Hi Xinxin.
In the current CRAN version of geiger treeTransform is not a valid
argument of fitDiscrete, instead you probably want to do:
fit<-fitDiscrete(tree,trait,transform="lambda")
Then the fitted value of lambda will be:
fit$opt$lambda
All the best, Liam
Liam J. Revell, Associate Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 10/22/2015 8:12 PM, xinxin xue wrote:
Hi,
how do i get the actual lambda value using fitDiscrete? it's for a binary
trait over a phylogeney. And would i need a p value too, for loglikelihood
ratio test between this lambda model and another model? thanks!
lambda<-fitDiscrete(tree,trait,treeTransform="lambda")
lambda
GEIGER-fitted comparative model of discrete data
fitted Q matrix:
1 2
1 -42.0543 42.0543
2 42.0543 -42.0543
model summary:
log-likelihood = -53.756148
AIC = 109.512296
AICc = 109.551900
free parameters = 1
Convergence diagnostics:
optimization iterations = 100
failed iterations = 0
frequency of best fit = 1.00
object summary:
'lik' -- likelihood function
'bnd' -- bounds for likelihood search
'res' -- optimization iteration summary
'opt' -- maximum likelihood parameter estimates
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