Automatic Shift Detection using a Phylogenetic EM

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Documentation for package ‘PhylogeneticEM’ version 1.8.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

allocate_regimes_from_shifts	Allocation of regimes to nodes.
allocate_shifts_from_regimes	Allocation of shifts to edges
check_parsimony	Check Parsimony, assuming no homoplasy
clusters_from_shifts	Clustering associated to a shift allocation, assuming no homoplasy.
compute_betas_from_shifts	Computation of the optimal values at nodes and tips.
compute_dist_phy	Phylogenetic Distances
compute_shifts_from_betas	Computation of shifts from the vector of optimal values
compute_stationary_variance	Compute the stationary variance matrix
compute_times_ca	Common Ancestors Times
correspondenceEdges	Correspondence between edges numbers
enlight	Make the result lighter
enlight.PhyloEM	Make the result lighter
enumerate_parsimony	Enumerate all the possible regime allocations, given a clustering of the tips.
enumerate_tips_under_edges	Tips descendants of nodes.
equivalent_shifts	Find all equivalent shifts allocations and values.
estimateEM	Perform One EM
extract	Extraction function
extract.enumerate_parsimony	Extract the result of 'enumerate_parsimony' at a node.
extract.equivalent_shifts	Extract the shifts values for one trait.
extract.parsimonyCost	Extraction of the actual number of solutions.
extract.parsimonyNumber	Extraction of the actual number of solutions.
extract.partitionsNumber	Extract from object 'partitionsNumber'
extract.simul_process	Extraction of simulated traits
find_grid_alpha	Find a reasonable grid for alpha
find_rotation	Test for rotation invariant datasets
get_criterion	Get Model Selection Criterion
imputed_traits	Ancestral State Reconstruction
imputed_traits.PhyloEM	Ancestral State Reconstruction
incidence.matrix	Incidence matrix of a tree.
incidence.matrix.full	Incidence matrix of a tree.
log_likelihood	Log Likelihood of a fitted object
log_likelihood.params_process	Log Likelihood of a fitted object
log_likelihood.PhyloEM	Log Likelihood of a fitted object
merge_alpha_grids	Merge PhyloEM fits on various grids of alpha values
merge_rotations	Merge fits from independent runs of PhyloEM.
model_selection	Model Selection of a fitted object
model_selection.PhyloEM	Model Selection of a fitted object
monkeys	New World Monkeys dataset
node_optimal_values	Computation of the optimal values at nodes and tips.
params_BM	Create an object 'params_process' for a BM
params_OU	Create an object 'params_process' for an OU
params_process	Create an object params_process
params_process.character	Create an object 'params_process'
params_process.PhyloEM	Parameter estimates
parsimonyCost	Minimal number of shifts needed to get a clustering.
parsimonyNumber	Number of equivalent parsimonious allocations.
partitionsNumber	Number of different models
PhyloEM	Model Estimation with Detection of Shifts
plot.enumerate_parsimony	Plot all the equivalent solutions.
plot.equivalent_shifts	Plot all the equivalent solutions.
plot.params_process	Plot for class 'simul_process'
plot.PhyloEM	Plot for class 'PhyloEM'
plot_criterion	Plot Model Selection Criterion
residuals.PhyloEM	Residuals of a fitted object
shifts.list_to_matrix	Compute the matrix of shifts.
shifts.matrix_to_list	Compute the list of shifts.
shifts_to_simmap	Simmap format mapping from list of edges
simul_process	Simulate a Stochastic Process on a tree
simul_process.params_process	Simulate a Stochastic Process on a tree
simul_process.PhyloEM	Simulate a Stochastic Process on a tree
transform_branch_length	Transform branch length for a re-scaled BM