simDepIndep: simDepIndep
In hferg/hfgr:

Description Usage Arguments

A function that simulates either dependent or independent evolution between two binary character over a tree, and then takes some number of clades of a specific size, and simulates dependent or independent evolution (whichever the rest of the tree isn't) within those clades. The tree and data are simulated, and the Q matrices for the two traits are fixed for both and independent evolution (at the moment).

1	simDepIndep(itts, treesize, mintax, maxtax, clades, base_mode, base_rate = 2)

`itts`	The number of trees and datasets to generate.
`treesize`	The size, in terminal taxa, of the tree to be simulated.
`mintax`	The minimum size for the clades that vary from the background model.
`maxtax`	The maximum size for the clades that vary from the background model.
`clades`	The number of clades to simulate the opposite model in.
`base_mode`	The model for the whole tree that the clades vary from. E.g. if "dependent" then the tree will be a dependent model, with n clades evolved as independent. If "independent" than vice versa.
`base_rate`	The model defaults to a "base transition rate" of 2 changes per mean path length, this changes that.