Tree: fix bug and add colored tree tips

• Resolved bug that incorrectly reordered tree
• Added a user input that plots the tree in the output PDF with color coded tips (e.g. by strain type).

Make tree structure uniform and add reconstruction progress statements

• Internal organization of tree structure is now always forced to "cladewise"
• Ancestral reconstruction progress statements are made after completing AR for 25%, 50%, and 75% of the genotypes in addition to 100% completion. This is important to tracking progress on very large (slow) datasets.

Increase stringency for choosing ARD model

Require a larger difference in AIC to choose ARD-based ancestral reconstruction over ER-based ancestral reconstruction. The previous difference: > 2; current difference > 10.

Better plotting for large trees

To improve readability of large trees I've made the following updates:

1. Line widths on trees decrease in size if there are more than 200 tree tips.
2. Genotype transition trees are plotted on their own page.
3. No more black outlines for the continuous phenotype tree
4. The user now has the option to choose between a phylogram (right facing, square tree) and fan tree. Phylogram is the default. The phylogram ignores tree edge length while the fan uses tree edge length.

Minor update to post-AR grouping

Post-AR grouping no longer incorrectly drops highly penetrant grouped genotypes.

All three algorithms now return unadjusted p-values in $raw_pvals object.

Two grouping methods

Users can now select between two grouping methods: pre- and post-ancestral reconstruction. Post-ancestral reconstruction was the default method in v1.0.0. Pre-ar was the default method in v1.1.0.

Update some object names and plot labels to reflect changes to nomenclature after hogwash paper revisions:

• convergence$intersection --> convergence$N
• Beta_genotype intersect Beta_phenotype --> Ntest

Grouped analysis fixed

Fixed bug in grouped analysis calculation of the genotype transition edges.
Added progress statements after ancestral reconstruction and permutation steps.
Phylogenetic signal now included in .rda output.
Set depends on R >= 3.6.0.

Preprint version

This is the version of the hogwash software used in the preprint: "hogwash: Three methods for Genome-Wide Association Studies in Bacteria."