5096db8316cb1fef555ca9034105e99a *DESCRIPTION
3c90058e28c5c2fc19ceb86b01a8d95b *NAMESPACE
31882a5c0028628365237bf9e60aa9ae *R/alignment_params_to_posterior_trees.R
ae899250e82d69ebbf440dc4ee4cdb7e *R/check_alignment.R
e3b290754fba0a4182f74ecc7a084866 *R/check_alignment_params.R
e90f195039296cb367d5452bcd72593e *R/check_beast2_installed.R
8286793758903919ed4cbee157de2d5d *R/check_error_fun.R
d671a10627279aed71a8d64ac80ff96c *R/check_error_measure_params.R
cfcf2c5d49f78e613304e3b14673a56a *R/check_experiment.R
ebecf0936543ac3cf6b80dacbba3d52f *R/check_experiments.R
7fb2f878af869f5b5530ab9c109ca59e *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
2b1931f353c39f184005719a8838c51b *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
7340a2df141140404001ac64492de46d *R/check_twinning_params.R
ea225ead4260d239c0101424863e42aa *R/check_twinning_params_names.R
e102da1a6a0b12dda148d8568b1c1f02 *R/collapse_tree_and_model.R
ade84ef4fa84a0570eafedc0f4fc9427 *R/collect_pir_outs.R
b82bb98bc02b425dcdea7a2802aea3a3 *R/combine_brts_and_topology.R
7251dc494bb570cd1373347b0e6c112d *R/combine_models.R
e416391d27b46770d822384b0cd86ff1 *R/complete_treelog_filename.R
83eaf67b4b2d8afe623df04ee8c9db50 *R/convert_pir_out_to_long.R
e93f2969a720331a1abf0511c98306df *R/copy_true_alignment.R
5fd9a9e0210b613efd765540997337cb *R/count_n_mutations.R
5920e251267c11a78fae31002d848cab *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
5a296cc01c3a95d38344580cf8b2cc97 *R/create_cand_experiment.R
468ed244433f58122f29a683486a72d4 *R/create_copy_twin_tree_from_true_fun.R
9953383ae63ba75c87bb384800f5a485 *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
02c85c5cfa32c3cd6e95c5f9bd2200f8 *R/create_gen_experiment.R
71599df1c6823055eebb6b4b81fad626 *R/create_generative_trees.R
81fd4fa0f0e2e22871adede3f8c3c56b *R/create_inference_conditions.R
5559c82250c1891a144bb02dd3497e7b *R/create_mono_nuc_dna.R
c93dbb7bc5e450f26ce962ef400bfb7f *R/create_pir_params.R
19b901d5fcf3a3fd375c497cf598cb68 *R/create_rate_matrix.R
83cd07baf3ad4feab4ff1fb094543c1a *R/create_sim_yule_twin_tree_fun.R
d85925310000a2712933e640b12812ac *R/create_standard_mutation_rate.R
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4e35f79b7eb62a2f9ba0b2ffe8bfd3f2 *R/create_std_pir_paramses.R
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adc29139879d8df2e5425f70d807b9f3 *R/create_test_marg_liks.R
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002f0bbb096283e83ba8fa12bf5d11bd *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
bcc129128c4aa51c8489369626f51cbf *R/create_true_alignment.R
8af8b869051c15c33bfb147c9d57ee38 *R/create_twal_file.R
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59bb1220bc565089a9434c0616592398 *R/create_twin_tree.R
a117ec721af7e05f64085552c7fc1fe0 *R/create_twinning_params.R
e988bade52063d9bdfe1121817c93917 *R/default_params_doc.R
42cd92cab571330c980705ca0ce3e151 *R/delete_beast2_state_files.R
df7220830bbc82dc5a154b759a9305de *R/errorses_to_data_frame.R
9a02121de94e2cf40f75d884b27a4760 *R/est_evidences.R
a670b61ab4341c3db09b0a2febcc95b0 *R/get_alignment_n_taxa.R
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1697c188421e180e5cc6d07ad2328eb3 *R/get_alignment_sequences.R
273beea25038b5c501eb3a7a1a4c8cf2 *R/get_copy_tral_fun.R
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b1d0fed6542dbf46979fec255f506f0a *R/get_experiments_filenames.R
0f9e8639135f7fa1d6a08484d0e35ddc *R/get_gamma_error_fun.R
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acc6fbf28794aa1eec2cab096a7a71d7 *R/get_pir_plot_fill_colors.R
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9ac767303148524dd605f5243617d9e5 *R/is_best_candidate.R
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