Hello,
This is Elaine.
I want to calculate lambda based on a bird data and a polygeny tree, using
geiger.
However, an error message below jumped out.
I do not understand it quite well.
Please kindly help explain its meaning and advise any code modification to
calculate lambda.
(BTW, I found Dr. Liam's modification (trend) on fitContinuous but do not
know how to apply it.)(# written by Liam J. Revell 2011)
Thank you very much.
Elaine
Error
> lambda_Mig_ML<-fitContinuous(phy= tree.pruned, data = birddata,
+ data.names = birddata$Family,model = "lambda")
Fitting lambda model:
Error in optim(foo, p = start, lower = lower, upper = upper, method = "L")
:
non-finite value supplied by optim
In addition: Warning message:
In var(ds$data) : NAs introduced by coercion
Code
Library(ape)
birddata <- read.csv("H:/ birddata_family_20130405.csv", header = TRUE)
birdtree <- read.nexus("H:/ birddata_family_20130405.nexus")
setwd("H:)
## prune the phylogeny to include only species which are in the data set
species.to.keep<-read.csv("H:/ birddata_family_20130405.csv", header = TRUE)
tree.pruned<-drop.tip(birdtree,tree.pruned<-drop.tip(tree,**
setdiff(tree$tip.label,ss))
library(geiger)
# compute lambda using fitDiscrete or fitContinuous functions of geiger
lambda_Mig_ML<-fitContinuous(phy= tree.pruned, data = birddata,
data.names = birddata$Family,model = "lambda")
lambda_GL_ML
[[alternative HTML version deleted]]
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