View source: R/fitDiversityModel.R
fitDiversityModel | R Documentation |
Fits a diversity-dependent phenotypic evolution model (similar to Mahler et al. 2010).
fitDiversityModel(tree, x, d=NULL, showTree=TRUE, tol=1e-6)
## S3 method for class 'fitDiversityModel'
logLik(object, ...)
## S3 method for class 'fitDiversityModel'
print(x, ...)
tree |
an object of class |
x |
a vector with tip values for a continuously distributed trait. For |
d |
a vector containing the inferred historical diversity at each node in the tree - if |
showTree |
optional logical value indicating whether to plot the tree transformation implied by the model. |
tol |
some small value by which |
object |
for |
... |
optional arguments for |
An object of class "fitDiversityModel"
consisting of the following elements:
logL |
log-likelihood of the fitted model. |
sig0 |
estimated starting value for the rate at the root of the tree, |
psi |
the estimated rate of change in the rate associated with the addition of a lineage. |
vcv |
a matrix with the variances and covariance of the estimated parameters (from the Hessian). |
Liam Revell liam.revell@umb.edu
Mahler, D. L, L. J. Revell, R. E. Glor, and J. B. Losos (2010) Ecological opportunity and the rate of morphological evolution in the diversification of Greater Antillean anoles. Evolution, 64, 2731-2745.
Revell, L. J. (2024) phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ, 12, e16505.
brownie.lite
, estDiversity
, evol.rate.mcmc
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