I thought I would give both make.simmap() and plotSimmap() a practical go, so I decided to map & plot a plausible scenario for island colonization in the Caribbean - shown below:
[Click here for higher resolution version.]
I made a couple of updates to both make.simmap() and plotSimmap() to make this possible.
First, in the ML transition matrix, estimated inside make.simmap() using ace(), some of the transition rates were 0.0 in the full, symmetric model for these data. This makes sense, given the large number of states (four - for the four main islands in the Greater Antilles) and small number of transitions between states. I decided to allow additional models - in this case, using the equal-rates model:
Next, plotting a relatively large tree created some graphical problems. First, I eliminated all the whitespace around the plot by setting the graphical parameter, par()$mar within the function:
Finally, I added the option to manipulate the font size for the tip labels. This just changes the graphical parameter cex.
I will shortly post these updated versions of make.simmap() and plotSimmap() to my R phylogenetics page and I will add them to the next version of "phytools."