c3d38b4085c4658f78e6d918015380b6 *CHANGELOG
15137cbb386deb5c6ac25efdcd052a0c *DESCRIPTION
ce972a93e562e74f8320fe45b50076b8 *NAMESPACE
f4f6293ad3a6a3ab1ac2b68b43c6e2bf *R/Claddis-package.R
cdcc61f032583283aa04f10801f0ec98 *R/add_polymorphisms_to_costmatrix.R
481e0d3256d1359173e651ad70b8360f *R/add_uncertainties_to_costmatrix.R
cf597d560e3e43114a807633cfc737bb *R/align_matrix_block.R
977c8d9fca09791de724ac05414f1c3f *R/assign_taxa_to_bins.R
70ce49bb85bda797ca29ea6d5ffb73f3 *R/bin_changes.R
b27c93ebe0de74c1188801f70f5dd9f5 *R/bin_character_completeness.R
d81670840f6e0ae74e1e6962e7d00ec4 *R/bin_edge_lengths.R
4dc9e341a7f35e995db38c8af95bccf3 *R/build_cladistic_matrix.R
e0278f6fef307049ac982629746a9998 *R/calculate_MPD.R
d7263db6b9511dd3100f74bc2262b657 *R/calculate_WMPD.R
98e969f711de21ecce6e3f3fd74c6892 *R/calculate_g.r
4f431e034c548ac6835a1c4a736baa8c *R/calculate_gmax.r
c9c737174ca3dc0e719446e54ae667e2 *R/calculate_kardashian_index.R
934dc8e26d75bc57f1d3d52f71e0766e *R/calculate_morphological_distances.R
a9f274afc9e058a0972a28eaa1bfe1b7 *R/calculate_tree_length.r
4c097dce18a1f51f0fdbb09a823f1191 *R/check_cladisticMatrix.R
f0fd5836c568d3de7f9e406ce853809d *R/check_costMatrix.R
7352376a5614aa668333f5010e4c8b25 *R/check_stateGraph.R
e81aa680a5d7e5b903bf70982531ec30 *R/check_taxonGroups.R
c6a68eb5810b0a74fe7ede8c3af23019 *R/check_timeBins.R
837988b6ed7263208e784530781da047 *R/classify_costmatrix.R
c7cb460bd17585c72893be99442d60fe *R/compactify_cladistic_matrix.R
fda458639bd9749d3b40b84ab0e3ec8a *R/convert_adjacency_matrix_to_costmatrix.r
8404081c43f2924590aa2edd7d26b627 *R/convert_costmatrix_to_stategraph.r
cdd7d4bf34bd53c9794a7e3c8a985e11 *R/convert_state_tree_to_adjacency_matrix.r
7a319b0215baafaa4206be72a9cacd9d *R/convert_stategraph_to_costmatrix.r
a2dfcacdda14c0e19b64f96fbc32ad22 *R/count_cherries.R
aa85fd2454761c0ccce2b97071a9d2d6 *R/date_nodes.R
fc8e282a2dbe684c5326924af7d4cc5e *R/drop_time_tip.R
e2131b41dfeb94bcce8aed6770996195 *R/estimate_ancestral_states.R
17fba49bd864ad0a1b15405f3735a538 *R/estimate_squared_change_ancestors.r
1292cb45a41ab0b4fb773ff36eb48691 *R/find_costmatrix_minimum_span.r
4587b0c6e2665384d8e2cd621fcea3f4 *R/find_descendant_edges.R
b974394fd2a9bd54c63b4dfb002e5125 *R/find_linked_edges.R
0c0482e74dcf290bc1eb5d23d0058816 *R/find_minimum_spanning_edges.R
ee2229d7abf12a11b68159b4b29cb42d *R/find_mrca.R
2d361803e1cb9fee98b63ae9a1495f5f *R/find_shortest_costmatrix_path.r
24aeaf3ab8110107bb0fdf036b7db9f6 *R/find_stategraph_minimum_span.r
50393f2762a3935446892a4dabe62f3e *R/find_time_bin_midpoints.R
cee127a139915b7072f27592acd6af04 *R/find_unique_trees.r
5d470ba3a44d00055ed15007974f8dfd *R/fix_costmatrix.R
75e69392181edb8ad710723497b9dc23 *R/fix_root_time.R
1ad2c7b5f787e559b56908b928298607 *R/is.cladisticMatrix.R
c0af3e58550c5727ce2f60cfb42a739e *R/is.costMatrix.R
5334c9e47f1df2bf4459495387c93d4a *R/is.stateGraph.R
7f76f9b09f8ec508cf911a5686db3d41 *R/is.taxonGroups.R
5fd52aa69a77252e86100962dbca6652 *R/is.timeBins.R
24d0ba8d0b68b3679ae53545ed7dc5ec *R/is_graph_connected.R
7901ee2999dac0178abc118d2b69d412 *R/locate_bracket_positions.r
623fde43680d5d71cab2be937eea4441 *R/make_costmatrix.r
da8babf6c4ba71691e8c400c03765c4f *R/make_labels.r
f1ac45a637417ca5ff5c36882f7e1b03 *R/map_dollo_changes.R
394202c3337514758808424f9cb3d4d7 *R/match_tree_edges.R
20a71dab883bf57f30b195259ef6e28a *R/ordinate_cladistic_matrix.R
1505a0e883943b0539400aae94161e00 *R/partition_time_bins.R
944c01d6bbf0af8b05c8a1b62238f185 *R/permute_all_polymorphisms.r
303339c19850c6da776f905503876023 *R/permute_all_treeshape_labellings.r
afcf9b54b20532b5a2ce6e41ac4b90f5 *R/permute_all_uncertainties.r
fb2dd9dff9e475597af5e8132610df24 *R/permute_connected_graphs.r
7e30e667b2c12e6652677274331ed7d5 *R/permute_costmatrices.r
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9458191d62845e974b2a9ec7a748d66b *R/permute_tipstates.r
53d295589f8a2707e0063e6231239af1 *R/permute_treeshapes.r
0ce65bd7383c27c1be4cbce30e8b8346 *R/plot_changes_on_tree.R
c52d65ac8dcb43b6a1396499dc1c8079 *R/plot_chronophylomorphospace.R
97047125f1a89d379f5974fe44f0a1b9 *R/plot_morphospace.R
88d718d2e008bc223adfcb7b657c722b *R/plot_morphospace_stack.R
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9ce2490ef25ada4bbca8d76f88ac4aba *R/plot_rates_time.R
b5f9ff2066b0656fc47fbb53d0a5ffa0 *R/plot_rates_tree.R
80268b3511cc1cc7ff771dc9f2515d0f *R/print.cladisticMatrix.r
160db68b634ba79151f078332805b826 *R/print.costMatrix.r
0917cd04361a66cbe601c976c415bd5a *R/print.stateGraph.r
8e53731b24e7bd3a6f1963505bd30df1 *R/print.taxonGroups.r
37f6b539dc6620a935347ca84a388498 *R/print.timeBins.r
70d84f280879b8143b094cd8248f2532 *R/prune_cladistic_matrix.R
1adf618e5bcd4af30b3029c69c61ef7d *R/read_nexus_matrix.R
fb02d28e81147c72e2fd43c7bb6c3c2f *R/reconstruct_ancestral_states.r
a8ed6bb441b7d0e2b0f3a08101f3d0ff *R/safe_taxonomic_reduction.R
e6df0206b130a4dca1cc404a32c02586 *R/safe_taxonomic_reinsertion.R
71e22fec6bfa13de2d658e7d71851de2 *R/split_out_subgraphs.R
7c3b787843a484c73107698cc878427d *R/test_rates.R
eeb17be4fe6852fec59487c39f5854c0 *R/trim_marginal_whitespace.r
a043c8118a3e93475b44eca501a41360 *R/trim_matrix.R
9c65afebe2f429b1533d5af3ca13c490 *R/write_nexus_matrix.R
29874a366dcca5ee033acf73d5ee7fa5 *R/write_tnt_matrix.R
ee80e0fdcef40c219496771f776b3cc5 *README.md
aa5e5a2cbfaea3d9b6cdbe378ac48cee *build/partial.rdb
f3a9c3374199d799689de4e89a4cb758 *data/day_2016.RData
415e1006c52c7e11214561624ec8f776 *data/gauthier_1986.RData
aad07fd1c5027a7d01ee57afe378bc36 *data/michaux_1989.RData
03f876ac575a40b52d00dfe2339af03b *inst/CITATION
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0ebe072fe1aee71f108e0db146ebb045 *man/assign_taxa_to_bins.Rd
a39c4d2ee521f6b41e1c45443db0d58f *man/bin_changes.Rd
f53f39631c022fa5752bb4ecb6549de7 *man/bin_character_completeness.Rd
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4b10c70a396a2a59e6374239e373a853 *man/calculate_MPD.Rd
fba2b427ce0512178a6bf6dbfe7e91e1 *man/calculate_WMPD.Rd
1e358561aa177253e9a03371b166746e *man/calculate_g.Rd
c25db25119a78406c37c918c1cfc8fe8 *man/calculate_gmax.Rd
1dfe26c393c8202468d992b8b1412be4 *man/calculate_kardashian_index.Rd
ba96c3c69b490cb456282c07178293fb *man/calculate_morphological_distances.Rd
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4ba544ee14b8f79a255cf60c77899604 *man/check_cladisticMatrix.Rd
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43099443a4da5b41fec8d266b7d549d7 *man/find_descendant_edges.Rd
932c6bde9f88911c87848f51b0bc0f02 *man/find_linked_edges.Rd
9ac7d6ad276146084128fe86daa10dae *man/find_minimum_spanning_edges.Rd
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36aa38a91c16338440e95b0d831200f9 *man/find_shortest_costmatrix_path.Rd
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64542363c489fe578a67fdad429bcb3e *man/fix_root_time.Rd
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8677b1f074bcc10472ae51575176ae09 *man/is.cladisticMatrix.Rd
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2b253c0e20628beb28f1461a7f8caa67 *man/read_nexus_matrix.Rd
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44af30cb3df1db0ca461a37625779145 *man/safe_taxonomic_reduction.Rd
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175940194c365173eafc47a7fa10e1f1 *man/write_tnt_matrix.Rd
d8c8d4e339fc863e4ad57a0b57fc2b06 *tests/testthat/test_bin_changes.R
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2b79be20a8941077c1cc0af4840fcc89 *tests/testthat/test_find_mrca.R
