ee27236765112bcb0c5a5d6d99ec4e1b *DESCRIPTION
a201c3bc9d391c994e8e288571ed6f2e *NAMESPACE
c943ff74a91b3a0ee24efe28dfc1684c *R/RcppExports.R
9a05b6f5fca5551459d999dc373bcacd *R/asr_empirical_probabilities.R
989b7786c5d618f4b4a278f60d277a71 *R/asr_independent_contrasts.R
5766739cbd484fff29a9e045252df4d8 *R/asr_max_parsimony.R
bf08bc01a160399c62c67d224ce49be6 *R/asr_mk_model.R
085126368e9a7434358a27646b8765a6 *R/asr_squared_change_parsimony.R
f6a1c71281b5713a4f8fe75745bbc76f *R/asr_subtree_averaging.R
992f71f4a5884df4e03de612a5ce69b8 *R/auxiliary_routines.R
ff6fded655000d2783244d6e2a0a09d5 *R/collapse_monofurcations.R
4dae7a5f9527b720f6aebec3e9e6cbf9 *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
e34742c851561fef3cb7b8938a677dc7 *R/date_tree_pl.R
d81ceeaec9a422307f401035a640debb *R/date_tree_red.R
5ca0e410c6967b748b8e0346666f9180 *R/exponentiate_matrix.R
3f734a938a3b46655dc1f4023876786e *R/extend_tree_to_height.R
89d51219463fd09b482247a91a11e316 *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
b665f4d0c723ab385c9bdd7ec8a0910e *R/fit_bm_model.R
8cfaa5a865389fbe8e8b403426467fe5 *R/fit_hbd_model_on_grid.R
a5f92b2ed81aa6fd3b4f0cd368c333e1 *R/fit_hbd_model_parametric.R
738b65daaeb66d5719e2ace3a4819e63 *R/fit_hbd_pdr_on_grid.R
bf7a22770705a13f55765595e7293060 *R/fit_hbd_pdr_parametric.R
8800b0e2632072c507a83dd2e5b19743 *R/fit_hbd_psr_on_grid.R
460549878b1d909a90f0e2eab6f75f31 *R/fit_musse.R
9202e805983da5833adc0d98f31367cf *R/fit_tree_model.R
e456b045eb2d76b45185ab98a120ffc4 *R/generate_gene_tree_msc.R
a1c8fe0076e80b6b1ed1cbbd7f898152 *R/generate_gene_tree_msc_hgt_dl.R
b846dcce6f2f3303fc0ee58eba09a63f *R/generate_random_tree.R
bb983bd9bf8afe3b6a266fcfed911e77 *R/generate_tree_hbd_reverse.R
75835cc961fb7789edc82cb62958e433 *R/generate_tree_with_evolving_rates.R
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
99218f67b88da59072522759d285d41c *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
4651cac19d8d910a9ad23963218a03cd *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
036544245befd90a69add4609491d2f8 *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
cd814daf121eb4407b0a831aadcc1f43 *R/hsp_max_parsimony.R
b3ea88cda823f496fe279812372abbce *R/hsp_mk_model.R
45828ded3c658ae6eae8959ed66ea542 *R/hsp_squared_change_parsimony.R
e15f8a274effe331434b51672d14de43 *R/hsp_subtree_averaging.R
27e8f0013e26c11ea335fe3573f48183 *R/is_monophyletic.R
04d1c8dddc3f419a7f557712f894097a *R/loglikelihood_hbd.R
b3effc09d0c3d17cc1d607197ba3282b *R/map_to_state_space.R
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
aa00b0d61a1d073a0d43fe8048874af0 *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
fc267ed11b0805a8b38ed083a9fe295a *R/simulate_deterministic_hbd.R
1834aa21281005649c81784a1edbaf7b *R/simulate_deterministic_hbd_msc.R
f4a0c1de8e67d35f3698a571dadc2805 *R/simulate_diversification_model.R
62ad96148d9f294de5b009d5f3dd058a *R/simulate_dsse.R
db223ac6c2ad93e431e07fdb83085223 *R/simulate_mk_model.R
d9382a5f7b6032a867eff406ed46754d *R/simulate_musse.R
896e3fcd5d6b4fd93094c7b6c2a9d9d6 *R/simulate_neutral_gene_evolution.R
473739c07568c4f017bf5580a687f534 *R/simulate_ou_model.R
91db8e678d574ffcb3e8e91108040d42 *R/simulate_rou_model.R
30c5fd4a5049cfccd0a7fc522fd88234 *R/split_tree_at_height.R
c6a348ff2c4e7d860fd69bf8ad683013 *R/tree_distance.R
8310d15bd0d98f4b35cb0cdf9893b2bf *R/tree_from_branching_ages.R
331e10dac76dd98c139c48f31b02b58e *R/trim_tree_at_height.R
b575b0d6f0e09a0ffab38403b4674c56 *R/write_tree.R
5ec58112eb169070e83d64cc1ca29b75 *inst/CITATION
48927d199ef125faf6e8c34cebaa980d *man/asr_empirical_probabilities.Rd
1be0b3893c94dc4c44f615c1358fe2bd *man/asr_independent_contrasts.Rd
bf190b498cc59cc4a655a21a617145ce *man/asr_max_parsimony.Rd
39d1078976a605a8875631cef3148a1d *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
af83e02d3db1ee6f9864d26dd57f7b8e *man/collapse_tree_at_resolution.Rd
ad0ac37de87e3623bca06e787cb618b8 *man/congruent_divergence_times.Rd
7c7ac6fbfc631fac539edcb5ba88a98c *man/count_lineages_through_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
6a50c9a60123e2fa4dfd817246452dab *man/extract_fasttree_constraints.Rd
1f8f19a1dbf406b0c66c10709bbae720 *man/find_farthest_tips.Rd
143bd53b4e1f419166e3c4efb24270e6 *man/find_nearest_tips.Rd
474164c84fb3892a906b791c416915dc *man/find_root.Rd
e5b3c517b235b600c18a27ef3ce044a3 *man/find_root_of_monophyletic_tips.Rd
98a238ff1ab994fd086a264640f0e121 *man/fit_bm_model.Rd
f33a5b3c6006405c2cb9ee0ee2c751cf *man/fit_hbd_model_on_grid.Rd
8693945dcee2335739490aa2e2fa2911 *man/fit_hbd_model_parametric.Rd
fa236fc440586200f5322b1306f83f82 *man/fit_hbd_pdr_on_grid.Rd
2940d6c1023f3d160e19fe07660f61da *man/fit_hbd_pdr_parametric.Rd
f3ccada5311f8ad943a5683c3f064d8d *man/fit_hbd_psr_on_grid.Rd
1b1fb57847dfb1a074469552f7df503b *man/fit_musse.Rd
d507c3041b9a70549c138aa0335dc5d4 *man/fit_tree_model.Rd
1b50a86cf79d1c6e7436644fbf16f443 *man/generate_gene_tree_msc.Rd
d26f75bcf59e5ca85c37d86186fff3a5 *man/generate_gene_tree_msc_hgt_dl.Rd
99eea713be1c992effd119da59fab068 *man/generate_random_tree.Rd
55b39f238899d98ed643dc71e1e4ca12 *man/generate_tree_hbd_reverse.Rd
ad86ddc60abbe42593c29f428aadd0d6 *man/generate_tree_with_evolving_rates.Rd
ae641e9d95c4a9a5600612d4359c09a6 *man/get_all_distances_to_root.Rd
6733a06c7d305c81b873580f0ad87812 *man/get_all_node_depths.Rd
c447f143f6e8efb3e2ccd4e81ea4fde8 *man/get_all_pairwise_distances.Rd
0ed6b6a9cfe603b8940793b30f5f33cb *man/get_clade_list.Rd
2cc9249608897c797081ddf2f8fa0721 *man/get_independent_contrasts.Rd
f9de754a3aa973f0f0c741d1d05a14d5 *man/get_mrca_of_set.Rd
58f810baee2f2f71d525ce2a03402c48 *man/get_pairwise_distances.Rd
445f8cb25aea57ce373e5ae656cc3c9c *man/get_pairwise_mrcas.Rd
babcc004d68152620e747b60732bd313 *man/get_random_diffusivity_matrix.Rd
1cbfd710b81b41140df8079bbe2b6c79 *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
34b9788f256e552c288515caa59f57f5 *man/get_transition_index_matrix.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
6333b1c992de9de180e93fb3d3bf145a *man/hsp_mk_model.Rd
0bd3ea01719e68eab5bc8b11ee5d06f7 *man/hsp_squared_change_parsimony.Rd
176cad8089d2dcbec43280c7d8b0591c *man/hsp_subtree_averaging.Rd
b9b079dda8b8a4242e34056581d5afbb *man/is_monophyletic.Rd
c5006277970c44167210619cf1be49c9 *man/loglikelihood_hbd.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
27e035cc9d3e3b1487ea5beba53848d6 *man/read_tree.Rd
962f27bb57367af18240d423ff161e36 *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
6e7967df83241e1f171b7d53f434a29b *man/simulate_bm_model.Rd
67da55a708abce92c05a4c201972567d *man/simulate_deterministic_hbd.Rd
4ee11a93fd9a06f909937759230955fd *man/simulate_diversification_model.Rd
bb49ed9352d79029856909af61622b90 *man/simulate_dsse.Rd
06efb099b73c51cfadf5f1ccfe86e021 *man/simulate_mk_model.Rd
8b9b9f3ae48f185056fd5aca983bc2b2 *man/simulate_ou_model.Rd
f91402ab1276c191222a9ca07ca725ce *man/simulate_rou_model.Rd
816fad55a79289820d2e97a595700dae *man/split_tree_at_height.Rd
c10add43e978486a3e629de4e3c7164e *man/tree_distance.Rd
b47b403c5f1815c2cd0dc5601636af09 *man/tree_from_branching_ages.Rd
6287a9db246b805a5ed2ea5f564abc2b *man/trim_tree_at_height.Rd
2d6d4490a937045e02b449eb19aac446 *man/write_tree.Rd
e70b97a3cf3972d9524547883d7a5143 *src/RcppExports.cpp
ded6e0dbe4b70b23ef196b149be98a7b *src/phylogenetics_cpp_routines.cpp
7c22b1b500cab25872924e218f1645f5 *src/registerDynamicSymbol.c
