• Exploring display of phylogeny. Unlabled, painted fan?
  • tweaking release-of-constraint plot - vary alpha, less strong? release at T/2? Animated version?

Creating paintings of phylogenies

Creating from a specified set of taxa is a somewhat common task for me. Wrightscape supports doing this for both ouch and ape trees.

intra_ancestor <- mrcaOUCH(c("Chlorurus_sordidus", "Hipposcarus_longiceps"), labrid$tree)
intramandibular <- paintBranches(intra_ancestor, labrid$tree, c("other","intramandibular"))
pharyngeal_ancestor<-mrcaOUCH(c("Bolbometopon_muricatum", "Sparisoma_radians"), labrid$tree)
pharyngeal <- paintBranches(pharyngeal_ancestor, labrid$tree, c("other","pharyngeal"))
two_shifts <- paintBranches(c(pharyngeal_ancestor, intra_ancestor), labrid$tree, 
c("wrasses", "pharyngeal", intramandibular") )

The ouch-trees can be converted back to ape trees in a way that can plot them, but for some reason break the fan-plot mode but not the standard phylogram plot mode. Writing to a nexus file and reading back in solves the backwards convert problem, but does not write the branch labels (at least not currently, which are stored in $regimes).

Warning signals

  • Parallelizing the prosecutors fallacy, following earlier post for MPI via snow