48f6ebb427bc2a5766f7a300b4534866 *DESCRIPTION
e281db6a52e221631088286747041591 *NAMESPACE
647f6b45b3d4b7d607b460fd4f60e0a4 *R/RcppExports.R
9a05b6f5fca5551459d999dc373bcacd *R/asr_empirical_probabilities.R
989b7786c5d618f4b4a278f60d277a71 *R/asr_independent_contrasts.R
8258435833fb0b2668b543b77c05a57e *R/asr_max_parsimony.R
54e59ca517f2f2bf91ec69b6084aa115 *R/asr_mk_model.R
085126368e9a7434358a27646b8765a6 *R/asr_squared_change_parsimony.R
f6a1c71281b5713a4f8fe75745bbc76f *R/asr_subtree_averaging.R
1582085403d2a11ecea6907fee738265 *R/auxiliary_routines.R
cb3a37fa03ea67ca6ace9d5859ef2645 *R/collapse_monofurcations.R
1813566e909da4774c9c61269a45a7fe *R/collapse_tree_at_resolution.R
bfe0fd12c907c06da622ed4fd7717a7e *R/congruent_divergence_times.R
aff21682f662bb9b4330af47703b6531 *R/count_clades_over_time.R
d736e8020a5799df6ce10fb5d6b3baae *R/count_tips_per_node.R
e34742c851561fef3cb7b8938a677dc7 *R/date_tree_pl.R
d81ceeaec9a422307f401035a640debb *R/date_tree_red.R
5ca0e410c6967b748b8e0346666f9180 *R/exponentiate_matrix.R
3f734a938a3b46655dc1f4023876786e *R/extend_tree_to_height.R
ade362b781a86e552fd2660103662dba *R/find_farthest_tips.R
282db5ffca1fde87785a7864d03e14c4 *R/find_nearest_tips.R
5e8a110182785dc41dcc0ac88f009ea0 *R/find_root.R
1ea97c12588e374ad6949df8e6c799d7 *R/find_root_of_monophyletic_tips.R
b665f4d0c723ab385c9bdd7ec8a0910e *R/fit_bm_model.R
4a1143f6901ea7536b39eef4bbda8e35 *R/fit_tree_model.R
67628d179a1792bc14fc195b792a55f9 *R/generate_random_tree.R
732c1aed06651e4ba377400ee92e590e *R/generate_tree_with_evolving_rates.R
28af55d0af57073595d3665f34e2d902 *R/get_all_distances_to_root.R
eb43f6c79321859ad6939b68ac12247c *R/get_all_node_depths.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
99218f67b88da59072522759d285d41c *R/get_random_mk_transition_matrix.R
3c16cad1b44e27ddd90804980a8137e6 *R/get_reds.R
f9de590cb60abf56cc29c154fccd9e85 *R/get_stationary_distribution.R
e7e0e8941aff2db2e10b6fed1a614c0a *R/get_subtree_at_node.R
15740d640257f2e35970281db98d6665 *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
d48bb3a6c7c50d6887c96a6a2b2602fb *R/hsp_empirical_probabilities.R
145eb14cf9b3dbd2b2c8934599304a14 *R/hsp_independent_contrasts.R
abce483f7fc45a136b675bd8efdffdf3 *R/hsp_max_parsimony.R
d2c7b5a74ce3c0354fab2321a73dec77 *R/hsp_mk_model.R
45828ded3c658ae6eae8959ed66ea542 *R/hsp_squared_change_parsimony.R
e15f8a274effe331434b51672d14de43 *R/hsp_subtree_averaging.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
7bca7b3341577fcccbdc2a3a9e5b4472 *R/pick_random_tips.R
ac4c08634508d4ed39b179af4a3715ba *R/read_tree.R
52173befbd946e1ecfafbb30abd0dc91 *R/reconstruct_past_diversification.R
99658e44e24f36812b905179f039d394 *R/reorder_tree_edges.R
0cc1271a7e9866d129fd7eafbb64df2f *R/root_at_midpoint.R
c826f8633301bd734ab8b4a9c836cef3 *R/root_at_node.R
460faaea40c0102f0dba39c677ee8734 *R/root_in_edge.R
a11ac7f05813f609e3d44deabc943baf *R/root_via_outgroup.R
0e1651281fc770cadfac3cfd557ef3cd *R/simulate_bm_model.R
84d0ab1609f196db0168f4a0d4068fca *R/simulate_diversification_model.R
db223ac6c2ad93e431e07fdb83085223 *R/simulate_mk_model.R
896e3fcd5d6b4fd93094c7b6c2a9d9d6 *R/simulate_neutral_gene_evolution.R
473739c07568c4f017bf5580a687f534 *R/simulate_ou_model.R
91db8e678d574ffcb3e8e91108040d42 *R/simulate_rou_model.R
c6a348ff2c4e7d860fd69bf8ad683013 *R/tree_distance.R
9ed667a5699194418f6aba50bd800f04 *R/trim_tree_at_height.R
c34d3c1dc4c0e949f06523ec3e8e918d *R/write_tree.R
5ec58112eb169070e83d64cc1ca29b75 *inst/CITATION
48927d199ef125faf6e8c34cebaa980d *man/asr_empirical_probabilities.Rd
1be0b3893c94dc4c44f615c1358fe2bd *man/asr_independent_contrasts.Rd
83631623a40714d58583ff562147cb91 *man/asr_max_parsimony.Rd
d5e411e6fb43901be96fcbda36803d61 *man/asr_mk_model.Rd
0f9d7d08aa0cd9caf75f700e7bdb69f1 *man/asr_squared_change_parsimony.Rd
176efc5d7871a86f6b3876703f0dcfd1 *man/asr_subtree_averaging.Rd
832d03b6d939a1cd46ef0e863fc5b297 *man/castor.Rd
24217936ec8ffb4627140552e02482ef *man/collapse_monofurcations.Rd
fc6a6634ebb8f3bbd7bf24d39606b650 *man/collapse_tree_at_resolution.Rd
ad0ac37de87e3623bca06e787cb618b8 *man/congruent_divergence_times.Rd
16f8e42e478fdc1dd5f3992966b6f46e *man/count_clades_over_time.Rd
55fc8df376f6820c4e892b418f63ad14 *man/count_tips_per_node.Rd
c5532d830fd70affe122a72814190a94 *man/date_tree_red.Rd
164411f08b5adabfdc2d15d87285fe55 *man/exponentiate_matrix.Rd
58d9586b71bea77c7e0122b13dd5dd49 *man/extend_tree_to_height.Rd
0a08e7af1be43d681b2e893631740769 *man/find_farthest_tips.Rd
2bf2db3bb8e5664b6ba13e952a579d43 *man/find_nearest_tips.Rd
474164c84fb3892a906b791c416915dc *man/find_root.Rd
e5b3c517b235b600c18a27ef3ce044a3 *man/find_root_of_monophyletic_tips.Rd
11807535e742affea945503fa161e3a0 *man/fit_bm_model.Rd
a3be0f0027947f602aa2f97db09d94f9 *man/fit_tree_model.Rd
ddfdb979cf156f6ac2c3c7c51508b41a *man/generate_random_tree.Rd
51c60decaa3f46989f5bd9fd22ff6bea *man/generate_tree_with_evolving_rates.Rd
ae641e9d95c4a9a5600612d4359c09a6 *man/get_all_distances_to_root.Rd
6733a06c7d305c81b873580f0ad87812 *man/get_all_node_depths.Rd
2cc9249608897c797081ddf2f8fa0721 *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
f28fb2a5194c5a684834370fc275870a *man/get_reds.Rd
ed439b4a11de01cb319be81f1b60d176 *man/get_stationary_distribution.Rd
3423e6b79ba3323f47dd660235b02c1e *man/get_subtree_at_node.Rd
ee56e69e8771934a6b3c4b0ee512c1d5 *man/get_subtree_with_tips.Rd
734f0758ba84ad13a2a2a9dc449dfdfd *man/get_tips_for_mrcas.Rd
40efc84abefe6b561f9dad8249ae07d2 *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
f91a9eb06bf340ea8521a1394baa3b01 *man/hsp_empirical_probabilities.Rd
a702695e01a65b118c63a78174dab873 *man/hsp_independent_contrasts.Rd
d359ef02ad84d465ed2cc39c1d64a678 *man/hsp_max_parsimony.Rd
333e03985e12ff60b296074904dc8e6b *man/hsp_mk_model.Rd
0bd3ea01719e68eab5bc8b11ee5d06f7 *man/hsp_squared_change_parsimony.Rd
176cad8089d2dcbec43280c7d8b0591c *man/hsp_subtree_averaging.Rd
b9b079dda8b8a4242e34056581d5afbb *man/is_monophyletic.Rd
9af14b79f52f18c84edec02ab0387d72 *man/map_to_state_space.Rd
f23b87dce36ac420b37c9eb913974a04 *man/merge_short_edges.Rd
272fc97c1aa0226120b0f1712a8d2ddd *man/multifurcations_to_bifurcations.Rd
cce605ef7ec59ba910a8b49f31c9fdda *man/pick_random_tips.Rd
7993de6191f2a702e851d85bed367959 *man/read_tree.Rd
358ee3881668bcee5cc1865400191c68 *man/reconstruct_past_diversification.Rd
c49b4a0bd43481c3e341f42ea48492d6 *man/reorder_tree_edges.Rd
f07d3a38b1781ba7615b1b8eec7ae9df *man/root_at_midpoint.Rd
ec7bfbe0d0515e62b7552d3868b7c500 *man/root_at_node.Rd
7223643ce5c3b9a4ec4563c23b9ccc78 *man/root_in_edge.Rd
15d6da71a09fe60f14505b63fb2159a3 *man/root_via_outgroup.Rd
8718d7438cf927ff1eb67334730d8969 *man/simulate_bm_model.Rd
c11b1fdb5d17ed7c9008fcd74ac2bcf2 *man/simulate_diversification_model.Rd
b833b9d41f8b480257e8d6ba5c7d9aab *man/simulate_mk_model.Rd
066570e339d8fc93284ea16b9d630bc1 *man/simulate_ou_model.Rd
2bbf6a07c19063755e483f17632ed16c *man/simulate_rou_model.Rd
c10add43e978486a3e629de4e3c7164e *man/tree_distance.Rd
86e2a12383bf2a7e29593fc9e1f033c7 *man/trim_tree_at_height.Rd
0b756907845e2b72ed893cf16073be19 *man/write_tree.Rd
fe17081825f0c0739a9206cf24a8e00a *src/RcppExports.cpp
0af7e0f28b3b4692ef21b9fd4d6e3b5c *src/phylogenetics_cpp_routines.cpp
7c22b1b500cab25872924e218f1645f5 *src/registerDynamicSymbol.c
