Add tests and various stuff

[Jean-Baptiste-Camps]

• added tests for the PCC.Stemma functions;
• rewrote part of the code, to make it less verbose and more efficient;
• corrected some minor bugs;
• improved documentation;
• added ask=TRUE and verbose=FALSE to the PCC.Stemma functions.

[Jean-Baptiste-Camps]

Apparently, a review is needed (sorry @floriancafiero ).

[floriancafiero]

Je suis dans le train je te fais ça dès que je suis devant mon ordi (navette entre opera de Rennes et opera de Marseille en ce moment, c’est un peu penible...)

Le 2 mai 2018 à 12:11, Jean-Baptiste-Camps notifications@github.com a écrit :

Apparently, a review is needed (sorry @floriancafiero ).

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[Jean-Baptiste-Camps]

Ok, en fait, pas de grosse vérification à faire a priori. J'ai juste ajouté des tests et optimisé le code, etc. Je comptais faire une seule grosse pull request en fin de semaine, mais je tronçonne, car j'expérimente avec igraph, là.

[Jean-Baptiste-Camps]

To go faster, I merged the igraph branch in this one. So, other improvements.

• Switched to igraph for stemma plotting ;
• enhanced visualisations:
  • stemmata plotted as tree
  • dotted lines for uncertainty;
  • created special layout where height in the stemma is proportional to the number of variants from the model;
  • added color, titles, etc.
• profiled the PCC.Stemma functions to gain efficiency (exec time /2);
• simplified PCC.Stemma outputs and documented it;
• added tests;
• various corrections and improvements;