fce2962a9d2807aeebddf166931b5757 *DESCRIPTION
fbd2792fe1b5e4a19de2847835be5fce *NAMESPACE
ea0531935275319d384aa16631b5a244 *R/RcppExports.R
93a1f04f79a55620c14af8dc4ce52ba0 *R/asr_empirical_probabilities.R
9dc91c47c8266a56bcb99176c4bca7ef *R/asr_independent_contrasts.R
042c306bc74cb8eee3d3c222a656bc5b *R/asr_max_parsimony.R
35a2b1d0b8db0de1cc10ccc20cc0dc36 *R/asr_mk_model.R
d27dd7b3fc2066d9a30c0d3107ba722f *R/asr_squared_change_parsimony.R
1b97a63388ff347440cc9da2613396b9 *R/auxiliary_routines.R
1813566e909da4774c9c61269a45a7fe *R/collapse_tree_at_resolution.R
4ff64a3b2d89f7b907f8f4f8119b7747 *R/count_clades_over_time.R
d736e8020a5799df6ce10fb5d6b3baae *R/count_tips_per_node.R
91fd2ea3fdc09636569dc2b69c42db26 *R/date_tree_PL.R
5ca0e410c6967b748b8e0346666f9180 *R/exponentiate_matrix.R
831999b4f255360557f5852d762f2208 *R/find_nearest_tips.R
5e8a110182785dc41dcc0ac88f009ea0 *R/find_root.R
b665f4d0c723ab385c9bdd7ec8a0910e *R/fit_bm_model.R
5723bf6569640c6734dfaf1569108758 *R/fit_tree_model.R
1c14dc00d8ce892750c9ecc6227159da *R/generate_random_tree.R
df15d44dce5a28b1561667ee2775b409 *R/generate_tree_with_evolving_rates.R
28af55d0af57073595d3665f34e2d902 *R/get_all_distances_to_root.R
e3f530defd25f1889a6d6bc9a620cec2 *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
99218f67b88da59072522759d285d41c *R/get_random_mk_transition_matrix.R
f9de590cb60abf56cc29c154fccd9e85 *R/get_stationary_distribution.R
00b53255287248cf9dfc1c9f8595a423 *R/get_subtree_at_node.R
bc1f107ad31e8d326321458eae7d9360 *R/get_subtree_with_tips.R
7533a04be559994c0f9e665a7d5b0411 *R/get_tips_for_mrcas.R
60d15cce8a438d078b3cf16d844cb8e3 *R/get_trait_acf.R
2dfd7ac058753bdb21b0641f1305f5ff *R/get_trait_depth.R
7c52d104a2e9e23893fc1086ffc08661 *R/get_trait_stats_over_time.R
00a390a11e5650d166fc45918e6e957d *R/get_transition_index_matrix.R
bf67c1a32504565d4bbc24c6841e1de6 *R/get_transition_matrix_from_rate_vector.R
6d61db3354ddd549aff2cdfea29d2414 *R/get_tree_span.R
4bf6536e16dfc47baf4d67cba0980822 *R/get_tree_traversal_root_to_tips.R
afdf6a82a6c3c6ac013b52a12ff580bb *R/hsp_empirical_probabilities.R
0fd951700483a9896115f01d7d5627b2 *R/hsp_independent_contrasts.R
3a22540645a0aaf46635a0a4e79f2b43 *R/hsp_max_parsimony.R
bf2cccda1750ee74c3af3adee5da63a5 *R/hsp_mk_model.R
9c55c080c8c8a675d3f3b10b19c90567 *R/hsp_squared_change_parsimony.R
27e8f0013e26c11ea335fe3573f48183 *R/is_monophyletic.R
b3effc09d0c3d17cc1d607197ba3282b *R/map_to_state_space.R
c6039e8f5534d7a124d959f14e68a440 *R/merge_short_edges.R
5b3deabdf27153dc6a0c53c57ea06278 *R/multifurcations_to_bifurcations.R
385c63ffd14beb5e9e92cf7002000e94 *R/pick_random_tips.R
b608327933ab59d13206929d369afbbc *R/reconstruct_past_diversification.R
99658e44e24f36812b905179f039d394 *R/reorder_tree_edges.R
c826f8633301bd734ab8b4a9c836cef3 *R/root_at_node.R
bc7121136c19e0a22dd31049eef650e6 *R/root_via_outgroup.R
0e1651281fc770cadfac3cfd557ef3cd *R/simulate_bm_model.R
94cccd35117b85072fd90275d3277c64 *R/simulate_diversification_model.R
c0b22daf4cce24f01a0715511aa3fc20 *R/simulate_mk_model.R
896e3fcd5d6b4fd93094c7b6c2a9d9d6 *R/simulate_neutral_gene_evolution.R
473739c07568c4f017bf5580a687f534 *R/simulate_ou_model.R
91db8e678d574ffcb3e8e91108040d42 *R/simulate_rou_model.R
9ed667a5699194418f6aba50bd800f04 *R/trim_tree_at_height.R
c34d3c1dc4c0e949f06523ec3e8e918d *R/write_tree.R
bd2e73fa7681814d1e25bdc82314599d *inst/CITATION
48927d199ef125faf6e8c34cebaa980d *man/asr_empirical_probabilities.Rd
dc33a67a6a76a8aa0bec1f5dc8b07fcb *man/asr_independent_contrasts.Rd
ef24f35424cfb489aaa2e570118931d7 *man/asr_max_parsimony.Rd
c608103684ce46e9bbd7db31a70ab157 *man/asr_mk_model.Rd
0f9d7d08aa0cd9caf75f700e7bdb69f1 *man/asr_squared_change_parsimony.Rd
b1f8fc4ae3eae76d5cbf3c935fb6c955 *man/castor.Rd
d77ceadba3f839e72ac4c450c6b6cb48 *man/collapse_tree_at_resolution.Rd
a5ceaea289601af13204ca0e938863c8 *man/count_clades_over_time.Rd
55fc8df376f6820c4e892b418f63ad14 *man/count_tips_per_node.Rd
164411f08b5adabfdc2d15d87285fe55 *man/exponentiate_matrix.Rd
2210b6577a9faa1a7adc46e624d3faf1 *man/find_nearest_tips.Rd
aee9db4fd3a47479b5cf46ddfb5723b7 *man/find_root.Rd
11807535e742affea945503fa161e3a0 *man/fit_bm_model.Rd
7509f7d961fee797ea0fd47237bdd5a2 *man/generate_random_tree.Rd
a47dfe2767aff16de176b91e81b53444 *man/generate_tree_with_evolving_rates.Rd
ae641e9d95c4a9a5600612d4359c09a6 *man/get_all_distances_to_root.Rd
4904568d20362f354666456db32e589f *man/get_independent_contrasts.Rd
f9de754a3aa973f0f0c741d1d05a14d5 *man/get_mrca_of_set.Rd
08f42ec1a2e6fb60cc6e073a08c6b00d *man/get_pairwise_distances.Rd
445f8cb25aea57ce373e5ae656cc3c9c *man/get_pairwise_mrcas.Rd
babcc004d68152620e747b60732bd313 *man/get_random_diffusivity_matrix.Rd
d9b6ce53d0a29ecbbd7bd1f4f30c7a61 *man/get_random_mk_transition_matrix.Rd
ed439b4a11de01cb319be81f1b60d176 *man/get_stationary_distribution.Rd
74948230b0cfdf76c435ab1aa3149000 *man/get_subtree_at_node.Rd
ea1e4a4ea6a2a66c0c2f94b0c16a65a1 *man/get_subtree_with_tips.Rd
734f0758ba84ad13a2a2a9dc449dfdfd *man/get_tips_for_mrcas.Rd
d9eb9ace0def54b057f028e6b243f1c5 *man/get_trait_acf.Rd
b6d0a32e987347d8770572b5943844a6 *man/get_trait_depth.Rd
02b60186def319a79ec442b5d417a8fd *man/get_trait_stats_over_time.Rd
89453e9c51d44f265dfb757553ef9a93 *man/get_tree_span.Rd
f95fb7fa4b50df705b4dbc4d52a5e0b2 *man/get_tree_traversal_root_to_tips.Rd
8fe9eb08aed894691c8350560517b4d0 *man/hsp_empirical_probabilities.Rd
912ae5c55a0d056e9df13bc8a658bc57 *man/hsp_independent_contrasts.Rd
ed36982524953e43a699295954302992 *man/hsp_max_parsimony.Rd
d1c987ca22a7c91e38a09ea683124e7c *man/hsp_mk_model.Rd
ac1545442081928c0033e7a8802d075b *man/hsp_squared_change_parsimony.Rd
b9b079dda8b8a4242e34056581d5afbb *man/is_monophyletic.Rd
9af14b79f52f18c84edec02ab0387d72 *man/map_to_state_space.Rd
f23b87dce36ac420b37c9eb913974a04 *man/merge_short_edges.Rd
8f3ebdd1c9310772e9746295e4339990 *man/multifurcations_to_bifurcations.Rd
4ca0232f910185e972ca2303a06606fd *man/pick_random_tips.Rd
f002f066a636811d5d646f8c5fed2ec5 *man/reconstruct_past_diversification.Rd
c49b4a0bd43481c3e341f42ea48492d6 *man/reorder_tree_edges.Rd
ee98da6906f83b423022f9833ceac986 *man/root_at_node.Rd
cc5ec02839af4855b803c41371c4c5f6 *man/root_via_outgroup.Rd
8718d7438cf927ff1eb67334730d8969 *man/simulate_bm_model.Rd
cf481d0a3525273c4c411c7b74e827d8 *man/simulate_diversification_model.Rd
b833b9d41f8b480257e8d6ba5c7d9aab *man/simulate_mk_model.Rd
066570e339d8fc93284ea16b9d630bc1 *man/simulate_ou_model.Rd
2bbf6a07c19063755e483f17632ed16c *man/simulate_rou_model.Rd
6eedd51c294e066c88a6e5e567a633bd *man/trim_tree_at_height.Rd
d9c5082b996e3a3af197e028cddac0e1 *man/write_tree.Rd
3add2b8f6122b0dc501b27f3a7d709cd *src/RcppExports.cpp
cd65820e799cc0c84335cd2b483e4e7e *src/phylogenetics_cpp_routines.cpp
7c22b1b500cab25872924e218f1645f5 *src/registerDynamicSymbol.c
