42bc89ba3bc786161836c7f25b5ddd1d *DESCRIPTION
7518105060ec14bce8f83ff5deb64b07 *NAMESPACE
d1a7066ae50bbcc6080a903c35157dae *R/RcppExports.R
90e3e84e252598a58a812a040e2bfced *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
1d704a8c09940811ee32c655120dbcc5 *R/auxiliary_routines.R
ff6fded655000d2783244d6e2a0a09d5 *R/collapse_monofurcations.R
f1724ff7c1d2a520fcf423a8a4668763 *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
7b4873234c78b02e2a5a7e9708a22a01 *R/evaluate_spline.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
e36d68451a40f8d85d4781f5e2de71db *R/fit_hbd_model_on_grid.R
291300efcdcabecd443c3b856b9b004f *R/fit_hbd_model_parametric.R
d31942759ea90d6ca8365e075403229f *R/fit_hbd_pdr_and_grid.R
0af5022f19e34fc5139cfc7d98aef2a1 *R/fit_hbd_pdr_on_grid.R
2a0e4f5fa6dbcbb4ab1b04ad1f78cd18 *R/fit_hbd_pdr_parametric.R
f9d21605a3a988319deafd5d1153daba *R/fit_hbd_psr_on_grid.R
1426d215b174240d1511b0f756a27c22 *R/fit_musse.R
9202e805983da5833adc0d98f31367cf *R/fit_tree_model.R
0eed8b7b366c3f7ec5f9e3e4b7536d96 *R/gamma_statistic.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
cc6969cc3874a7ad62f840bb671e3cf2 *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
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
4651cac19d8d910a9ad23963218a03cd *R/get_subtree_with_tips.R
1299c215867f026a451fe0cd8cf82391 *R/get_subtrees_at_nodes.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
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fc0ae53019a185ef1d410ce0ff585470 *R/hsp_binomial.R
633c42a80b16cdd9718692723a8fb8ee *R/hsp_empirical_probabilities.R
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27e8f0013e26c11ea335fe3573f48183 *R/is_monophyletic.R
a827832d811ba5cf9e236b3e39316f80 *R/loglikelihood_hbd.R
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c2b6a32c402ca7c5478724c8710a82fc *R/merge_short_edges.R
9322e57d5311a475d660535093cbf5a6 *R/multifurcations_to_bifurcations.R
7bca7b3341577fcccbdc2a3a9e5b4472 *R/pick_random_tips.R
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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
175b4a100431d5312959758064c5ed0e *R/simulate_dsse.R
db223ac6c2ad93e431e07fdb83085223 *R/simulate_mk_model.R
a09f1724a2961fdcf3f2049b3259ec11 *R/simulate_musse.R
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473739c07568c4f017bf5580a687f534 *R/simulate_ou_model.R
91db8e678d574ffcb3e8e91108040d42 *R/simulate_rou_model.R
e77a42186407f6c3b45c13dff0be9a4f *R/simulate_tdsse.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
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7c7ac6fbfc631fac539edcb5ba88a98c *man/count_lineages_through_time.Rd
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1f8f19a1dbf406b0c66c10709bbae720 *man/find_farthest_tips.Rd
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8b9b9f3ae48f185056fd5aca983bc2b2 *man/simulate_ou_model.Rd
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f8e1699f613374c57cd50e353719cc09 *man/simulate_tdsse.Rd
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2d6d4490a937045e02b449eb19aac446 *man/write_tree.Rd
9724d10dfcccd6fe9b297dce89df703c *src/RcppExports.cpp
03a5d8a6232a8cd451aed767506cdac7 *src/STMathExpression.cpp
c63909f744c3da0df38702e3b4c9c767 *src/STMathExpression.h
89c279f2a99eee1f80500ebcf1e7bcdd *src/phylogenetics_cpp_routines.cpp
7c22b1b500cab25872924e218f1645f5 *src/registerDynamicSymbol.c
