FPK_sim_traitgram {BBMV} | R Documentation |
Simulates a trait evolving according to the FPK model and also plots evolution along branches of this tree using a traitgram.
FPK_sim_traitgram(tree, x0, a, b, c, bounds, sigsq, time_step, res.x = 200 , ylim.plot = NULL, return.trait = FALSE)
tree |
The phylogenetic tree on which to simulate the trait evolving. |
x0 |
The initial value of the trait (at the root of the tree). |
a |
The coefficient for the x^4 term of the potential. |
b |
The coefficient for the quadratic term of the potential. |
c |
The coefficient for the linear term of the potential. |
bounds |
The bounds on the trait interval. |
sigsq |
The evolutionary rate. |
time_step |
The time step for incremental simulations (should be smaller that the shortest branch in the tree). |
res.x |
The number of points to use for discretizing the trait interval. |
ylim.plot |
The y limits of the plot. If left to NULL, the bounds of the trait interval will be used, but you might want to zoom in a bit more if the bounds are not reached. |
return.trait |
If set to TRUE, the function returns a named vector of trait values at the tips of the tree. |
The function is slower than Sim_FPK since it simulates step by step along branches. It should be used to visualize trait evolution, but Sim_FPK should be preferred for quick simulations.
The function is mainly designed to produce a plot, but eventually returns a named vector of trait values at the tips of the tree.
F. C. Boucher