fit.continuous {geiger}R Documentation

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

Details

Value

Prints out results - I think?

Note

Author(s)

Wendell Challenger and Luke J. Harmon

References

PAGEL

See Also

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)


[Package geiger version 0.2-6 Index]