Katie Saund

Advanced enhancement: Instead of checking for convergence on each individual edge, could create contiguous edge blocks

an advanced feature that would improve sophistication of the method is instead of treating edges as binary (yes variant present in AR or not), perform stochastic mapping and look at...

For the "Both" setting - reuse the AR data to save time. Currently, it runs AR once for PhyC and then again for Synchronous.

In continuous test return raw delta(phenotype) as columns/entries in: $phenotype_transition_edges $delta_pheno_table and $delta_pheno_list To help with downstream analysis. Check if binary tests return directional phenotype data or not (add if...

add a paragraph to wiki about ClonalFrame for missing genotype data

This is a suggestion from Nate: reduce run time by running only 1,000 permutations for each genotype. Then only continue to run more permutations for genotypes that have p <...

update dependency to 4.0 (Phytools is now a 4.0 ape dependency)

Return more objects

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- Return grouped presence/absence pattern on grouped runs - Return tree - Return AR results

People shouldn't run the tests if the phenotype doesn't converge enough, but let's add stop() to prevent the wasted compute time.

Implement intermediate data saves

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Save intermediate data after slow steps and implement hogwash starting from save points.