NEWS.md

In treeducken: Nested Phylogenetic Tree Simulator

treeducken 1.1.0

treeducken 1.1.0

Major changes

• Function names shortened to be more user friendly
• Added functionality for plotting events on cophylogeny from event_history data frame
• sim_cophyloBD (formerly sim_cophylo_bdp) now has two arguments:
  • host_limit controlling the number of hosts a symbiont is allowed to have at one time
  • hs_mode which changes host expansion events to host switch events (h_exp_r is still used to change the rate)
• Added new simulation mode sim_cophyloBD_ana which adds anagenetic events (i.e., happening between speciation nodes) to the functionality of sim_cophyloBD
• Changed event history to output only major events (description of abbreviations added to documentation)
• show_div_bar option added to plot. This outputs a bar showing the different events as tick marks.
• swapped output of association_mat from hosts in columns and symbionts in rows to hosts in rows and symbionts in columns.

Bug fixes

• Fixed typo in README.md

treeducken 1.0.0

Major changes

• First release of software can currently simulate:

  • species trees
  • host-symbiont paired trees
  • locus trees within host, symbiont, or species trees
  • gene trees within locus trees using the multilocus coalescent
  • gene trees within species trees using the multispecies coalescent

• Other features:

  • plotting of host-symbiont paired trees that include extinct tips
  • limited functions for using the simulated trees

Bug fixes

treeducken documentation built on March 3, 2021, 1:11 a.m.