Samples gene family trees that evolved on a species tree with various conditions.

Description

Samples gene family trees that evolved on the branches of a species tree under the birth-death process. Trees may be conditioned on various priors for the number of reconstructed gene lineages at the root of the species tree, on the total number of genes in the gene tree, on the number of genes in each tip of the species tree, on at least one gene in each tip of the species tree or some combination of those conditions.

Usage

rgenetree(n, spec.phy, lams, mus, root = NULL, genetips = NULL, alltips = FALSE)

Arguments

.

Details

root sets the prior distribution of the number of reconstructed gene lineages at the root node of the species tree. If is.null(root), then the prior on the number of lineages is flat, but if is.null(genetips) then root must have some value. If root is a single positive integer, then all gene trees will start with root reconstructed gene lineages at the root. To establish a more complex prior root should be a numerical vector for which the ith element represents the prior probability that there are i gene lineages at the root, so that sum(root)==1. In that case root can be of any length and the prior probability of any number of lineages greater than length(root) will be 0. It should be noted that this is the prior probability assuming is.null(genetips) & !alltips, changes to those values will affect the probabilities (Hallinan 2012?).

genetips sets the conditions on the number of genes in the tips of the spec.phy. If is.null(genetips) then there are no conditions. If genetips is a single integer, then that value will be the total number of genes in each sampled gene tree, although the number of genes in each species may vary from sample to sample. One can set the number of genes in each tip of the spec.phy with a genetips of length length(spec.phy$tip.label), where the ith member of genetips will be the number of genes in spec.phy$tip.label[i].

Value

If n==1, a tree of class “phylo”. Otherwise, multiple trees in a list of class “multiPhylo”.

Author(s)

Nathaniel Malachi Hallinan

References

N. Hallinan. Null models for gene family trees, Math. Biosci. (In review).

See Also

recon.score,plot.phylo,plot.recon(coming soon)

Examples

##First we need a simple species tree
spec<-read.tree(text="((A:0.5,B:0.5):0.5,C:1);")
##Now we sample ten gene trees starting with 3 reconstructed gene lineages
phy.all<-rgenetree(10,spec,0.5,0.5,3)
plot(phy.all)

##Now let's make sure that every tip has at least one gene and set an exponential prior on the root
phy.full<-rgenetree(10,spec,0.5,0.5,exp(-(1:20))/sum(exp(-(1:20))),NULL,TRUE)
plot(phy.full)

##Now lets force the whole gene tree to end in 10 genes and set a flat prior for the root
phy.10<-rgenetree(10,spec,0.5,0.5,NULL,10)
plot(phy.10)

##Now lets start with 3 genes, set the number of genes at each tip of spec and vary mu between the branches of spec 
phy.253<-rgenetree(10,spec,0.5,c(0,1,0.2,0.5),3,c(2,5,3))
plot(phy.253)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(HyPhy)
Loading required package: ape
Loading required package: R.utils
Loading required package: R.oo
Loading required package: R.methodsS3
R.methodsS3 v1.7.1 (2016-02-15) successfully loaded. See ?R.methodsS3 for help.
R.oo v1.20.0 (2016-02-17) successfully loaded. See ?R.oo for help.

Attaching package: 'R.oo'

The following objects are masked from 'package:methods':

    getClasses, getMethods

The following objects are masked from 'package:base':

    attach, detach, gc, load, save

R.utils v2.3.0 (2016-04-13) successfully loaded. See ?R.utils for help.

Attaching package: 'R.utils'

The following object is masked from 'package:utils':

    timestamp

The following objects are masked from 'package:base':

    cat, commandArgs, getOption, inherits, isOpen, parse, warnings

> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/HyPhy/rgenetree.Rd_%03d_medium.png", width=480, height=480)
> ### Name: rgenetree
> ### Title: Samples gene family trees that evolved on a species tree with
> ###   various conditions.
> ### Aliases: rgenetree
> 
> ### ** Examples
> 
> ##First we need a simple species tree
> spec<-read.tree(text="((A:0.5,B:0.5):0.5,C:1);")
> ##Now we sample ten gene trees starting with 3 reconstructed gene lineages
> phy.all<-rgenetree(10,spec,0.5,0.5,3)
> plot(phy.all)
> 
> ##Now let's make sure that every tip has at least one gene and set an exponential prior on the root
> phy.full<-rgenetree(10,spec,0.5,0.5,exp(-(1:20))/sum(exp(-(1:20))),NULL,TRUE)
> plot(phy.full)
> 
> ##Now lets force the whole gene tree to end in 10 genes and set a flat prior for the root
> phy.10<-rgenetree(10,spec,0.5,0.5,NULL,10)
> plot(phy.10)
> 
> ##Now lets start with 3 genes, set the number of genes at each tip of spec and vary mu between the branches of spec 
> phy.253<-rgenetree(10,spec,0.5,c(0,1,0.2,0.5),3,c(2,5,3))
> plot(phy.253)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>