geiger (version 0.2-5)

fit.continuous: Model fitting for continuous data

Description

Fits macroevolutionary models to phylogenetic trees

Usage

fit.continuous(tips, phy, lambda = FALSE, kappa = FALSE, delta = FALSE, alpha=FALSE, r = FALSE, bounds=NULL, print=TRUE, meserr=0)

Arguments

tips

Tip data

phy

Phylogenetic tree

lambda

Estimate lambda?

kappa

Estimate kappa?

delta

Estimate delta?

alpha

Estimate alpha?

r

Estimate r?

bounds

Range to constrain estimates?

print

Verbose mode?

meserr

Measurement error for each tip species

Value

• Prints out results - I think?

References

PAGEL

Examples

data(geospiza)
attach(geospiza)


V1 			<- log(geospiza.data[,1])
names(V1) 	<- rownames(geospiza.data)

drop.tip(geospiza.tree, "olivacea")->g.tree


#---- PRINT RESULTS
fit.continuous(V1, g.tree, print=TRUE)
 
#---- STORE RESULTS 
brown.fit <-  fit.continuous(V1, g.tree, print=FALSE)
#----------------------------------------------------
#   PHYLOGENETIC SIGNAL: FIT LAMBDA ON OFF-DAIGS
#----------------------------------------------------
fit.continuous(V1, g.tree, lambda=TRUE, print=TRUE)
#----------------------------------------------------
#    FIT TIME PROPORTIONALITY: DELTA 
#---------------------------------------------------
fit.continuous(V1, g.tree,  delta=TRUE, print=TRUE, bounds=list(delta=c(0.001, 5)))
#----------------------------------------------------
#    FIT TIME PROPORTIONALITY: KAPPA 
#---------------------------------------------------
fit.continuous(V1, g.tree,  kappa=TRUE, print=TRUE)