Description Usage Arguments Value Author(s) See Also Examples
Functions that builds the likelihood function of the FPK or BBMV model
1 2 |
tree |
A phylogenetic tree in 'phylo' format |
trait |
A named vector of trait values for the tips of the tree. It should match tip labels in the phylogeny. Alternatively, a named list with one element per tip in the tree, each element being in turn a numeric vector with multiple measurements of the trait for this tip. |
bounds |
The two bounds that constrain trait values when fitting the BBMV model. Specified by a numeric vector containing the minimum and maximum bound of the trait interval as the first and second element, respectively. |
a |
The value of the x^4 term in the evolutionary potential. If set to NULL (the default), this parameter will be estimated. If a numeric value is provided, this parameter will be fixed to the value specified. |
b |
The value of the quadratic term in the evolutionary potential. If set to NULL (the default), this parameter will be estimated. If a numeric value is provided, this parameter will be fixed to the value specified. |
c |
The value of the linear term in the evolutionary potential. If set to NULL (the default), this parameter will be estimated. If a numeric value is provided, this parameter will be fixed to the value specified. |
Npts |
The number of points used in the discretization procedure. |
A list of several items, including the data and model call, but most importantly the likelihood function ($fun element).
F.C. Boucher
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | ## Not run:
# Simulate data: tree + continuous trait
library(geiger)
tree=sim.bdtree(stop='taxa',n=10) # tree with few tips for quick tests
tree$edge.length=100*tree$edge.length/max(branching.times(tree)) # rescale the tree
# Simulate trait evolving on a macroevolutionary landscape with two peaks of equal heights
x=seq(from=-1.5,to=1.5,length.out=100)
bounds=c(min(x),max(x)) # the bounds we use for simulating
V6=10*(x^4-0.5*(x^2)+0.*x) # this is the evolutionary potential: it has two wells
TRAIT= Sim_FPK(tree,x0=0,V=V6,sigma=10,bounds=c(-5, 5))
# create a likelihood function for the FPK model:
ll_FPK4=lnL_FPK(tree,TRAIT,Npts=25,a=NULL,b=NULL,c=NULL) # the full model
## End(Not run)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.