read.gtree.samples: reads gene tree samples from the posterior generated by...
In fmichonneau/starbeastPPS: A posterior predictive check for the multispecies coalescent model implemented in *BEAST
Description
Usage
Arguments
Details
Value
Author(s)
Examples
Description
this function will read in a .trees file generated by *BEAST and store the among-branch rate variation in a vector called "rate" appended to each tree
Usage
1
Arguments
file
the path and file name of a .trees nexus file generated by *BEAST corresponding to the posterior distribution of a coalescent genealogy for a single locus.
Details
this function uses ape's read.nexus and another function, taken and reconstituted from package 'phyloch' by Christoph Heibl to get the trees and branch rate scalar vector from the posterior distribution of gene trees from a *BEAST run.
this function is unfortunately very slow compared to read.nexus.
Value
a phylo or multiphylo object, each with a vector of among-branch rate variation named "rate" appended.
Author(s)
Noah Reid
Examples
1
2
3
##---- Should be DIRECTLY executable !! ----
##-- ==> Define data, use random,
##-- or do help(data=index) for the standard data sets.
fmichonneau/starbeastPPS documentation built on May 16, 2019, 1:47 p.m.
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Description Usage Arguments Details Value Author(s) Examples
Description
this function will read in a .trees file generated by *BEAST and store the among-branch rate variation in a vector called "rate" appended to each tree
Usage
1 |
Arguments
file |
the path and file name of a .trees nexus file generated by *BEAST corresponding to the posterior distribution of a coalescent genealogy for a single locus. |
Details
this function uses ape's read.nexus and another function, taken and reconstituted from package 'phyloch' by Christoph Heibl to get the trees and branch rate scalar vector from the posterior distribution of gene trees from a *BEAST run.
this function is unfortunately very slow compared to read.nexus.
Value
a phylo or multiphylo object, each with a vector of among-branch rate variation named "rate" appended.
Author(s)
Noah Reid
Examples
1 2 3 | ##---- Should be DIRECTLY executable !! ----
##-- ==> Define data, use random,
##-- or do help(data=index) for the standard data sets.
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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