fit.continuous {geiger} | R Documentation |
Fits macroevolutionary models to phylogenetic trees
fit.continuous(tips, phy, lambda = FALSE, kappa = FALSE, delta = FALSE, alpha=FALSE, r = FALSE, bounds=NULL, print=TRUE, meserr=0)
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 |
Prints out results - I think?
Wendell Challenger and Luke J. Harmon
PAGEL
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)