Function check_parsimony
Check for parsimony at the M step.
Check for parsimony at the M step.
Merge branch 'check_parsimony_in_lasso' of github.com:pbastide/Phylogenetic-EM into check_parsimony_in_lasso
Change prod into any.
Add scale_tree to generic functions.
re-write enumerate_tips_under_edges.
parcimony -> parsimony
Rename parcimonyNumber.R to parsimonyNumber.R
Coherence fixes in arguments calls.
Compute the actualized incidence matrix and use it in lasso initialization.
This allows lasso to work for non-parametric trees.
Change function equivalent_shifts_values, to actualize on incidence matrix rather than on shifts values (handle non-parametric trees).
Minor fix on plot_equivalent_shifts.
Handle case where clusters are not nice integer in enumerateParsimony.
Re-define parsimony checks.
In initialization, take some random (parsimonious) edges better than NULL if default initialization.
Random shifts in M step if really unlucky : all segmentation algorithm failed, and no old shifts to start with.
missing -> !exists
check_parsimony -> check_parsimony_ism
sum() == 0 -> !any
Function to attempt to find K independent selected variables in a regularization path.
Merge

Merge branch 'check_parsimony_in_lasso' into develop

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