Question: Phangorn bootstrap option
0
gravatar for Speed.Lee
2.6 years ago by
Speed.Lee30
Speed.Lee30 wrote:

I am using phangorn, maximum likelihood to estimate tree.

optim.pml process, I used rearrangement = "stochastic",

fit <-optim.pml(fit, multicore=TRUE, rearrangement = "stochastic")

so when bootstrap I should use optnni = TRUE or go straight forward? What is the difference, and the

bs <- bootstrap.pml(fit, bs=100, optnni = TRUE)

Sorry for the silly question but I cannot find an answer by search.

phangorn R • 752 views
ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by Speed.Lee30
0
gravatar for Speed.Lee
2.6 years ago by
Speed.Lee30
Speed.Lee30 wrote:

I just read a Phangorn vignettes, in appendix:

fit = optim.pml(fitNJ, rearrangement = "stochastic", optInv=TRUE,optGamma=TRUE)

fit

bs = bootstrap.pml(fit, bs=100, optNni=TRUE, multicore=TRUE)

This solves the problem.

But I still do not know the difference.

ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by Speed.Lee30
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1812 users visited in the last hour