PhylogeneticEM 1.2.1

CRAN maintenance
- Added references in Description
- Reduce checking and vignette building time

PhylogeneticEM 1.2.0

Added Options:
- option_is.ultrametric to control the ape::is.ultrametric check.
Deprecation Fix:
- Go back to updated version of gglasso (faster than grplasso). This should not change the results of PhylogeneticEM.
Added functions:
- Functions find_rotation and merge_rotations to deal with datasets that are equal up to a rotation.
- Functions get_criterion and plot_criterion to get and plot the criterion used for model selection easilly.
New feature:
- Function PhyloEM can now allow for negative values of alpha, to fit an EB model.
Bug fix:
- In function plot, fixed bug that led to the wrong parameters being selected when doing ancestral trait reconstruction.

Deprecation Fix:
- Remove dependency from gglasso (replaced with grplasso). This should not change the results of PhylogeneticEM.
Bug Fixes:
- Issue an error message when the tree has some zero-length branches.
Minor Changes:
- Added options to plot.equivalent_shifts.

Minor Changes:
- Impose a maximum value for alpha in find_grid_alpha to respect machine max double.
New Features
- added argument label_font to plot function to control the label font.
- added argument axis_las to plot function to control the axis las.
Bug fixes:
- Plotting missing values correctly in plot.PhyloEM.
- Bug fixes in plotting PhyloEM object when p = 1.
- When p=1 and nbr_alpha is not missing, do not switch to estimated mode for alpha.
Technical:
- registration of c++ code to comply with R 3.4 new standards.

Initial Release.