c3e41ff05d626d0225de91c872640c42 *DESCRIPTION
e8c1458438ead3c34974bc0be3a03ed6 *LICENSE
95370787c3a210a43be56a27aec2d323 *NAMESPACE
cc76b4b50169860ca89d79ec252c11d5 *NEWS.md
216bb308cebf519018d89ef8337dcd1f *R/E_step.R
eb44977f9f195e6c1bacdebc5cf348ba *R/M_step.R
d4c8e63463f2abcb8dc8c66738870333 *R/RcppExports.R
26a86c9c2f751de34ec82646493124be *R/data.R
202dc84cb42c74c3dd1425bf29cbd7fd *R/estimateEM.R
0d5ce39746d41989f9b3aa4d55ab61cd *R/generic_functions.R
08d39adfeb53bf7fd8aaca9f44ebeec9 *R/init_EM.R
569bed33c20883c956fe67d1b38d9760 *R/model_selection.R
09692a1d8d7e0be05f2ee44dce7c59c1 *R/parsimonyNumber.R
5e50883574235a3186d5d34392515f53 *R/partitionsNumber.R
aa905e9fb0d46dc19acf230c32c36ea2 *R/plot_functions.R
7c5732678798d204a07fe307f20a61ae *R/shifts_manipulations.R
d403da302e77a05fddf1bb5ef1c2185a *R/shutoff.R
b5db4034c59752dbde71a2353607a96b *R/simulate.R
4b87e7faa63ec0b488470791fc1c1f90 *build/vignette.rds
5c66fe8f813e13ce24f0e7da420d882d *data/monkeys.rda
0f3c2dd9ecf85298dc5406ed0b234b73 *inst/CITATION
623d9fc12d66116505288a7d72dca6ca *inst/WORDLIST
358edcca37bef876c1c2da05a5764f30 *inst/doc/monkeys.R
2847b58e0b3e4466aabc22aa7bfc26e1 *inst/doc/monkeys.Rmd
871611d584373949dc244a302eec76ac *inst/doc/monkeys.html
054b50699db19148e795e8c03af018ae *inst/doc/tutorial.R
c51d8de6126e5e1bee4697cc1523a014 *inst/doc/tutorial.Rmd
eac163de5ee69a0986cbab37d9dcf6ef *inst/doc/tutorial.html
a7d8c63964797db7eab8cd9cc0fb3bf7 *man/PhyloEM.Rd
5091bb49622e86d7162b4ba76b963150 *man/add_complementary.Rd
b86e7e918ed324665750c999d74b88bf *man/allocate_regimes_from_shifts.Rd
8f9e69baf1d184a7c803ef856191aa26 *man/allocate_shifts_from_regimes.Rd
f88624b0f6a90f66a0c0e22f2a26a60a *man/allocate_subset_node.simulate.Rd
4a19d5a3e2bff7332c6fa136e2c27ec9 *man/check.selection.strength.Rd
12e08258896019513b21333df5cb4f87 *man/check_data.Rd
93ed463f641c634a2a7ded63fd59c043 *man/check_dimensions.Rd
1af0bcbb18fb24ba17037c0dfb1a7511 *man/check_parsimony.Rd
791775525e0a28e80a26f39544c180b0 *man/check_parsimony_clusters.Rd
38fdc54517faea4b2840e5dab3e9ecdd *man/check_range_alpha.Rd
2185352ba7b1994382fd12ad525ea005 *man/clusters_from_shifts.Rd
53a75a71ef0bafc8123c2fded32b030c *man/compute_E.simple.Rd
016502612588bd92cbbb7bee24bdf10d *man/compute_actualization_matrix_ultrametric.Rd
e1e1f11e732ab4397b869875c14ab5f9 *man/compute_betas_from_shifts.Rd
391f3060e57cd7287dadacd4b31dd2a1 *man/compute_diff_exp.BM.Rd
a0e466528b2e8578cf14a35e9315015f *man/compute_dist_phy.Rd
c468ffb02fc1897b5fcc1f803d2b73f2 *man/compute_expectations.BM.Rd
e1222880136942a06756ed0d659f0391 *man/compute_expectations.scOU.Rd
15556ade833cb4953997d0953bc17594 *man/compute_fixed_moments.Rd
28d66c19f5bb99e94c50d612578443e0 *man/compute_gauss_lasso.Rd
9af7b75663165699e3623758e9d1f804 *man/compute_log_likelihood.simple.Rd
bfab2247674c57a76b6e3382975c171c *man/compute_mahalanobis_distance.simple.Rd
402fcec26f70ccef56261eb4fd69e847 *man/compute_mean_variance.simple.Rd
ab79d9d74b7c6605221e8d59c46330f7 *man/compute_residuals.simple.Rd
438f46de62e927a36966d3302cc4c6b1 *man/compute_shifts_from_betas.Rd
918d97cf2261c239d100f81d30f1168c *man/compute_state_filter.Rd
2cf8b921e77ea65dfe6b7f5770c6c9bf *man/compute_stationary_variance.Rd
7c86ac8d3231b2a498138fd4dd738a43 *man/compute_sum_var_diff.Rd
1cc8149f88ea2fd67ea9a1bc20977508 *man/compute_times_ca.Rd
1775ec15b21da3caaa5a4bc5edc9fc79 *man/compute_tree_correlations_matrix.BM.Rd
d94acb214366b9f2c3184756db222a76 *man/compute_tree_correlations_matrix.scOU.Rd
32da1cd62de9d41934d04212117f1d2c *man/compute_var_M.BM.Rd
e9a7fbf04cf47f909efd0445923fefcb *man/compute_var_diff.BM.Rd
d8ba82f121a39209db152d189d2f8f28 *man/compute_variance_block_diagonal.BM.Rd
77d286e8f2df959da2688b759e31cf6a *man/compute_variance_block_diagonal.OU.Rd
3f68b0e03ab381bf22967d0bdb26ca71 *man/compute_variance_covariance.BM.Rd
26804da62bb1a36785d3d6c8fcab6bd9 *man/compute_variance_covariance.OU.Rd
27770cee3e872cc8abfa38462169d85d *man/compute_variance_covariance.OU.nonsym.Rd
9f5ef7fa58b71daa523e4c4361fc2747 *man/compute_variance_covariance.scOU.Rd
3ef52303964c8f6bc2b8abb688cf6b39 *man/correspondenceEdges.Rd
8d9a8d55e959a2eeb4761402cc0515e0 *man/enlight.Rd
9eaac144bb61973a356829391bcdd35b *man/enumerate_parsimony.Rd
ea93ffa26957a258eecf7691ee5c5cb5 *man/enumerate_tips_under_edges.Rd
84698ddd6782a6b66c629c98a934f95c *man/equivalent_shifts.Rd
068dae73324683ea93b625836d7bd841 *man/equivalent_shifts_edges.Rd
2b1496107a4e12fc5df5e88d68f8fe0f *man/equivalent_shifts_values.Rd
faa1fdd71399ba87c85ca4a584acf87b *man/estimate.alpha.Rd
7163ce210463473b91c7f8b359acb4fd *man/estimateEM.Rd
a77738880c9a6b04fc05d3f6bce11f13 *man/extract.Rd
8d3f87ecd6a4f075d4ef79bf074783ea *man/extract.enumerate_parsimony.Rd
0741106c33754875e44aed51b28dc9fc *man/extract.equivalent_shifts.Rd
dbf8a81837676fee09ea0f4d0e64f441 *man/extract.parsimonyCost.Rd
017bfae927a86a5232bc1072a912a5e1 *man/extract.parsimonyNumber.Rd
bd745f7a9172a40d037b81b3d7412132 *man/extract.partitionsNumber.Rd
6395c8f3b881e76a832cfe79cfaa01cb *man/extract.simul_process.Rd
fad879eb90d7eaffe014c075f0e8cd96 *man/extract.variance_covariance.Rd
bb532aff0517cc1166bd1bed8bf78e40 *man/find_grid_alpha.Rd
4669e304f279702a24b305fb5185aaee *man/find_independent_regression_vectors.glmnet_multivariate.Rd
d7b30acbe20a8b56fb4c4531bee2f07a *man/find_rotation.Rd
11b4a2bd2a3e8ae2167408a2b2fa10d4 *man/find_shift_values.Rd
02c6ec8d709beb8d32f34f0b9848287f *man/format_output.Rd
f917c0c25e0edc2f486cd411d3d9720a *man/get_criterion.Rd
c84b6c17ebc96e24e26e83b342e65c8c *man/get_variance_node.Rd
3e66011cd08bd016c4e72cbf657bb215 *man/go_back_to_original_process.Rd
aad9ade5ae3746a1914251a48d4bc6a2 *man/imputed_traits.Rd
d4c7d58096b51564bd8ebfbfda383ef3 *man/incidence.matrix.Rd
0eb505797d91b876f1f29411b6f09a4c *man/incidence.matrix.full.Rd
cefe82b1c621ad3289ef16db85d08695 *man/incidence_matrix_actualization_factors.Rd
28e8f530616b0177212927c06a119289 *man/init.EM.lasso.Rd
d0d2c6759b9369c3b06bb6d13194bd2a *man/init.allocate_regimes_from_shifts.Rd
6119be222d03fd1aab552dc99fbfebcf *man/init.alpha.gamma.estimation.Rd
e485365f0b6eefc4a0c2cbad5061928f *man/init.compute_betas_from_shifts.Rd
373f5de3fb97a7cef2438669a43b39f9 *man/init.enumerate_parsimony.Rd
c7028aad5d83d2a564ad5736874d5e7f *man/init.incidence.matrix.Rd
68fdd209553353474ed05c746d26ef50 *man/init.incidence.matrix.full.Rd
16a794bcb0ccdb2cfe72cb439f4eadc7 *man/init.parsimonyCost.Rd
3b58d82745147be5818b7365530d24fe *man/init.parsimonyNumber.Rd
1931737f202e6f1c0ddc51ee84f04210 *man/init.simulate.BM.Rd
f7534dc02bdea30afb3ca8147b2de2bd *man/init.simulate.OU.Rd
9975c4318b3382f866cd8b8c32d032ff *man/init.simulate.StateAndExp.Rd
0bc5097407c2f8e58f4c8a258e74a54b *man/is.in.ranges.Rd
86fb6a1495c8cb67a622c423d1d81beb *man/lasso_regression_K_fixed.glmnet_multivariate.Rd
6d7233ee0bf6e3178d9c4e62450bf376 *man/log_likelihood.Rd
3a37461c2187911010ddfb7ced899c35 *man/matrix_of_possibles.Rd
5faf6c8f0d5cb0aba66f7eb47150dc8c *man/merge_complementary_vectors.Rd
842022aa72c53ba130ee0d516d322fd1 *man/merge_params_independent.Rd
ab235b0cdf34a2b04cb281c3ced26257 *man/merge_rotations.Rd
74ee73558b5b24f2696f373d31b8e3a9 *man/model_selection.Rd
3095f5d5336099b63cf399187e3f985b *man/monkeys.Rd
92b4604c0700f3791def41c9d42e6dd5 *man/params_BM.Rd
2cc96cf209c4cfee9b56ae34d57afabe *man/params_OU.Rd
6b699ac15d1978fff023b72ea340381e *man/params_process.PhyloEM.Rd
1cdd27b44cea44cdfd8669e9ce565bf1 *man/params_process.Rd
3bdebdf11cacf2474e61a1a6729365cb *man/params_process.character.Rd
aacbcd35a53cea42a16dcc3e58ff98e5 *man/parsimonyCost.Rd
7373576de0be8003246baeb571600013 *man/parsimonyNumber.Rd
8ae960bff6a864f0c6f6e3839033ce89 *man/partitionsNumber.Rd
c3d1373f068ad4b77e497d61b64e3868 *man/penalty_BaraudGiraudHuet_likelihood.Rd
b0ea18ca20a5d985aa144bf7798c7ba1 *man/penalty_BirgeMassart_shape1.Rd
090371d988b03e17a3ac7e12c9f3e096 *man/penalty_BirgeMassart_shape2.Rd
1574776eb7ebf091f72191b8cc97aa4d *man/penalty_pBIC.Rd
0b89b21cf9189b608b68aaa20a8736fd *man/plot.PhyloEM.Rd
67c8256772aa50b939749c40e634ce99 *man/plot.enumerate_parsimony.Rd
ff2f521caedfeeee9212313845d984f1 *man/plot.equivalent_shifts.Rd
2ccaf4abbac4281f996e96d1efc004b3 *man/plot.params_process.Rd
92bbec400bf6e392aa3339be238230cf *man/plot_criterion.Rd
7a0f17f09f969ce59a59e1dec0db4049 *man/prod.index.Rd
4f47b99e9d173f2f4a4c844a89cdc7ab *man/qr.solve_exact.Rd
99d220c65cf55cd0617d201bcc8e0af9 *man/recursionDown.Rd
3f8ebe642e31ac00112f698c3ee8881c *man/residuals.PhyloEM.Rd
8c9ec6410063618400606c11e18721d6 *man/sample_edges_intervals.Rd
320c29add6990ad4722215a397e31740 *man/sample_shifts_edges.Rd
baecbc4857d7707deb26c5eddbb9deed *man/scale_params.Rd
28e74737502bcf9f71a6ecd41085de48 *man/segmentation.BM.Rd
948a30d1114ca4ce855e0b1d195e1ed0 *man/segmentation.OU.specialCase.lasso.Rd
2f44567ef19a74e3aeb3649703a8a414 *man/segmentation.OU.specialCase.same_shifts.Rd
2d3a6b1a4c91c5f0e1b6d8ad4a40ae9f *man/shifts.list_to_matrix.Rd
1aa69955439180f0f2f8f11d44123bcd *man/shifts.list_to_vector.Rd
5e2ef8aaaec6cfbc4f5693ce1ba83b95 *man/shifts.matrix_to_list.Rd
88e930188087a823a9d764a5c3e2957c *man/shifts.vector_to_list.Rd
b5f5290a0f40dc382bcbf8d990280597 *man/shifts_to_simmap.Rd
4766f7399bae0aa6a210944f4f8847f4 *man/simul_process.Rd
4e6c12732e9a623c88694c4fce86c7e0 *man/simulate_internal.Rd
27196b9a536a907cdf3b96fd3d16ab4b *man/split_params_independent.Rd
c7245bed2750bd6d756553d3ac41504e *man/sum.partitions.Rd
f0020bb5c70eda56fcdf4e130b455576 *man/sum.partitions.cardFixed.Rd
31d66dd1db2c3ff5bee1750d41d805a3 *man/sum.prod.comb.Rd
7be6fc27527d7bc877a0c697c251de3a *man/sum.simplex.Rd
3e1119aaf7ae679dd9e9cf910d498a13 *man/test.root.state.Rd
8d54b16f231147e05b5f055d91d5ce2f *man/transform_branch_length.Rd
999a72ed25f5ebb4e3aa725fc1636e62 *man/transform_shifts_values.Rd
eb30103600e62f7ecbf1fe0588980245 *man/update.allocate_regimes_from_shifts.Rd
ee105441d998894d26ff77954267b996 *man/update.compute_betas_from_shifts.Rd
9cc76a9461478da9c35b3ba6c1b37076 *man/update.enumerate_parsimony.Rd
f0e12ce229451ee1f53f9b37b5c2ccfd *man/update.incidence.matrix.Rd
55be2483e1435b4c63c579067f058482 *man/update.incidence.matrix.full.Rd
db42f282e8c93bed48a28186c9f38ddc *man/update.parsimonyCost.Rd
070c30068d0c343f040ecda318cc7842 *man/update.parsimonyNumber.Rd
c53432f3b9c9dfc96576d087d5e29db2 *man/update.partitionsNumber.gen.Rd
83bd75ee73bf9b1fe8972010e7e60283 *man/wrapper_E_step.Rd
2a6f9e9e044a78154d3cfda5936d6f48 *src/Makevars
2a6f9e9e044a78154d3cfda5936d6f48 *src/Makevars.win
5721dec944628cc5cbcc84ea681d1501 *src/RcppExports.cpp
0a0e431e880e66d97ce206dd610a7f5f *src/init.c
f546663a3962fd9cff0162461a6990bb *src/upward_downward.cpp
5d08ef47493bc82d592a57dce6ef1aa8 *src/upward_downward.h
eaa0087f7e3f8d2ff56adfe8d1cf65bc *tests/testthat/test-EM-initialization.R
fc9aa381677b130328723504600ed82f *tests/testthat/test-EM-no_missing.R
2f6a575cb527fb2cd23add3ebee6c0fa *tests/testthat/test-core-compute_variance_covariance.R
579a7dad1c75cacfe89b6f33187a2b91 *tests/testthat/test-core-log_likelihood.R
9d9a0e30a121758108dd6029a8bfd183 *tests/testthat/test-independent_multivariate.R
b11c0c8143627cbddebc06fe35749d4e *tests/testthat/test-shifts-model_selection.R
bf1145c65c15af8fe2cb895a83f08338 *tests/testthat/test-shifts-parsimonyNumber.R
696cd749b118da2474e2d4698c746a9f *tests/testthat/test-shifts-partitionsNumber.R
515209fdb5045364fd7027c9d633fb6b *tests/testthat/test-upward_downward.R
2c74c027e162ce9237c055db0bf68fd9 *tests/testthat/test-utilities-handling_parameters.R
a10e77f0b01c8af437ccf6d5b8e6427c *tests/testthat/test-utilities-impute-traits.R
5c2b577436b2617fbd0a9585078ca3e2 *tests/testthat/test-utilities-rotations.R
4787f608a54df542c43dea40bfdb63ba *tests/testthat/test-utilities-simulate.R
e253777db9bb888f51b3a547117731ec *tests/testthat_EM.R
c6f18619aef4700b747e795669901d1a *tests/testthat_core.R
421192bd4221e436b1f03f1745dbe836 *tests/testthat_independent.R
9fde9f10de579d1d05c0ff2ca2e5f3d9 *tests/testthat_shifts.R
4a2dbfa934a8a2eb3c23b0370576ab14 *tests/testthat_upward.R
2ccbd66711847ff97a9982fdd813005b *tests/testthat_utilities.R
2847b58e0b3e4466aabc22aa7bfc26e1 *vignettes/monkeys.Rmd
c51d8de6126e5e1bee4697cc1523a014 *vignettes/tutorial.Rmd
