Files in PhylogeneticEM
Automatic Shift Detection using a Phylogenetic EM

MD5
NEWS.md
DESCRIPTION
LICENSE
NAMESPACE
vignettes/tutorial.Rmd
data/monkeys.rda
R/shifts_manipulations.R R/model_selection.R R/parsimonyNumber.R R/M_step.R R/simulate.R R/estimateEM.R R/generic_functions.R R/RcppExports.R R/partitionsNumber.R R/init_EM.R R/data.R R/shutoff.R R/E_step.R R/plot_functions.R
build/vignette.rds
tests/testthat_EM.R tests/testthat_core.R tests/testthat_upward.R tests/testthat_independent.R tests/testthat_shifts.R tests/testthat_utilities.R tests/testthat/test-utilities-handling_parameters.R tests/testthat/test-independent_multivariate.R tests/testthat/test-EM-no_missing.R tests/testthat/test-upward_downward.R tests/testthat/test-utilities-simulate.R tests/testthat/test-utilities-impute-traits.R tests/testthat/test-core-log_likelihood.R tests/testthat/test-core-compute_variance_covariance.R tests/testthat/test-shifts-model_selection.R tests/testthat/test-shifts-parsimonyNumber.R tests/testthat/test-EM-initialization.R tests/testthat/test-shifts-partitionsNumber.R man/sum.prod.comb.Rd man/init.simulate.OU.Rd man/lasso_regression_K_fixed.glmnet_multivariate.Rd man/init.simulate.StateAndExp.Rd man/shifts.list_to_vector.Rd man/compute_expectations.scOU.Rd man/segmentation.OU.specialCase.lasso.Rd man/compute_state_filter.Rd man/matrix_of_possibles.Rd man/penalty_pBIC.Rd man/init.EM.lasso.Rd man/compute_mean_variance.simple.Rd man/scale_params.Rd man/compute_diff_exp.BM.Rd man/plot.enumerate_parsimony.Rd man/transform_shifts_values.Rd man/test.root.state.Rd man/format_output.Rd man/simulate_internal.Rd man/go_back_to_original_process.Rd man/compute_tree_correlations_matrix.BM.Rd man/extract.partitionsNumber.Rd man/plot.PhyloEM.Rd man/check.selection.strength.Rd man/check_data.Rd man/incidence.matrix.Rd man/compute_shifts_from_betas.Rd man/sample_edges_intervals.Rd man/check_parsimony_clusters.Rd man/extract.parsimonyNumber.Rd man/get_variance_node.Rd man/compute_E.simple.Rd man/equivalent_shifts_edges.Rd man/estimateEM.Rd man/extract.parsimonyCost.Rd man/init.simulate.BM.Rd man/parsimonyNumber.Rd man/penalty_BirgeMassart_shape2.Rd man/sum.simplex.Rd man/compute_var_diff.BM.Rd man/update.partitionsNumber.gen.Rd man/compute_times_ca.Rd man/correspondenceEdges.Rd man/params_process.PhyloEM.Rd man/extract.Rd man/parsimonyCost.Rd man/update.parsimonyCost.Rd man/incidence_matrix_actualization_factors.Rd man/add_complementary.Rd man/impute.data.Rphylopars.Rd man/init.incidence.matrix.full.Rd man/plot.equivalent_shifts.Rd man/penalty_BirgeMassart_shape1.Rd man/init.parsimonyCost.Rd man/find_independent_regression_vectors.glmnet_multivariate.Rd man/split_params_independent.Rd man/wrapper_E_step.Rd man/merge_complementary_vectors.Rd man/compute_variance_covariance.scOU.Rd man/sample_shifts_edges.Rd man/clusters_from_shifts.Rd man/update.incidence.matrix.Rd man/log_likelihood.Rd man/update.parsimonyNumber.Rd man/compute_mahalanobis_distance.simple.Rd man/find_grid_alpha.Rd man/partitionsNumber.Rd man/segmentation.OU.specialCase.same_shifts.Rd man/compute_actualization_matrix_ultrametric.Rd man/update.compute_betas_from_shifts.Rd man/is.in.ranges.Rd man/update.incidence.matrix.full.Rd man/simul_process.Rd man/init.alpha.gamma.estimation.Rd man/params_OU.Rd man/update.enumerate_parsimony.Rd man/extract.variance_covariance.Rd man/allocate_subset_node.simulate.Rd man/extract.simul_process.Rd man/merge_params_independent.Rd man/compute_fixed_moments.Rd man/params_process.character.Rd man/incidence.matrix.full.Rd man/compute_betas_from_shifts.Rd man/compute_variance_covariance.OU.Rd man/equivalent_shifts_values.Rd man/enlight.Rd man/check_dimensions.Rd man/penalty_BaraudGiraudHuet_likelihood.Rd man/init.incidence.matrix.Rd man/compute_var_M.BM.Rd man/compute_residuals.simple.Rd man/transform_branch_length.Rd man/PhyloEM.Rd man/compute_gauss_lasso.Rd man/check_parsimony.Rd man/params_BM.Rd man/shifts.list_to_matrix.Rd man/params_process.Rd man/compute_sum_var_diff.Rd man/recursionDown.Rd man/compute_tree_correlations_matrix.scOU.Rd man/residuals.PhyloEM.Rd man/shifts_to_simmap.Rd man/init.allocate_regimes_from_shifts.Rd man/compute_expectations.BM.Rd man/update.allocate_regimes_from_shifts.Rd man/compute_stationary_variance.Rd man/find_shift_values.Rd man/plot.params_process.Rd man/init.compute_betas_from_shifts.Rd man/model_selection.Rd man/enumerate_tips_under_edges.Rd man/imputed_traits.Rd man/allocate_shifts_from_regimes.Rd man/prod.index.Rd man/segmentation.BM.Rd man/extract.equivalent_shifts.Rd man/shifts.matrix_to_list.Rd man/estimate.alpha.Rd man/allocate_regimes_from_shifts.Rd man/sum.partitions.Rd man/sum.partitions.cardFixed.Rd man/shifts.vector_to_list.Rd man/enumerate_parsimony.Rd man/init.parsimonyNumber.Rd man/equivalent_shifts.Rd man/compute_log_likelihood.simple.Rd man/qr.solve_exact.Rd man/init.enumerate_parsimony.Rd man/monkeys.Rd man/extract.enumerate_parsimony.Rd man/compute_variance_covariance.BM.Rd man/compute_dist_phy.Rd
inst/CITATION
inst/doc/tutorial.html
inst/doc/tutorial.Rmd inst/doc/tutorial.R
src/Makevars
src/init.c
src/RcppExports.cpp
src/upward_downward.h
src/upward_downward.cpp
src/Makevars.win
PhylogeneticEM documentation built on Sept. 9, 2017, 1:03 a.m.