wadedismukes/treeducken: treeducken 1.1.0

Published April 22, 2021 | Version 1.1.0

Software Open

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

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

Files

Name	Size	Download all
wadedismukes/treeducken-1.1.0.zip md5:7fcaa8fbd34c5be8ae49d47827e1a6af	150.3 kB	Preview Download

Is supplement to: https://github.com/wadedismukes/treeducken/tree/1.1.0 (URL)