# Automatic Shift Detection using a Phylogenetic EM

## Documentation for package ‘PhylogeneticEM’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## 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_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
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