cb53fa93d95b50f304ebce020 *man/create_clock_models_from_names.Rd
583f01d60a33573b188a5f85c4d042d7 *man/create_clock_rate_param.Rd
75ff75fd9a49ceef96292fe9b22b17eb *man/create_clock_rate_state_node_parameter_xml.Rd
15ef35a53c33459bf7d64b7ae54cf3c0 *man/create_data_xml.Rd
7b2d0c78c395a3753f0bea052f687dfe *man/create_distr.Rd
d725f1f8f5821185c30a1f7f766b91aa *man/create_exp_distr.Rd
ca6a062bb9bf1c07ca94c4b44ada856d *man/create_freq_param.Rd
94deb15fcd6dd3b9b7f4cc4017a8f65b *man/create_gamma_distr.Rd
fb57db9f6e62e9dcb34f7b49a386c94e *man/create_gamma_site_model.Rd
84a561e8ef21f4d397fe6e37f64b11d9 *man/create_gtr_site_model.Rd
0df300ea336852b005abc3b36c40fdd5 *man/create_gtr_subst_model_xml.Rd
b24c16ad1baa3f899fdf4add056e141b *man/create_hky_site_model.Rd
7461fa2f5c32890b532cfed9f42b2cfb *man/create_hky_subst_model_xml.Rd
da95be34e608b90bcd6c3f008693eb09 *man/create_inference_model.Rd
45c8bbc0c758258f25b7c993ebf0cc51 *man/create_inv_gamma_distr.Rd
3b75d0d4340bd58d5f14da85a9dadef0 *man/create_jc69_site_model.Rd
f65d6603fcc4dad968e25033193f5bd0 *man/create_jc69_subst_model_xml.Rd
96db2901cc5ba0e7ef22f19386a8b1f8 *man/create_kappa_1_param.Rd
b8247607a98192fa80d0f07dce47a57a *man/create_kappa_2_param.Rd
a3f4cfd87a00230b5363c4b75c1cdd5f *man/create_kappa_param.Rd
5b0dbca8a73c438ce3efc0211b4870da *man/create_lambda_param.Rd
d2d9b22034781b69c5ccc0ac20f3aaf9 *man/create_laplace_distr.Rd
a7e3f354f416edf28ff8e9971d885b47 *man/create_log_normal_distr.Rd
b631f3d70c8c30f47495c88734a16499 *man/create_loggers_xml.Rd
8fa62d617b8cbb354e20668b3110c4c2 *man/create_m_param.Rd
b52e8faece50c22011db069522ca0208 *man/create_mcmc.Rd
26c3f11ff07656f0b3dfd054cb6b7071 *man/create_mean_param.Rd
da9372df7021e136fd3ca1b32b140289 *man/create_mrca_prior.Rd
5ebf0cb9239d7738947f5164de729c03 *man/create_mu_param.Rd
d1356e67efa20568022fd1793aa081e8 *man/create_normal_distr.Rd
42879fe2d40f01d133d228a75221886a *man/create_ns_inference_model.Rd
1711584fbc3e43814a755d1b527f433f *man/create_ns_mcmc.Rd
ee3eb2bc4e12efe9237366e364275d22 *man/create_one_div_x_distr.Rd
b5db9f7bdbc20b16022cbf536c7dcf13 *man/create_param.Rd
7d4bca619c66771f2051be1cf91d526e *man/create_poisson_distr.Rd
859c0e457967a9b7cca382ba18f26dbe *man/create_rate_ac_param.Rd
61750430780281dca27a2deae568c468 *man/create_rate_ag_param.Rd
466b73c0abb48959ec9fb145f20d343a *man/create_rate_at_param.Rd
bd44e8d4fae1d0f427eeb04105db7fb8 *man/create_rate_categories_state_node_xml.Rd
06ee74e142d62d15ac249c8c28cba1d8 *man/create_rate_cg_param.Rd
3e28cb267e84bc22337e3a151b7ff907 *man/create_rate_ct_param.Rd
e6b8dd9a27764152a214129abfd72382 *man/create_rate_gt_param.Rd
e7ba4d5fab7f6e0de5627a684dba2eed *man/create_rln_clock_branch_rate_model_xml.Rd
695ff9d94c0c52ba55ff7f8c689e315f *man/create_rln_clock_model.Rd
d14820098a7fee32e15882182c56b0af *man/create_s_param.Rd
951984c2fdb56738fc95d58f52154e37 *man/create_scale_param.Rd
0709d8fbbe4ceba9feb598a791b5d10d *man/create_screenlog.Rd
40ce3c6cfd7eee90f75a946927defab6 *man/create_screenlog_xml.Rd
dd00395661102dcffdf53a708ee9518f *man/create_sigma_param.Rd
b43d3de79dfd40e6f956f8cdd396ca60 *man/create_site_model.Rd
8f6f18015995e8daa8c4bd238e729e2d *man/create_site_model_from_name.Rd
fbcab65d311f2d8af507e4d9d2d94b47 *man/create_site_model_parameters_xml.Rd
cedddaceca6d9aa36b1f1292ab3b98bf *man/create_site_model_xml.Rd
c4b080b9776fc9da9bfd5c3622b32d89 *man/create_site_models.Rd
e97319cb70cfc81b1ddaf1135b7e9709 *man/create_site_models_from_names.Rd
9b7eac567a824264fce4fb1904f9faaa *man/create_strict_clock_branch_rate_model_xml.Rd
81b96e469a800cd0c185fa17e2f5e38f *man/create_strict_clock_model.Rd
b6302e7da7209624f1d02bf17fccb3f6 *man/create_strict_clock_rate_scaler_operator_xml.Rd
e2ef1212c94e4b97cfa64f03432358c7 *man/create_subst_model_xml.Rd
c17eb5bf25dc9e95e400dc4727d1a0ad *man/create_temp_screenlog_filename.Rd
4dc999c4ed06c1b03d427b924c1398c3 *man/create_temp_tracelog_filename.Rd
2ed220ddcf489b74f659946618728d0d *man/create_temp_treelog_filename.Rd
f0a6158a5ca88eb0f333b84627d645a6 *man/create_test_inference_model.Rd
73bfaa42908348de4a60a65e609eeeba *man/create_test_mcmc.Rd
1e358233145ee737dd4732d41f5c3443 *man/create_test_ns_inference_model.Rd
741dd3aa85a64b0777b30f149fce9cec *man/create_test_ns_mcmc.Rd
cf34b6b3190dbaf7dd7d989fe29e5876 *man/create_test_screenlog.Rd
5bfd7d5c80694c7c7470fc6d39428a4f *man/create_test_tracelog.Rd
0bbcb5ffcbefdfe58ddbe54995af0e63 *man/create_test_treelog.Rd
013bae8a9b4d2598662dd425dc598d87 *man/create_tn93_site_model.Rd
58611448eb9b04db4b4b7d2c9d3128f5 *man/create_tn93_subst_model_xml.Rd
74f3baadb8296f42509945ae89a3f6f0 *man/create_tracelog.Rd
57f23fb597857bdd634956b3875c573f *man/create_tracelog_xml.Rd
89be7d79c4f49cc451966d007ed91209 *man/create_trait_set_string.Rd
f167fc2915312434ec02534b3a5b077e *man/create_tree_likelihood_distr_xml.Rd
6fdea7ca248f1f1eb5c64311080ef170 *man/create_tree_prior.Rd
0512cf8c96b4a422327414ee9755344c *man/create_tree_priors.Rd
f91c6ebdfb99027f7fe2c8f1d467268f *man/create_treelog.Rd
c7e13e28dd62caf648bfeb958c6b6d13 *man/create_treelog_xml.Rd
73520712df5fa9786dc3683cd9317daa *man/create_ucld_mean_state_node_param_xml.Rd
f80e063ee222ef0c0de74536aeb69b4b *man/create_ucld_stdev_state_node_param_xml.Rd
09de83f84a3c5aa74dfd75fa311b01a0 *man/create_uniform_distr.Rd
b23581731a82c238a126964d65cba380 *man/create_xml_declaration.Rd
ad054cde0f95c846ba70639221970b44 *man/create_yule_tree_prior.Rd
a4f0a2470425a4c4202f901d7f308239 *man/default_parameters_doc.Rd
685c521209effcfade111a876716e9f0 *man/default_params_doc.Rd
5c4d9b5f966f1fc6f7187a524d9c34e2 *man/distr_to_xml.Rd
13244cbf0210c692a60ce62f406b7ad5 *man/distr_to_xml_beta.Rd
c33650453023c5784350be7b4e548fba *man/distr_to_xml_exp.Rd
f63bd4e01e2d4c5321bebeb48cb1661a *man/distr_to_xml_inv_gamma.Rd
3d049cb72c45f13296e5564c58579b14 *man/distr_to_xml_laplace.Rd
ac9909225d5618b5054c4667f4a6da24 *man/distr_to_xml_log_normal.Rd
f1a2e757b7510c1b9b853bc91c4d1ef5 *man/distr_to_xml_normal.Rd
652c1dcc9c7c97af6cf299de9be94d3c *man/distr_to_xml_one_div_x.Rd
689808fba540c88fc71b22acd8605e61 *man/distr_to_xml_poisson.Rd
401e6de47717bf985e5135e6b7cf46e7 *man/distr_to_xml_uniform.Rd
1131698964c92e6dac0ba2e4ea3e33f0 *man/extract_xml_loggers_from_lines.Rd
28e3e8620cd5f99b892ab8c6181d1383 *man/extract_xml_operators_from_lines.Rd
eff8b4e9fb31f912db4791eaf88a4ff1 *man/extract_xml_section_from_lines.Rd
029b7761471e5ddc7ae10d404cf9b128 *man/fasta_file_to_sequences.Rd
f7de71e5ff24145a37bf281e4d155cfa *man/figures/AppVeyor.png
3f25ab37a1f6270f76c025cf6eda5421 *man/figures/Codecov.png
b55c56f3943a394162527954ca4a3009 *man/figures/GitHubActions.png
cefa8b5db1c53b4ff2bdc0c66e3f55a9 *man/figures/beautier_logo.png
e29af2f267ba0de0ef88e1c0a2d53716 *man/find_clock_model.Rd
a1acddbbbb6f4cb1baeacc9b1362e922 *man/find_first_regex_line.Rd
393ebf7a2cae75a8e96b10ebb215e9e6 *man/find_first_xml_opening_tag_line.Rd
3cbe0970aa0ae51223fb4587660933a9 *man/find_last_regex_line.Rd
07b9c0c84d2d6143d8c8dc4f50fa770b *man/find_last_xml_closing_tag_line.Rd
d4a79696533ae4db8798e5b516bfe0f5 *man/freq_equilibrium_to_xml.Rd
849b37577b603998800d9b7e7e2b7e57 *man/freq_param_to_xml.Rd
945b4dac67c465db5a6fa05a18b6a1a3 *man/gamma_distr_to_xml.Rd
6402082189796e8135afaab044849b03 *man/gamma_site_model_to_xml_prior_distr.Rd
997fd447953ad225f9d78410e7c1d633 *man/gamma_site_model_to_xml_state.Rd
d7a0505c82b150c30253e4acaa6f0c88 *man/gamma_site_models_to_xml_prior_distr.Rd
d6afa42274bab08a5e1060ca6894f9a5 *man/get_alignment_id.Rd
99e332bc2eb6fe56259de278bb5cfae2 *man/get_alignment_ids.Rd
565f9a2cdc720e3a6a0ef96c1f3bb2af *man/get_alignment_ids_from_fasta_filenames.Rd
9a132c7d1dc3902eb071e89028c3d266 *man/get_beautier_folder.Rd
da87da5a59da3779f82fb1a76467860a *man/get_beautier_path.Rd
7df5757d010e41f7dbf172432d07b8cb *man/get_beautier_paths.Rd
175791aae1d3aa658e147a6b651f4189 *man/get_beautier_tempfilename.Rd
92691073898c8ba32819fa783bcd592d *man/get_clock_model_name.Rd
6397c3530e5b723cb8cc5da549e528bb *man/get_clock_model_names.Rd
f18f9508bb8a608c4c54d02a91095ba1 *man/get_clock_models_ids.Rd
99a5a914be9c8abf684f040c3c680998 *man/get_crown_age.Rd
6113daec3a10753a754b9f39594b0219 *man/get_default_beast_namespace.Rd
7831d5254d4fdab25081eecc3afcb843 *man/get_default_beast_namespace_v2_4.Rd
d1f38f467ed58013a88a7b4f615820ab *man/get_default_beast_namespace_v2_6.Rd
0f34e0d243a4c270e27f2b4bb8dafdef *man/get_distr_n_params.Rd
05968ddc498f474cf28dec7211ade9da *man/get_distr_names.Rd
5314006e8a12acadc98c4356a67ee1ca *man/get_fasta_filename.Rd
cb1fb936abfc7d747440425770e46ed6 *man/get_file_base_sans_ext.Rd
8a6f3e8e457a20fdcde30c3c839199c5 *man/get_freq_equilibrium_names.Rd
5d3aa5cd0fda0e23f61016e163140b26 *man/get_gamma_site_model_n_distrs.Rd
0b724e805c880747c6af123c78cf3657 *man/get_gamma_site_model_n_params.Rd
891d52a79c3f735c2fc70959d0beaec5 *man/get_has_non_strict_clock_model.Rd
1a265459338c1ad18b38eb2857552d48 *man/get_inference_model_filenames.Rd
c6237816028d942b685aef48f57e1a77 *man/get_log_modes.Rd
ebc08795912299ad3d4aaa7416e8e792 *man/get_log_sorts.Rd
1b7218692c62164c5c152396fc3d6aba *man/get_mcmc_filenames.Rd
0699ab01b2880273c331a489ad2b71c7 *man/get_n_taxa.Rd
6973d1cef2988f2019c4423517c97ff4 *man/get_operator_id_pre.Rd
4ce20f747889472148cd867321749a41 *man/get_param_names.Rd
e1e6f95bff5682dfafc97ec86204df40 *man/get_remove_dir_fun.Rd
4a5a75fae9ad6868b10f5d039e6fab5d *man/get_remove_hex_fun.Rd
9dc1bb4fd47611d5d8f2a92f4540f106 *man/get_replace_dir_fun.Rd
86c031d93ee5b1b0b2834772b6e7cee1 *man/get_site_model_n_distrs.Rd
526aa248badb343a3f607fe364f5d47b *man/get_site_model_n_params.Rd
ccab41f6ad978c7ef9fa0244bd81a434 *man/get_site_model_names.Rd
f7a0e4edf6c73904b057a92c7cd03bec *man/get_site_models_n_distrs.Rd
78b326c0c288c657e7e97f4dcf09216c *man/get_site_models_n_params.Rd
c972ee18fa8eeaddd400b1ae6802fd88 *man/get_taxa_names.Rd
a8dbe36b65b855c9f0d067811beddefc *man/get_tree_prior_n_distrs.Rd
65872054fcb255a47157f7e976a7efd3 *man/get_tree_prior_n_params.Rd
a8b45f63e58b88045cb3eedbbe788ab6 *man/get_tree_prior_names.Rd
a4f20f2083057dce02af09ade6771231 *man/get_tree_priors_n_distrs.Rd
439fcd5d4b80771d2ae9bb57749e76aa *man/get_tree_priors_n_params.Rd
4e3c9fcb23268cda9fc93cb2267f5d7f *man/get_xml_closing_tag.Rd
73bcd88cc23d14dd4e561befec66bbe4 *man/get_xml_opening_tag.Rd
03614724a7fcc170c91b1b1b9d2c37b1 *man/gtr_site_model_to_xml_prior_distr.Rd
67e1739e7ed50149e6e6aa9aad5ddc82 *man/gtr_site_model_to_xml_state.Rd
cc6e51408fe70ec678238feb19745afc *man/has_mrca_prior.Rd
593e1dcd60c29509cdb8aa4c8b765c5b *man/has_mrca_prior_with_distr.Rd
a554c965f5025d07983b47a987f6e754 *man/has_rln_clock_model.Rd
43365221b96b35fb1ce0f4cd24bd4d34 *man/has_strict_clock_model.Rd
d21db03606579a7a43c2a9e7b7075e29 *man/has_tip_dating.Rd
63d2ea659f4b30624ee986587302921d *man/has_xml_closing_tag.Rd
ad69b9617768511256b35c4b7b2c9aae *man/has_xml_opening_tag.Rd
e2b5508b4f6ac1c4dc389121212f670b *man/has_xml_short_closing_tag.Rd
715888ab376908d348b6d3cac0082fd3 *man/hky_site_model_to_xml_prior_distr.Rd
99b301a5945ebf162f95c13e7e917736 *man/hky_site_model_to_xml_state.Rd
8e0fc9008fc5d590758d5e334a3c1a64 *man/indent.Rd
80122289f64a76d2320906ec6650db14 *man/init_bd_tree_prior.Rd
1ffc522aa2952d4ef7fe4788a88d841e *man/init_beta_distr.Rd
0255cbaa57ffbb1ee8f1892fc40a4510 *man/init_ccp_tree_prior.Rd
ff19e7712631ca0e4ebe1c3d0977c53c *man/init_cep_tree_prior.Rd
d2f93bfca9870003724f1602271f61e7 *man/init_clock_models.Rd
c56da38e783c10482cd6058729cf94be *man/init_distr.Rd
ba31dee9233c659edba388d4a48017cc *man/init_exp_distr.Rd
2f0fe70ab34bd956a7ca4cef2e97a703 *man/init_gamma_distr.Rd
b0f28068b7140955c43c2b42cd4f90aa *man/init_gamma_site_model.Rd
933b13bc8519f83276a01d759928792e *man/init_gtr_site_model.Rd
d130decbf610e81bb1c661dbec3a866b *man/init_hky_site_model.Rd
64c09efc6806235b664f451da1e59302 *man/init_inference_model.Rd
e9fb6d32565b2040eb2f1869b2bce238 *man/init_inv_gamma_distr.Rd
3287445684c9d65ab7e68de357f2da13 *man/init_jc69_site_model.Rd
eba87917cd38f437fa18b714a43b58eb *man/init_laplace_distr.Rd
728ae657ff3818a1773a45e78723d641 *man/init_log_normal_distr.Rd
7904e9ab161212853d6062900c4f9050 *man/init_mrca_prior.Rd
6842d6f630dcdbc68d82a399b3692b4e *man/init_mrca_priors.Rd
74016074fbc1989e7e88c9d9a45fc5bd *man/init_normal_distr.Rd
2934a8a5d98cfcbcae809a7cf03e879b *man/init_one_div_x_distr.Rd
2e8f1add3a5afddb27881213769b0af6 *man/init_param.Rd
69e6b997cde4eda19c83d1544716c8dc *man/init_poisson_distr.Rd
4b484b3ec5d00e3bcaa01d8df5bda0f2 *man/init_rln_clock_model.Rd
8b7d933c8969a3e5137342e2f8b9b88f *man/init_site_models.Rd
e43f81be3c69255d3b2ff54b4c073a1c *man/init_strict_clock_model.Rd
176d1db841360ef6997e50a9e33e950f *man/init_tn93_site_model.Rd
3ff7bfd35de62c9926a1a2a9b9d3b04d *man/init_tree_priors.Rd
f6f781f7f76e804eb7933247cc6e5235 *man/init_uniform_distr.Rd
45be1bc0e1e2e540b4f365c1d7d8b1c3 *man/init_yule_tree_prior.Rd
6cd738193473dde2a8a109de13e10a50 *man/interspace.Rd
a62174ddd83f2c71a7dabf921f82210c *man/is_alpha_param.Rd
be5210b9e6877f9900db52148ced4395 *man/is_b_pop_sizes_param.Rd
3e8f49f7058a1fd15f9c0c80f803a25b *man/is_bd_tree_prior.Rd
66fec5ce6ae5fb741a51f36d15e8bbd4 *man/is_beauti_options.Rd
daeb7b2235e5fefce51405f00459f0e9 *man/is_beta_distr.Rd
9a1eaf3c67ca77f9c7ea895841b1aa63 *man/is_beta_param.Rd
ca622351bee4dde5054cd66484a76652 *man/is_cbs_tree_prior.Rd
45dc73bdc68b3e733f0bc27f2c314c8d *man/is_ccp_tree_prior.Rd
7791efdbba437a0b887a38f7bda74806 *man/is_cep_tree_prior.Rd
7d1bb0f6a3a5fa59d0a9ee5466dca92b *man/is_clock_model.Rd
dc698b59a1b9d7377688472324bd907f *man/is_clock_model_name.Rd
a2a9dfd2e00ec3c8e585b87893808efa *man/is_clock_rate_param.Rd
b19376eb9671ee9061d4df1266be89f2 *man/is_default_mcmc.Rd
56e52366033bde5b77c6b2e9e71a89e2 *man/is_distr.Rd
dee04e2134cacf363b3052c11f109151 *man/is_distr_name.Rd
b891e123bf2f6a05d9ac1bd4cdf7d376 *man/is_exp_distr.Rd
74b193a03e67379dddee858266a089ab *man/is_freq_equilibrium_name.Rd
72ddf7b1af3db617f01123056d60b9d0 *man/is_freq_param.Rd
311c8d36af92101d617374a5bf77bee2 *man/is_gamma_distr.Rd
abbcabae79956bed443c6667b7ef2ff1 *man/is_gamma_site_model.Rd
980a035eed388ad03141a082fac42f11 *man/is_gtr_site_model.Rd
86717aab600a14b6f4c911bafe1a9d08 *man/is_hky_site_model.Rd
78eb87f12cf41994712372fdf07f7774 *man/is_id.Rd
6f8ec74a0316d8050d5de15141d4c19a *man/is_in_patterns.Rd
cf5d899c2eb395263c0473d139aecd5e *man/is_inference_model.Rd
217d9424369d551df5bcc8532f085eec *man/is_init_bd_tree_prior.Rd
1ce51667fd3047cb6b07f61fec114b1f *man/is_init_beta_distr.Rd
bdc74e3ab626918aaaf4bfae03d47e71 *man/is_init_cbs_tree_prior.Rd
bf9606104cf15b62ac836fb5d410cf3a *man/is_init_ccp_tree_prior.Rd
125721fde8d0315b8e36f5688b139266 *man/is_init_cep_tree_prior.Rd
b482aa5b4890c0512c7c77aee053be76 *man/is_init_clock_model.Rd
005abe4eb03ae7b057eb0179bf241c0c *man/is_init_distr.Rd
7390b3990f376f5a1cd26ee3c33ab445 *man/is_init_exp_distr.Rd
38983dcd03d25eb1e1245481e5375b85 *man/is_init_gamma_distr.Rd
b532c0a48a1704663773f6d3dbcb90ee *man/is_init_gamma_site_model.Rd
9533d8ad0cea629044382f3c2c845e00 *man/is_init_gtr_site_model.Rd
37d8fc3f0afd6250eecc8db306525bd7 *man/is_init_hky_site_model.Rd
bbbdb45b4c61b350b96d0c5eef02b0b5 *man/is_init_inv_gamma_distr.Rd
35e0f356d096ef5ba27bdb53b461ae36 *man/is_init_jc69_site_model.Rd
0f5380ae16d1549a464e910533a43d5f *man/is_init_laplace_distr.Rd
63d2a4b78ace833bc210d085c29d1744 *man/is_init_log_normal_distr.Rd
062555ec2ddf49f7dd817cb78d38550d *man/is_init_mrca_prior.Rd
3fbbf28118a1abe708310f8409506d60 *man/is_init_normal_distr.Rd
23ddba4a18464beffab89f351766b4dc *man/is_init_one_div_x_distr.Rd
8a683501c6d3c8819c74c95ed852873e *man/is_init_param.Rd
02f872ff1933bce8baef739836be66c6 *man/is_init_poisson_distr.Rd
9a67965f30c94e4ec37fb9e613616c78 *man/is_init_rln_clock_model.Rd
5d2ffd5f90bae2d59afd7d808c8de87d *man/is_init_site_model.Rd
6418fb49f1f4aefa8d582d7a8d0f32e0 *man/is_init_strict_clock_model.Rd
a2085b4bff5774e41675a446c767c556 *man/is_init_tn93_site_model.Rd
599d2eaabfde68218794080b1cca741c *man/is_init_tree_prior.Rd
10843248f7b8cf92616b402a2a406dcd *man/is_init_uniform_distr.Rd
3a41c9df5b76eed828fcb219376894d0 *man/is_init_yule_tree_prior.Rd
adb59e3d84f0b58cfa4abe867edb14bd *man/is_inv_gamma_distr.Rd
97095e214c66b1f9d958d8863a49d8c2 *man/is_jc69_site_model.Rd
7d604839c798c5be0773a1454cfd3489 *man/is_kappa_1_param.Rd
f1d9e9853843262e30979364da4ae4f8 *man/is_kappa_2_param.Rd
4ad117cbc2fd29bb450cfbaf57e61461 *man/is_kappa_param.Rd
7dc63de5d92df77062d51f26fe2e3898 *man/is_lambda_param.Rd
358c7ae0a251717df75e4aad86520666 *man/is_laplace_distr.Rd
ba435697539cad45f1a85cad3f05e022 *man/is_log_normal_distr.Rd
6d3fab03eb7c6c512af0d4405901da20 *man/is_m_param.Rd
877f7ba8dfd7935bf52022dfc77e31d0 *man/is_mcmc.Rd
27fbb602fa30322f283fd00255189bb9 *man/is_mcmc_nested_sampling.Rd
be763dbf234ec049fa4ea58119ae6b4b *man/is_mean_param.Rd
10777216cc30898d3f6a7bbb74f694eb *man/is_mrca_align_id_in_fasta.Rd
4ee4e1b912dd5c500e7e8c63c5eb5d3f *man/is_mrca_align_ids_in_fastas.Rd
2c5dfe2398176c969545f2be54783f77 *man/is_mrca_prior.Rd
1e31776fe0292d8ae1e233a7d3d5a999 *man/is_mrca_prior_with_distr.Rd
69411b47a1c863bdcf92ed321609013e *man/is_mu_param.Rd
1cc977823a6233f797e06f9802390e3f *man/is_normal_distr.Rd
1940b05f4aa240f792116e0c95879f86 *man/is_on_appveyor.Rd
ad20185a0f55104517e17c40347a57f7 *man/is_on_ci.Rd
ee2e5882c8e83a6fc7283ddb58ab61bd *man/is_on_github_actions.Rd
6bdfaecd7856b2a4576b73e2633311cc *man/is_on_travis.Rd
e6f24fbb41fff55ff408a4a171cbff21 *man/is_one_bool.Rd
dda28351f28f80eef62903cde2fd1f87 *man/is_one_div_x_distr.Rd
66fe1cae4aa05f58f311c353267e73aa *man/is_one_double.Rd
e71d1cdf950b62bcc35a5d01d23733a4 *man/is_one_empty_string.Rd
b83c7dc87e44523b797b23c71fa64569 *man/is_one_int.Rd
a3ad97e8243a7bbb6379e1f7615cd55e *man/is_one_na.Rd
95540af7a58115be79b05b25644bb975 *man/is_one_string.Rd
3b1d69cab45c42ddebf2095a53d455db *man/is_one_string_that_is_a_number.Rd
379c85d2f019df8ad17b3d4c1b73b303 *man/is_param.Rd
d7bf234ac89c02c7e8aeb0399db641e4 *man/is_param_name.Rd
53059a8b861934687b143afb093e7f83 *man/is_phylo.Rd
44a15828bc2dfc2e706136b172e4d027 *man/is_poisson_distr.Rd
e3e345499ca99894593d6bee67566abf *man/is_rate_ac_param.Rd
4525ae0b39e94ff914b23b7d9179d39e *man/is_rate_ag_param.Rd
d82a495a5cdfeb46a59920a6a235f387 *man/is_rate_at_param.Rd
092c5c40f62633b8d5756eafc673767f *man/is_rate_cg_param.Rd
489c2c02d23a74430d8f6a975afce107 *man/is_rate_ct_param.Rd
de5a26fed2d484098322d0f39747c8e5 *man/is_rate_gt_param.Rd
e897829a18ba54c30cbd8181ea14e7e0 *man/is_rln_clock_model.Rd
ed940239ddf54156aee3caa1c28158bc *man/is_s_param.Rd
13547a1cb4e8e1babbdd304692c5d0ce *man/is_scale_param.Rd
ef3194491cae6bb504f9fa9bce3e784d *man/is_sigma_param.Rd
faab5599a73bf7a3280521e12c2220ff *man/is_site_model.Rd
1caa64cf867bc3c9b65b49a621dd549b *man/is_site_model_name.Rd
52ee642b7831e4d402f46985485b0375 *man/is_strict_clock_model.Rd
abee24f7fe9c167fcae92374ea8e8ac0 *man/is_tn93_site_model.Rd
e31dddc5eb203a695044e2ac741d0feb *man/is_tree_prior.Rd
896aaab2fdcf3a7664e23d1a0f0fe266 *man/is_tree_prior_name.Rd
14fbfecae2f8af7e5ce0016b46eb9610 *man/is_uniform_distr.Rd
7adcc5b6610ffe27cc3fe990e0398791 *man/is_xml.Rd
65a344ae5c498b6f17389525e8b8766b *man/is_yule_tree_prior.Rd
a85e45ecf28f8aa918164726071174b5 *man/jc69_site_model_to_xml_state.Rd
9754fc226b8f60abe07e4d524dfb769b *man/kappa_param_to_xml.Rd
ee8a01c71f1c13c867fda9b501e9cc17 *man/m_param_to_xml.Rd
6d0acd537acd9bfeac94e8e1750805c5 *man/mcmc_to_xml_run.Rd
1571eec008c31bbd40d1c4f12717b55b *man/mcmc_to_xml_run_default.Rd
60dbdf3901f858b2d8d742d997f936bf *man/mcmc_to_xml_run_nested_sampling.Rd
5ab9cc47877612f5db3ccd879b9320db *man/mrca_prior_to_xml_prior_distr.Rd
5b2e79b4ecc1071b84bd2361263b7a85 *man/mrca_prior_to_xml_state.Rd
3d73da0f010a7408c2056e6e5b8b3699 *man/mrca_prior_to_xml_taxonset.Rd
57e8cdd0fc77ec786c67e1e5a54e1a22 *man/mrca_prior_to_xml_tracelog.Rd
9276327aa05b2c49ec237eff6e92d826 *man/mrca_priors_to_xml_prior_distr.Rd
641b1ba881b63530d1f599e0956c7d0a *man/no_taxa_to_xml_tree.Rd
2d53e4724cc85b78bef49956e790d88a *man/parameter_to_xml.Rd
52d457fe7a77155feefa299463cae690 *man/parameter_to_xml_kappa_1.Rd
4a95e40e9db3e9c9bafaf45445c7e895 *man/parameter_to_xml_kappa_2.Rd
c378ff7dc2fb3d6e18fd654ae3f2b175 *man/parameter_to_xml_lambda.Rd
b251b52fc004250f93dd7a4badabcfa9 *man/parameter_to_xml_mean.Rd
cb2a9758d63a4477ca499460cda696c1 *man/parameter_to_xml_mu.Rd
42f7f31edbb4331f2979841cbfd07c4f *man/parameter_to_xml_rate_ac.Rd
022540ef21a5217526ab735eb4089d0a *man/parameter_to_xml_rate_ag.Rd
ab91b7d01035fa48c5739491e6876183 *man/parameter_to_xml_rate_at.Rd
e5cc37af98fbdafd987710206246b4cd *man/parameter_to_xml_rate_cg.Rd
af86f7402543c505282ef5c5ca0a9746 *man/parameter_to_xml_rate_ct.Rd
d759bae267db48e0b7c16bf45584b951 *man/parameter_to_xml_rate_gt.Rd
a61e42795d4c8aa8f6ad2e2d0c8d7e9f *man/parameter_to_xml_scale.Rd
b2768629757f2b0b2f3f70739c2559af *man/parameter_to_xml_sigma.Rd
e81c37b4542764c6e5f6d63b038fe640 *man/remove_beautier_folder.Rd
2a72e8852602cae18788b76c0a612d3b *man/remove_empty_lines.Rd
4084607ad70612743d09b057d73c0618 *man/remove_multiline.Rd
d14aba670f3847ef91bb0d0f8cb76e9c *man/rename_inference_model_filenames.Rd
c6e43c6f2a3ae6bd2efb99f15725c8d8 *man/rename_mcmc_filenames.Rd
a7dc7aef6e2a14766332996f20453394 *man/rln_clock_model_to_xml_mean_rate_prior.Rd
825a7cfaf5fadb1312795c0a2aadde4e *man/rln_clock_model_to_xml_operators.Rd
41b53cbd9e9c4150b97cfda65dd3c137 *man/rln_clock_model_to_xml_prior_distr.Rd
679160d2b0ebb304ecc233d4efe652ec *man/rln_clock_model_to_xml_state.Rd
76a2c1e74b3ade8d93caddc5fc74117a *man/rln_clock_model_to_xml_tracelog.Rd
ce40abb157319aa447f01f771732ebd2 *man/rnd_phylo_to_xml_init.Rd
aefa5374bb143d54efec3d0f58b34880 *man/s_parameter_to_xml.Rd
23c08e055056b9ee6e601c14d66e28e8 *man/site_model_to_xml_operators.Rd
72b8fd3a633c46745ea27e41d7b27dc7 *man/site_model_to_xml_prior_distr.Rd
e76d52cb62deb9d1e0ba8acd143b4ee4 *man/site_model_to_xml_state.Rd
1a7609e19281aa843c037117768a0aa7 *man/site_model_to_xml_tracelog.Rd
8740d41f367005649119c6476e93521e *man/site_models_to_xml_operators.Rd
88083725a5fcbf13e0f63cff58fcbe6f *man/site_models_to_xml_prior_distr.Rd
7be02fed690fd44853669a81ed66bb86 *man/site_models_to_xml_tracelog.Rd
50f9176a1a656b77afd35117cd44300c *man/strict_clock_model_to_xml_operators.Rd
a271e34ed03913e6837451ba09be5f8c *man/strict_clock_model_to_xml_prior_distr.Rd
cb54885fb3566d03b9bcd7504042deb4 *man/strict_clock_model_to_xml_state.Rd
fbbc7c9e6e4a767172d84b3eb96ee007 *man/strict_clock_model_to_xml_tracelog.Rd
ec6ef4f8f2f1ea2fd7e0e0fef19089f8 *man/taxa_to_xml_tree.Rd
e133964b0cbbac25e8b24b850e525670 *man/tipdate_taxa_to_xml_trait.Rd
1a2aa2dcef6007f711c14b10a6e2fa5d *man/tipdate_taxa_to_xml_tree.Rd
810d1a7741d9229643596cb431b00208 *man/tn93_site_model_to_xml_prior_distr.Rd
8697f5c50645a697fb60a9bf93f8373b *man/tn93_site_model_to_xml_state.Rd
86df59b4284a7a09d176c187d420dec5 *man/tree_model_to_tracelog_xml.Rd
33af265c23dd5d8e98353c0b6128de82 *man/tree_prior_to_xml_operators.Rd
d2ccefaaf89566cd0a7a1ad0043440e1 *man/tree_prior_to_xml_prior_distr.Rd
0b99a1577b5eeb0d8d2d0aeed789fe3a *man/tree_prior_to_xml_state.Rd
6fc8d1aaee6569f0d0da3aa20c00e4ad *man/tree_prior_to_xml_tracelog.Rd
53ce57f86560ff71add440be9bb93722 *man/tree_priors_to_xml_prior_distr.Rd
2301b24f43efae826f05a1273121f9b8 *man/tree_priors_to_xml_tracelog.Rd
76efcb7d3bdd3dc65859d8eddfbd4588 *man/unindent.Rd
f0124ac393f5c6b40fd2417008eb237b *man/yule_tree_prior_to_xml_operators.Rd
51cd51bfd4964abef5fcf024cfc332c5 *man/yule_tree_prior_to_xml_prior_distr.Rd
699b225e2fcf1925f72ee30fdad50d41 *vignettes/aco_hky_nd2_tn93.png
c375e47bf1cf8a0c7a3062643977d1e3 *vignettes/all_default.png
f68d71c5c72424064ec3cdb6ac780b29 *vignettes/anthus_2_4.png
dcd81e1e57c3aeb20d563cb5a402fd4e *vignettes/bd_2_4.png
cefa8b5db1c53b4ff2bdc0c66e3f55a9 *vignettes/beautier_logo.png
3f3480fba0410971d3ca06cb0b9a7b19 *vignettes/birth_rate_normal_2_4.png
2c9503f5c6de0bedc889ddf6d68cdadf *vignettes/demo.Rmd
c73a2f81d34a803062d0a2886b5b76fc *vignettes/examples.Rmd
31581bf78fb7f262230ffc82fc482feb *vignettes/hky_prop_invariant_0_5_2_4.png
b25ff646358933ce64e49a50b6680fcb *vignettes/inference_models.Rmd
bcee737a390f78e407da15d318aa66e1 *vignettes/jc69_2_4.png
ab4a28c306b1e17872f4b9f4c389a699 *vignettes/mrca_crown_age.png
9aefe293b1aade94f089f9f4bb0cb882 *vignettes/mrca_prior_all.png
75053f6a1e99116811bbc966b24339a8 *vignettes/mrca_prior_crown_age.png
0e61f1d25dc5b57f0be8c0d6163deff9 *vignettes/rln_2_4.png
9c0d1af25a7b3c0bae7ccd66a1614d0c *vignettes/strict_clock_rate_0_5_2_4.png
