960460794533bd5a627bd2e31f391db7 *DESCRIPTION
169bb16de27b912bf1883f400134af72 *NAMESPACE
3a92958e94ca93b4ce4d15c035b8cd17 *R/alignment_params_to_posterior_trees.R
72e6bbb2daab73f03e30ed669c4dd48b *R/check_alignment.R
54f1a0a9356e97339a437b50a96086fd *R/check_alignment_params.R
9cad0abbe7f2914082c449d73ad614f0 *R/check_beast2_installed.R
f73a7f3507ed5e7bb3b444a59065c75b *R/check_error_fun.R
476a0afae58ae6e53028bb0e224c7aec *R/check_error_measure_params.R
037fee525e79aa35a7a324037cb02281 *R/check_experiment.R
f82db79b0b3bc00ea393382b6219b08b *R/check_experiments.R
139dd106bf3b26d510553a9cff5d307d *R/check_experiments_all_inference_models_are_unique.R
5506cb064c83e0603555a05ef8aae764 *R/check_experiments_candidates_have_same_beast2_files.R
fb9a3a6258a4a13c3c96d6913f899eba *R/check_experiments_candidates_have_same_mcmcs.R
93f94e70f1bfb567018f35ec9b040dcd *R/check_gen_and_cand_save_to_different_files.R
42916179ecd820e9ad4194786c2f4130 *R/check_inference_conditions.R
424a5d1db72153dd2e4d074e54b38d5a *R/check_inference_model_type_names.R
fe7815bb0049d8edd19decaca7d2dea0 *R/check_inference_model_weights.R
26c3e1b5a5a908151c3c68b9d820137e *R/check_init_pir_params.R
42ac2e06ccc4da23d8e35f8989fa712a *R/check_is_ns_beast2_pkg_installed.R
6ec69665a48c1af5dea8f8840a9f8e22 *R/check_model_type.R
32bc3d1f0cb4f3af75da4e2cba4fe985 *R/check_mutation_rate.R
5ae0996286c1827431d0338f4f02ec49 *R/check_pir_out.R
f75ef8251500f9eb0fd9f59cd6364efc *R/check_pir_out_errors_above_zero.R
778fc285948d965d7a9170df08c18e0a *R/check_pir_params.R
60ac7943ca4643eda45635e8f6e7d59c *R/check_pir_paramses.R
a1927b9bed97258e19286f11de9ab5f2 *R/check_reconstructed_phylogeny.R
45997fb25b886375a13205b1b2f5efae *R/check_root_sequence.R
33a09eab47acee59aae3c9a39d09ee20 *R/check_sim_tral_fun.R
d390016f95e5ea280fcb93387e7aaf1d *R/check_sim_twal_fun.R
dc67abe1614129fef33e085719b103e7 *R/check_sim_twin_tree_fun.R
4fa2aefcfc95574e52801325491f4ab5 *R/check_tree_and_model.R
939c2bca9b2f7f76c745b428e31a9cef *R/check_tree_and_model_errors.R
ce36413c5277b4e8633dc1082f8c2b73 *R/check_tree_and_models.R
9b5b5dda928622b6473228878c2cd7bd *R/check_tree_type.R
8fb1c5ab882f8addc0a6e5911a1271d9 *R/check_tree_types.R
824e9089a5d45ddef29b438551b947d1 *R/check_twin_phylogeny.R
66dd93f773be71432c96cc31c8d0f21f *R/check_twinning_params.R
ea225ead4260d239c0101424863e42aa *R/check_twinning_params_names.R
e102da1a6a0b12dda148d8568b1c1f02 *R/collapse_tree_and_model.R
f10fb4f59fc4dd1417059a6ba74559e9 *R/collect_pir_outs.R
b82bb98bc02b425dcdea7a2802aea3a3 *R/combine_brts_and_topology.R
7251dc494bb570cd1373347b0e6c112d *R/combine_models.R
bc1ca40062e02c3420920998a7d019f5 *R/complete_treelog_filename.R
7e7de8e7bce93dffcee8bb28a374be77 *R/convert_pir_out_to_long.R
a211f1a2d2d428c2c5b99b75c50c1a03 *R/copy_true_alignment.R
be013203d8bdaa4f5eb8656564eb19de *R/count_n_mutations.R
fd59e1a495c98b9ce585cceb939ed4a2 *R/create_alignment_params.R
d5bf50a4a1b3a38ef2f61fc0562ad8f1 *R/create_all_bd_experiments.R
0b290890f74077ee8fa59d726f005f32 *R/create_all_coal_experiments.R
f7f97517836b3241cad67cb1134ca7a1 *R/create_all_experiments.R
be03adf8af44295e94cdc1c32d141547 *R/create_blocked_dna.R
86e106dd5e0a45912d80ea928e2bac5a *R/create_cand_experiment.R
468ed244433f58122f29a683486a72d4 *R/create_copy_twin_tree_from_true_fun.R
5fcdebdb3b70f45e092fcfbb947c7406 *R/create_error_measure_params.R
2b52f7d6e280f0639e9e93248999b725 *R/create_exemplary_dd_tree.R
d1e0b2870109f90985b8a85aaa6adbac *R/create_exemplary_dd_tree_giappo.R
0291037044aee1f080803eb3d7d0f165 *R/create_experiment.R
cf0dea50c8385c39dbd75dfd4bb48edb *R/create_gen_experiment.R
71599df1c6823055eebb6b4b81fad626 *R/create_generative_trees.R
918c556b6e7bf4ddbe3e6e96901276dd *R/create_inference_conditions.R
5559c82250c1891a144bb02dd3497e7b *R/create_mono_nuc_dna.R
29f45fbb4cd71a26bbae6d8fe0364f10 *R/create_pir_params.R
bd289a23ffd6334d8aad58a526508da9 *R/create_rate_matrix.R
83cd07baf3ad4feab4ff1fb094543c1a *R/create_sim_yule_twin_tree_fun.R
d85925310000a2712933e640b12812ac *R/create_standard_mutation_rate.R
3fe9b05cdf0c8d3efc628ef3177956fc *R/create_std_pir_params.R
4e35f79b7eb62a2f9ba0b2ffe8bfd3f2 *R/create_std_pir_paramses.R
70b00a99bf3aa1deb5573cef081082d9 *R/create_test_cand_experiment.R
3a4a8753e29424c2d065493127f01cff *R/create_test_experiment.R
bf1f7545431044b0fbd208c26c0febd7 *R/create_test_gen_experiment.R
adc29139879d8df2e5425f70d807b9f3 *R/create_test_marg_liks.R
cb9cb68eba625babb3a3ce2fd82c4ae0 *R/create_test_phylogeny.R
acaa100e1abab4c9acf140feb112a661 *R/create_test_pir_params_setup.R
b8afea5b4eee66e1a76fa32b13491a6f *R/create_test_pir_run_output.R
cf14dc08d8180cd90332a1d4fff890e4 *R/create_tral_file.R
27f59dc67024f29741b91c16a749d4c3 *R/create_tree_and_model_errors_from_folder.R
aab4f8c944314706bbde727dcda8129c *R/create_tree_and_model_errors_from_folders.R
da623349a953ef569293387677aec3d9 *R/create_true_alignment.R
b5cfb065180daea8c1ad631cc4500c22 *R/create_twal_file.R
e8bd39534061c7f5de17da5e2b66728f *R/create_twin_branching_times.R
0820a083c210bb5a745b53a31bff1553 *R/create_twin_tree.R
06a0f77ef6e07c5221066282d57bd18a *R/create_twinning_params.R
e988bade52063d9bdfe1121817c93917 *R/default_params_doc.R
42cd92cab571330c980705ca0ce3e151 *R/delete_beast2_state_files.R
f7329fe02f4466e29816977ff7f81edc *R/errorses_to_data_frame.R
88e3b018c06e52fafb5ed950f3d62016 *R/est_evidences.R
a670b61ab4341c3db09b0a2febcc95b0 *R/get_alignment_n_taxa.R
6f9088db4f07df18b617ae800f56939b *R/get_alignment_sequence_length.R
1697c188421e180e5cc6d07ad2328eb3 *R/get_alignment_sequences.R
273beea25038b5c501eb3a7a1a4c8cf2 *R/get_copy_tral_fun.R
2dceb7c08a21deeab2d610c688f95b3d *R/get_experiment_filenames.R
b1d0fed6542dbf46979fec255f506f0a *R/get_experiments_filenames.R
0f9e8639135f7fa1d6a08484d0e35ddc *R/get_gamma_error_fun.R
a7fa9b5a0009a87c9e949e187dd808f1 *R/get_model_selections.R
e86e6ba1738b3c38a0ef85a25444b732 *R/get_nltt_error_fun.R
f4a5f289aadf4ddf1acfdbd5cfbd7930 *R/get_pir_params_filenames.R
acc6fbf28794aa1eec2cab096a7a71d7 *R/get_pir_plot_fill_colors.R
79c5c6bfe63bc133d09c2a80d4f8c19a *R/get_pir_plot_line_colors.R
128ec7e9274df51dd526e33863bf16e9 *R/get_pir_plot_theme.R
b83ef0a9f133ca0dc9f8412a1d4cebc3 *R/get_pir_plot_tree_and_model_descriptions.R
bdf1184e17617c48735dfe850f59eb8b *R/get_remove_hex_twin_fun.R
402c2f21753f6722d8782c72087eea2a *R/get_sim_bd_twin_tree_fun.R
d3bbd2dcac540ac80e9aac56152d14e0 *R/get_sim_tral_with_lns_site_model_fun.R
65c8d5716e82e2cc0bfe73e388580a76 *R/get_sim_tral_with_std_nsm_fun.R
648cd8463da797584dfed8c7048e7eae *R/get_sim_tral_with_uns_site_model_fun.R
6412b111af56ffecc96c1267f7557064 *R/get_sim_twal_with_same_n_mutation_fun.R
0e3a84207bb1d0d8d90416ec7fdbae81 *R/get_sim_twal_with_std_nsm_fun.R
0f109acc474e9e885b1ce52b27b70fef *R/get_sim_yule_twin_tree_fun.R
02b9993981716962b42f683dcf7ab677 *R/get_temp_errors_filename.R
12e4298f243435db1d5277080eaf6e1b *R/get_temp_evidence_filename.R
ef483b4f99f2ccc2438f686981ee8a83 *R/get_temp_fasta_filename.R
df977d7490e125837da66658dec581af *R/get_temp_tree_filename.R
de11063d91a0bd80847274504de6c098 *R/get_test_alignment.R
0efc2e39dcf60ce563f9a51eb8c93368 *R/get_tree_and_model_descriptions.R
b965df89604d109a69f35c98cf324ba9 *R/get_tree_and_model_values.R
c0a7b6396600e93e895556eae9d53dcc *R/has_candidate_experiments.R
56e5893166d5d08c903a6d20a7431d5f *R/has_twinning.R
4a78e2806d244fc1db5505f0d6a7256b *R/init_experiment.R
0d50391c4c5fd13033bd76a62944d291 *R/init_pir_params.R
b721210b3b54c400cd18d660562fc89d *R/is_best_candidate.R
01861fa197f8ce3a85036aa3fedd4105 *R/is_dna_seq.R
ddca972926f19d145515cb733b32b55d *R/is_pir_params.R
4d1691b8e89aa48e2b8978d99ea70d35 *R/phylo_to_errors.R
97f75cdc5623423683ec670f35360354 *R/pir_plot.R
8ca9ada03f4053df84ea5dfeb3270cf9 *R/pir_plot_from_file.R
e51651371ddc613735c29eccb5a5ba69 *R/pir_plot_from_long.R
680dcf3cd334f0155ca5cfa40373a59d *R/pir_plots.R
251cb3d87fca08ad78dbeec9ecd06d64 *R/pir_rename.R
9d03daef3572b95eda60c41e32b24f19 *R/pir_rename_to_std.R
5ef8471f58eaa7d46045845eeea83d63 *R/pir_run.R
ac8da3b7adf496f16f58883d7c3bfac1 *R/pir_run_distribution.R
b30fef1f6cacf9ecefb283985328316d *R/pir_run_true_tree.R
cb5344a445c5d9a8f74b1f5276ea9d02 *R/pir_run_twin_tree.R
31afdf4d124e74f8a954f5f183bc6ff9 *R/pir_runs.R
9d2a41618e69a3347764dbd1e37afd22 *R/pir_save.R
f406d9383db1fb747b82fb9f0419f6db *R/pir_to_pics.R
ca3f083fc968c70f88a5abcde701cbc3 *R/pir_to_tables.R
14777dd76ea7ba84f49a15fd5a62886a *R/pirouette-package.R
9aaf2a9377d14c35b315368e01ea45fe *R/plot_alignment_from_file.R
7f601726c4ff7b6d92a26b27f7b88e7a *R/read_errors_csv.R
6bd490af3a7e742653877d1191747074 *R/relevel_inference_model.R
382ded8eb3e7f1a4046d06abe194fc6b *R/relevel_tree_and_model.R
6d797fe07d8b03f9c31218c5586a8848 *R/renum_rng_seeds.R
1c6da12edfae8ac29990d22af27bbdaa *R/replicate_pir_params.R
e3f05182b75e1aed6aa98199370186bf *R/rm_pir_param_files.R
60cfa386a05474030e8a28b7edd1e76b *R/select_candidate_evidences.R
05b58ce182a9b54fb3fe43298a53f35c *R/select_experiments.R
5cc65976a22b36b4b0ae1ec550a5b558 *R/shorten_experiments.R
4b35a2a6e99850fb6ea0d2330824342f *R/shorten_pir_params.R
542d11c8962d3ac178ac37920a87df93 *R/shorten_pir_paramses.R
639b102036056c27c9ecafcbab9ad4fb *R/sim_alignment_with_n_mutations.R
68e122a134db3970769526d8999485bb *R/sim_alignment_with_std_nsm.R
60f0269d9dd45b2c538b8531126eda15 *R/sim_alignment_with_std_nsm_from_params.R
4f0f45e3d25b10cc995d2da6534976da *R/sim_bd_twin_tree.R
fb3ef0fe9a36812c69f428100f0bb9d7 *R/sim_tral_with_lns_site_model.R
3c5036d202005fb506d43733a9c129fe *R/sim_tral_with_nsm.R
2fca000f67eff6836c44f8782a2ec411 *R/sim_tral_with_uns_site_model.R
0596f93f85ddc913f48e0a1dce5f5ef3 *R/sim_true_alignment.R
94b440b499078b4be855b44dbebff3e2 *R/sim_twal_with_lns_site_model.R
49c7a0e77d133516d41bf075d9d8b037 *R/sim_twal_with_nsm.R
c3201cca909eb349e5ca9ad7ebcee7c4 *R/sim_twal_with_same_n_mutation.R
77bcb2232534101108d1c36cbe53d93e *R/sim_twal_with_uns_site_model.R
57014be0328799fac767dfd4d56c82cd *R/sim_twin_alignment.R
f7694b6c77a26b92218e3d3f890ee67f *R/to_evidence_filename.R
b27087c8b9963a1879d9d51eced8d5a0 *R/to_twin_filename.R
d013cfe98f72a5e1ab9788394e4b5649 *R/to_twin_filenames.R
82431673cede222804f36eb14aeb6f1a *R/twin_to_yule_tree.R
8d2487dbf45064f33b08e5a80830b68e *R/utils-pipe.R
d1c88457b43a074f32be947435ce2153 *R/utils.R
1ca0199bfcf3a89ce87e3e7b3200e081 *R/will_measure_evidence.R
be9ce4435fe882d3884440c994f4bd93 *build/vignette.rds
05d865a35909055180f5b8535abe11e5 *inst/CITATION
90242b0779dc0425e5baea4abc51dd70 *inst/doc/create_twin_tree.R
3cc84122d4d130971fcb022297c8c496 *inst/doc/create_twin_tree.Rmd
fe86026da1faf3aead9fd20ddff44027 *inst/doc/create_twin_tree.html
181fac3cb0c834f8e120373bc0afd469 *inst/doc/demo.R
c972df06ac4ff0a6774129106b81cead *inst/doc/demo.Rmd
886771c6cdbb582554646f25db6e07b2 *inst/doc/demo.html
50fed54090c2d0f218e1380cf4bc0690 *inst/doc/experiment.R
8c573d51e0c72cfb412712f05ed94a59 *inst/doc/experiment.Rmd
e79b786e2bbce9f197ada804f9fa46c3 *inst/doc/experiment.html
af83309d04a346d319b1a0a006e6d1fc *inst/doc/partial_function_evaluation.R
a8eaaf168891e4c4f6f4fe0412a2c21c *inst/doc/partial_function_evaluation.Rmd
a0b4f4fb1d410c6d9ca6ad3b33f4b68f *inst/doc/partial_function_evaluation.html
7138e5c05f6f1801ccd3300614a0f7cf *inst/doc/tutorial.R
2f5993359bcef5aa55af1ac62a1fe9a7 *inst/doc/tutorial.Rmd
23f84ed392714f91c48c24f77cae2fdf *inst/doc/tutorial.html
4ce0ec8ae5231ca7a5f41ecbbcee4425 *inst/doc/twinning.R
92b1f50eafc27dbefa1d60672855b084 *inst/doc/twinning.Rmd
48e519e5d91b3a4b131515efa36e00e3 *inst/doc/twinning.html
ec083e238606229bcc5ad0a2ea17a456 *inst/extdata/alignment.fas
ec083e238606229bcc5ad0a2ea17a456 *inst/extdata/alignment_evidence.fas
2b54f39ee9abed1d4f82d03b6111c675 *inst/extdata/test_output_3.fas
2b54f39ee9abed1d4f82d03b6111c675 *inst/extdata/test_output_3_evidence.fas
f1b33b5d07537d8adeb0ce41c700a5a5 *man/check_alignment.Rd
1db63ea07ebe320ecbb53d3b5ae4e610 *man/check_alignment_params.Rd
a9c24cc2706591c574cd3d2fe0c4093d *man/check_alignment_params_names.Rd
0ff2f8d5548d1915f34b1480a9c53639 *man/check_beast2_installed.Rd
f3f780e00799bc98091918c7450aa8f2 *man/check_candidates_save_to_same_files.Rd
00436f61cb4c6d29efb9b05501fc5cc5 *man/check_error_fun.Rd
d1a36971690cfc22f8ff3c2ba23e6630 *man/check_error_measure_params.Rd
5a91465205caf9ce133353d84821d623 *man/check_experiment.Rd
4e37fdc3c92615cdea963fce07469712 *man/check_experiments.Rd
0c775251632c60829e76d9c27ca801ff *man/check_experiments_all_inference_models_are_unique.Rd
f734e63d430195a8eac3b900a9ec6f71 *man/check_experiments_candidates_have_same_mcmcs.Rd
8449832493ea5eb13f39cb66e650e46d *man/check_gen_and_cand_exps_save_to_different_files.Rd
88024de778d2a557b436cd3692e9d392 *man/check_inference_conditions.Rd
2eaffb546676948025bdb51562159d19 *man/check_inference_model_type_names.Rd
1e073a6020957071c4ff3574c0f538b0 *man/check_inference_model_weights.Rd
df66d7d37412a6ea384cd65fc9c14a56 *man/check_init_pir_params.Rd
5acab27e99570004a5a82b27045b4d19 *man/check_is_ns_beast2_pkg_installed.Rd
2c9cfbba20a46d9f9250a8012ebc802b *man/check_model_type.Rd
502acee3315e4b12ca4c286bf43ec4d5 *man/check_mutation_rate.Rd
d362d109da1f4d8b2e027732bd870607 *man/check_pir_out.Rd
72d31e9fa53349211c58a92425c54621 *man/check_pir_out_errors_above_zero.Rd
4f383fce6c7982e3232915ac958b5414 *man/check_pir_out_names.Rd
ce00d04ff34fb78ec0b35a71853eab76 *man/check_pir_params.Rd
4373ae88c3eb432f2cf2252d451847cf *man/check_pir_params_data_types.Rd
75211da74002b9149f61e0372c303a1f *man/check_pir_params_names.Rd
57d26ba8e99b1e53aa9162871bcd6bce *man/check_pir_paramses.Rd
d82ed3877043315fffc4c4c653bf9b3b *man/check_reconstructed_phylogeny.Rd
71b0b8274c23ddbc2306a586c9133bf1 *man/check_root_sequence.Rd
c9e4a397b0916641e3ec56f036cdaf0d *man/check_sim_tral_fun.Rd
dc0ec4f4a44d983c21bdf4d56baa003b *man/check_sim_twal_fun.Rd
3e20330afe1c5fb160e7355ad91e05d6 *man/check_sim_twin_tree_fun.Rd
65e90748a81794d4322bf527511d3355 *man/check_tree_and_model.Rd
b74dac409e90a26b47df71c017d70a2c *man/check_tree_and_model_errors.Rd
c9e27fecf1f11edbc8e88f38a5a3af92 *man/check_tree_and_models.Rd
96d58cbfe3f83853909f995d7617975f *man/check_tree_type.Rd
3ed6cf35b01b60d626b3522c4b5014c1 *man/check_tree_types.Rd
f72ea15f261311832a201a4dd164ec0b *man/check_twin_phylogeny.Rd
71f2fa803673e3b8bc518ed76fb99ffc *man/check_twinning_params.Rd
55122e68f31ac040aa1ce9de32387789 *man/check_twinning_params_names.Rd
d2cdd4167bef7da1a183d2de55d20fc9 *man/collapse_tree_and_model.Rd
54edf157c1ffba125f67c5e6c241c994 *man/collect_pir_outs.Rd
51c6d325363b99262626056b5383b65e *man/combine_brts_and_topology.Rd
b1440e678ee24f4cbf7ae7fdc64a09e9 *man/combine_models.Rd
37eb83d23f029d919a846c62cc1bc5fc *man/complete_treelog_filename.Rd
5a0df7cf8d865e096c186ba217d24143 *man/convert_pir_out_to_long.Rd
c22efdc12853ccf1b47e9100df4dfb75 *man/convert_tree2brts.Rd
d9938c91df786a7e9b228d0306ae74d9 *man/copy_true_alignment.Rd
1f0f001064cb376c1354674721ee96e8 *man/count_n_mutations.Rd
a43191f0a239c4dc4d0b14657e0cf260 *man/create_alignment_params.Rd
5598f0484b27251008b85e6d4c434e33 *man/create_all_bd_experiments.Rd
81680e56be7868353f4b07ad0acec26f *man/create_all_coal_experiments.Rd
6978ed6a32b85059d3421bd41aa8170c *man/create_all_experiments.Rd
21811fe8ac24f2ee35a735fddf7cad55 *man/create_bd_tree.Rd
cb75c79a7a42b88acd9d8513554d8c2c *man/create_blocked_dna.Rd
0df271b2fc6a64708c8cc3aea5cca6c5 *man/create_cand_experiment.Rd
fef0db759c1f8a2b8391bc539691b52e *man/create_copy_twtr_from_true_fun.Rd
516aca38cf13de38cd410e86e2e73ca7 *man/create_error_measure_params.Rd
232728d221b49da61bf2182aab0a91da *man/create_exemplary_dd_tree.Rd
1682ae0a0d7c1bccb1048154ed4d9c72 *man/create_exemplary_dd_tree_giappo.Rd
dbb7278c3da98a3a14373b731ed36da0 *man/create_experiment.Rd
99b54416d8af4daf63d1ee0fc0b2b973 *man/create_gen_experiment.Rd
dffeaa13048117c5cec8d39caea9a8ab *man/create_inference_conditions.Rd
a1c3bcd06cbfac52f06940309cb8a806 *man/create_mono_nuc_dna.Rd
94920400cfcf473f4d00d269cd0b6d54 *man/create_pir_params.Rd
58bb38e598e548d3bc9f1ba5c4e06f14 *man/create_sim_yule_twin_tree_fun.Rd
7b2eedc76f3cddc6aec9592025628546 *man/create_standard_mutation_rate.Rd
95b552a73c5b016f1f42bf1ffa6ce167 *man/create_std_pir_params.Rd
fd15360f32b65c3fd9d97e8f9d528a81 *man/create_std_pir_paramses.Rd
fd69b5ac428210b29d0d9aca9c002931 *man/create_test_alignment_params.Rd
ac490084ba9afbe7f45d1d7420563770 *man/create_test_cand_experiment.Rd
26a765db15c6e8586231d221babe7055 *man/create_test_experiment.Rd
95dfd79859edd84f46e25eee45154bb1 *man/create_test_gen_experiment.Rd
92cd9381f044da80bce5e4688a30d84a *man/create_test_marg_liks.Rd
50aae6a8b62d9dc1e88802658e0af68e *man/create_test_phylogeny.Rd
1aa6ebb75a932c5fa3644605469d08dc *man/create_test_pir_params.Rd
c6c741c72c4f4b1b556147a40827eeee *man/create_test_pir_params_setup.Rd
207cb565949ab4823c51b1a1aad33c1e *man/create_test_pir_run_output.Rd
dd5f795323046669049937c6700b327e *man/create_test_pir_run_output2.Rd
b8e0e50d32503dc2660377d0fc8dd4f5 *man/create_tral_file.Rd
1bbb7820f612cecc33a055a29a9ff066 *man/create_tree_and_model_errors_from_folder.Rd
4d1d8bc485f55bcefaf945bb4821a2ec *man/create_tree_and_model_errors_from_folders.Rd
d6d2d2e46be1ceefc8ff4cb7d62d8223 *man/create_true_alignment.Rd
db946d01b312913a7218a2a29c34cfc5 *man/create_twal_file.Rd
b1199cf323bec8236d9d10adbaeb8dff *man/create_twin_branching_times.Rd
f4237734f3fe42fb892cdccf45ec0b9a *man/create_twin_tree.Rd
036dbb52cd742071252d171c9d8e3a06 *man/create_twinning_params.Rd
0b82c11c3a34e07dfb8116ea5a76e6c4 *man/create_yule_tree.Rd
43e166920dca55fcfa65c7583243b2b4 *man/default_params_doc.Rd
0b1fc9544de70ec26624e39d6eb8f9e4 *man/delete_beast2_state_files.Rd
159ed222f4c161d0ce97f22451c18b52 *man/errorses_to_data_frame.Rd
c33cd4f7b5b212b7f30a37f807f1acae *man/est_evidences.Rd
3f25ab37a1f6270f76c025cf6eda5421 *man/figures/Codecov.png
b55c56f3943a394162527954ca4a3009 *man/figures/GitHubActions.png
2ee2ff334273b5637ab8270ae5023e8f *man/get_alignment_n_taxa.Rd
1a7c3242f1d1f7f12f8c3fe669be295c *man/get_alignment_sequence_length.Rd
a2bafa0d4cd9378609ac28cb8c47f50a *man/get_alignment_sequences.Rd
34b9802dffce8e15b40e8f658d953115 *man/get_copy_tral_fun.Rd
f8a36274472f26107367360e150e4a5a *man/get_experiment_filenames.Rd
9eda1dd65cf8d36ada8c9ba8a79545cf *man/get_experiments_filenames.Rd
b817c1176a56f1554a8ffb0e87e8866f *man/get_gamma_error_fun.Rd
c60c813cd8df9d113b75dce9b7141639 *man/get_model_selections.Rd
814cfdf18760339e1e3547e58e7b5a1c *man/get_model_type_names.Rd
1a36067d73cb8317d72dcc3e64d78342 *man/get_nltt_error_fun.Rd
48c6791eed95d7625ab26fe97364dd6c *man/get_pir_params_filenames.Rd
19de91df04e8c43deca7c3beb66fd533 *man/get_pir_plot_fill_colors.Rd
6a98af7d0b0ea4c974500f84264d13c7 *man/get_pir_plot_line_colors.Rd
49a8a65bfeac73fd7602ed17070a0a4a *man/get_pir_plot_theme.Rd
f1dc6a8b550c52c153248597939f59d5 *man/get_pir_plot_tree_and_model_descriptions.Rd
92c8bb6299e432331a532f21d3e32f8d *man/get_remove_hex_twin_fun.Rd
599285702fd810f954b704e98707bb0a *man/get_sim_bd_twin_tree_fun.Rd
6733b53574197c2462bf2aae0340ca94 *man/get_sim_tral_with_lns_nsm_fun.Rd
e85a6b10b661aed350ece6a6c23e5a8c *man/get_sim_tral_with_std_nsm_fun.Rd
11dd7b9d8e53e14b7d40d3eaaed24e55 *man/get_sim_tral_with_uns_nsm_fun.Rd
2b047c77d59f31ae35d57ee319b2411b *man/get_sim_twal_same_n_muts_fun.Rd
3d2c2b270c99afae3d475a6e3fbcbdcc *man/get_sim_twal_with_std_nsm_fun.Rd
f74d63b360e3d7c11aa5b44108aebd5f *man/get_sim_yule_twin_tree_fun.Rd
cf6288c742c9acda67bc5d833b3fb82b *man/get_temp_errors_filename.Rd
31630806da86fc2f137aac41f1416a21 *man/get_temp_evidence_filename.Rd
22dd10332bf8d193873c42c64de0669a *man/get_temp_fasta_filename.Rd
e9c3ca8425890345d5d02d8f0c2a9a6c *man/get_temp_tree_filename.Rd
953aaa374f05f843411a343c5fcdb003 *man/get_test_alignment.Rd
08d0f3b4579cad817aaa29dedb32a554 *man/get_tree_and_model_descriptions.Rd
01592c3811d022b0e9693ecf30d22542 *man/get_tree_and_model_values.Rd
5c8f058f3ac44a7f1c7693345f121996 *man/get_tree_types.Rd
308bec0774002232882e7986e246e71e *man/get_twin_methods.Rd
236e7fa23e9b7189daadaf77a68ddc13 *man/get_twin_models.Rd
a8df16ac255c9bd28ff20f3b60b11913 *man/has_candidate_experiments.Rd
9f5bf61bb8cd2e99bd5f75c03d6311ff *man/has_twinning.Rd
5cbb8f02d77aba6972f1c3c2e4a86a7e *man/init_experiment.Rd
2a906d53dc4feeedc42eaf1a15ab9fc2 *man/init_pir_params.Rd
acbb698b04dfd2d2a7deb9789f7c5b15 *man/is_best_candidate.Rd
659e48b49e80bc64283e8e567bd63d87 *man/is_dna_seq.Rd
543af898017614e7271c9dfced676906 *man/is_pir_params.Rd
fb6e33d01e9f184bf8928726b57b04fb *man/phylo_to_errors.Rd
1f7896a1b866ff9ae89ba35be7c7b6f1 *man/pipe.Rd
4f9e445659f8b299f19fd9d81876b079 *man/pir_plot.Rd
f1cc6a08cca72e20a2920e443c6a0fd2 *man/pir_plot_from_file.Rd
48b61b8dd6e56fad371ef402934bb3b3 *man/pir_plot_from_long.Rd
5e03341c68fdbd6a278f9fa3b5ebbeb2 *man/pir_plots.Rd
dbcc498300b9bf468e6ecbb01e325a0b *man/pir_rename.Rd
6740d16027db4fe4436476f53e2abb34 *man/pir_rename_to_std.Rd
946e1e1450e85213fb7f0f5d531fc4d7 *man/pir_run.Rd
d56d320918b8f351aae810768e8149f1 *man/pir_run_distribution.Rd
1121fa46aabc8bb9b5d7f93f8bef33bb *man/pir_run_true_tree.Rd
b5b58165703c992915dffaaa77b9aa5b *man/pir_run_twin_tree.Rd
0203bd7c9e241b5da5a6f4da1836c7bf *man/pir_runs.Rd
a1c1e0072fd5a92fb15f87c3aae8ef9e *man/pir_save.Rd
73eb4f96d1d5f285f9efd86604520310 *man/pir_to_pics.Rd
3301ea3fceabf3a5492728d2aed64d34 *man/pir_to_tables.Rd
e20008864623b65ccdec18b8372383d0 *man/pirouette-package.Rd
81847e256a538bd84fc3dbdd58ab4eb8 *man/plot_alignment_from_file.Rd
e6e5684fb1e136178abd482e8d42d40b *man/read_errors_csv.Rd
bde87a25b0b97e5fb7ac7741f86379f4 *man/relevel_inference_model.Rd
f23d1d420373c1209a99a9caec812e2e *man/relevel_tree_and_model.Rd
488d645d2217d70bae086a35055bc0d9 *man/renum_rng_seeds.Rd
babd59c01e83891ec56a4ad53178ff2a *man/replicate_pir_params.Rd
b06684b3c426221d138975c7732a3b80 *man/rm_pir_param_files.Rd
84d3190b09f06e113ba17200771f9f16 *man/select_candidate_evidences.Rd
95343a5ca2c2e0edd4f1da898a759913 *man/select_experiments.Rd
c4e3f5ec78fd0ba2ccba4f74a9a72625 *man/shorten_experiments.Rd
e4cf09855d7221960e4e14dec8a5f19d *man/shorten_pir_params.Rd
77939cb1812f6cdf983cfcc0faf61d4f *man/shorten_pir_paramses.Rd
a83a9c99c7ee1ccd4b073a1d029f45a6 *man/sim_alignment_with_n_mutations.Rd
95efad542a852807c19819af18b19cdf *man/sim_alignment_with_std_nsm.Rd
a5a831d4c9a37a551f2344ab963d3dde *man/sim_alignment_with_std_nsm_from_params.Rd
83d3f7fb5ee469fd23a5450e56d6b43e *man/sim_bd_twin_tree.Rd
9a7c1746ebfebf52d8a7b1c023f7651a *man/sim_tral_with_lns_nsm.Rd
774830dcc4e7cec704a55f41dbe33b50 *man/sim_tral_with_std_nsm.Rd
dc9d4feef7bde8dd4efda2f88ef2323a *man/sim_tral_with_uns_nsm.Rd
143e494e169b4f1a063ec5d4ecc1b9d0 *man/sim_true_alignment.Rd
849f0c5753e8441442e12e10aa0b9d29 *man/sim_twal_with_lns_nsm.Rd
69f9640e4d7feee93e1901f593a6fb30 *man/sim_twal_with_same_n_mutation.Rd
6ccd511d96781133d070293137de5756 *man/sim_twal_with_std_nsm.Rd
26aa58f1f336b750b804d902c041ae9e *man/sim_twal_with_uns_nsm.Rd
25f7c1c882df87c5523254464ab93cd6 *man/sim_twin_alignment.Rd
51d009beb4c4b00f578724bd6018c635 *man/sim_yule_twin_tree.Rd
35c3e401bf0b12729d2cea08c9b66c3f *man/to_evidence_filename.Rd
7f6b2945a060eb2205959c5a00fee719 *man/to_twin_filename.Rd
f5cd575982602ba02f3e7b3ef41ad05f *man/to_twin_filenames.Rd
722c141285c02cc5a5de345bd95af005 *man/will_measure_evidence.Rd
3cc84122d4d130971fcb022297c8c496 *vignettes/create_twin_tree.Rmd
c972df06ac4ff0a6774129106b81cead *vignettes/demo.Rmd
8c573d51e0c72cfb412712f05ed94a59 *vignettes/experiment.Rmd
a8eaaf168891e4c4f6f4fe0412a2c21c *vignettes/partial_function_evaluation.Rmd
2f5993359bcef5aa55af1ac62a1fe9a7 *vignettes/tutorial.Rmd
92b1f50eafc27dbefa1d60672855b084 *vignettes/twinning.Rmd
