c64305890be40f23535b959c03dd105a *DESCRIPTION
97acaf7186f4719b9fc90d5cc088af42 *NAMESPACE
09966fe4c22b0f614930049f44d4a42d *R/RcppExports.R
90e3e84e252598a58a812a040e2bfced *R/asr_empirical_probabilities.R
989b7786c5d618f4b4a278f60d277a71 *R/asr_independent_contrasts.R
5766739cbd484fff29a9e045252df4d8 *R/asr_max_parsimony.R
942b9eaa32dc69a89b027ecc06b056be *R/asr_mk_model.R
085126368e9a7434358a27646b8765a6 *R/asr_squared_change_parsimony.R
f6a1c71281b5713a4f8fe75745bbc76f *R/asr_subtree_averaging.R
822232ed8faad6dc9921541af5de243a *R/auxiliary_routines.R
1c15800df049bcc1a2833ca818225313 *R/collapse_monofurcations.R
ca3a8f5b310f31342c77c7e4ad07f4eb *R/collapse_tree_at_resolution.R
bfe0fd12c907c06da622ed4fd7717a7e *R/congruent_divergence_times.R
b064cb759b01e504b9e7a79cd6c98dfc *R/count_lineages_through_time.R
d736e8020a5799df6ce10fb5d6b3baae *R/count_tips_per_node.R
d81ceeaec9a422307f401035a640debb *R/date_tree_red.R
71e74f8639654538b13df6db5a863e7f *R/evaluate_spline.R
5ca0e410c6967b748b8e0346666f9180 *R/exponentiate_matrix.R
3f734a938a3b46655dc1f4023876786e *R/extend_tree_to_height.R
b82080762190bce93df3c0a2bbe3b8a8 *R/extract_fasttree_constraints.R
f2609325246e3e12067277b78c354d91 *R/find_farthest_tips.R
282db5ffca1fde87785a7864d03e14c4 *R/find_nearest_tips.R
5e8a110182785dc41dcc0ac88f009ea0 *R/find_root.R
1ea97c12588e374ad6949df8e6c799d7 *R/find_root_of_monophyletic_tips.R
22eacf16320ee46824574a2078dd803b *R/fit_and_compare_bm_models.R
6fe0775dcdda2a4b52b318f242891960 *R/fit_bm_model.R
e36d68451a40f8d85d4781f5e2de71db *R/fit_hbd_model_on_grid.R
20c6449921a3ca4c3762367def903c3c *R/fit_hbd_model_parametric.R
d31942759ea90d6ca8365e075403229f *R/fit_hbd_pdr_and_grid.R
12b132b523841e709a37fb69ec2b2c18 *R/fit_hbd_pdr_on_grid.R
c8be531ba3d8aadc38591c7fc0311d3b *R/fit_hbd_pdr_parametric.R
0418e5262b28a920f4d01a04b578b58c *R/fit_hbd_psr_on_grid.R
0a244354b133e9b02a56e999b522c94c *R/fit_hbds_model_parametric.R
3f2aa8880f5ba9a456231d22e3edc880 *R/fit_mk.R
1cf984ceb84881328ec1d9f4d7c190b5 *R/fit_musse.R
5c0bab7d542d5e65bd830cd40da18c69 *R/fit_sbm_const.R
5c9e9f29c75fd059286694ff0107930e *R/fit_sbm_const_biased_sampling_unfinished.R
0ef886110950ed4a9919eafed29b3c56 *R/fit_sbm_linear.R
2dd1d2c19d9625600104fb9b5e81e779 *R/fit_sbm_parametric.R
9202e805983da5833adc0d98f31367cf *R/fit_tree_model.R
0eed8b7b366c3f7ec5f9e3e4b7536d96 *R/gamma_statistic.R
e456b045eb2d76b45185ab98a120ffc4 *R/generate_gene_tree_msc.R
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b846dcce6f2f3303fc0ee58eba09a63f *R/generate_random_tree.R
3d5e48734f093ea1150c5365e6251911 *R/generate_tree_hbd_reverse.R
93a685f9202426f8021eb5d4cf12814a *R/generate_tree_hbds.R
cc6969cc3874a7ad62f840bb671e3cf2 *R/generate_tree_with_evolving_rates.R
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28af55d0af57073595d3665f34e2d902 *R/get_all_distances_to_root.R
eb43f6c79321859ad6939b68ac12247c *R/get_all_node_depths.R
46c7f78022eebcf7fb69d69e36161fb6 *R/get_all_pairwise_distances.R
1ff57e6c9244cf199fb235da349e9da3 *R/get_clade_list.R
dc6bd12fb89c8790dc9071d5876a0155 *R/get_independent_contrasts.R
10714e99dc514dcf8735baec012f43e7 *R/get_mrca_of_set.R
ca4e0d3d97450c056cf8e6bc50b782f1 *R/get_pairwise_distances.R
c91a89675f18c56273fc10c600a21df3 *R/get_pairwise_mrcas.R
c6e21e4e0479b619d499d959c1891089 *R/get_random_diffusivity_matrix.R
6e05cd29c225f59083dab5374159e6cb *R/get_random_mk_transition_matrix.R
3c16cad1b44e27ddd90804980a8137e6 *R/get_reds.R
f9de590cb60abf56cc29c154fccd9e85 *R/get_stationary_distribution.R
deb4fe36a3a9122b4eba7b78b7a3d479 *R/get_subtree_at_node.R
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7533a04be559994c0f9e665a7d5b0411 *R/get_tips_for_mrcas.R
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4bf6536e16dfc47baf4d67cba0980822 *R/get_tree_traversal_root_to_tips.R
fc0ae53019a185ef1d410ce0ff585470 *R/hsp_binomial.R
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145eb14cf9b3dbd2b2c8934599304a14 *R/hsp_independent_contrasts.R
1963139ac502b8bf4885e6d8584e683e *R/hsp_max_parsimony.R
a4ec81b4d40c4b6defb304c5c67056ec *R/hsp_mk_model.R
1c2a998ed4d45fbfa0d76452ac5b49ac *R/hsp_nearest_neighbor.R
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c2b6a32c402ca7c5478724c8710a82fc *R/merge_short_edges.R
9322e57d5311a475d660535093cbf5a6 *R/multifurcations_to_bifurcations.R
7bca7b3341577fcccbdc2a3a9e5b4472 *R/pick_random_tips.R
b0aed7b28cb1cc91933ba0a806036a57 *R/read_tree.R
5101df5ddc1816a1d427aa471ab5b3ca *R/reconstruct_past_diversification.R
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51f21392f2e0030910da1c33a4495cbe *R/root_in_edge.R
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d999ed3f935d8eddcdb44108c672b422 *R/simulate_bm_model.R
fc267ed11b0805a8b38ed083a9fe295a *R/simulate_deterministic_hbd.R
1834aa21281005649c81784a1edbaf7b *R/simulate_deterministic_hbd_msc.R
0ba11734b0b804e5469295b2a155ba6b *R/simulate_deterministic_hbds.R
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175b4a100431d5312959758064c5ed0e *R/simulate_dsse.R
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a09f1724a2961fdcf3f2049b3259ec11 *R/simulate_musse.R
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75cd6635acc1924e888e1d3fe8bdd05d *R/simulate_sbm.R
e77a42186407f6c3b45c13dff0be9a4f *R/simulate_tdsse.R
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912fad991efe2e61d091e85ee8f0ac58 *R/trim_tree_at_height.R
b575b0d6f0e09a0ffab38403b4674c56 *R/write_tree.R
5ec58112eb169070e83d64cc1ca29b75 *inst/CITATION
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