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 |
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 |