simtrees: Simplistic simulation of gene trees with outliers

In phylter: Detect and Remove Outliers in Phylogenomics Datasets

Simplistic simulation of gene trees with outliers

Description

Simple (simplistic) simulation of trees with outliers.

Usage

simtrees(Ngn, Nsp, Nsp.out = 0, Ngn.out = 0, Nb.cell.outlier = 0, 
brlen.sd = 0, out.type="topology",bl.mult=2)

Arguments

Ngn	Number of gene trees to simulate.
Nsp	Number of species (tips) per tree.
Nsp.out	Number of outlier species (also called rogue taxa). 0 = none.
Ngn.out	Number of outlier genes. 0 = none.
Nb.cell.outlier	Number of times one species in one tree is an outlier. 0 = none. The type of outlier is set by out.type=.
brlen.sd	Heterogeneity of branch lengths in trees. A value with mean 0 and standard deviation equal to brlen.sd is added to each branch length. If the resulting branch length has a negative value, its absolute value is taken.
out.type	The type of cell outlier. Can be "topology" (the default), where outlier species are simulated by branching them elsewhere (randomly) in the tree, "brlength", where terminal branches of outlier species are multiplied by bl.mult (see after) or "both" where half of the outliers are "topology" and the other half are "brlength". In the latter case, if the number of outliers (Nb.cell.outlier) id odd, there is one more topology outlier than brlength outlier simulated.
bl.mult	Multiplier of terminal branches of outlier species when out.type="topology" or out.type="both". Ignored otherwise.

Details

The simulation process is as follows: a first tree is generated with the rtree() function and is then duplicated and modified according to the parameters chosen by the user.

Value

A list X containing a list of trees in multiPhylo format (X$trees) and a list of outliers (X$outl).

Examples

 
# Very basic simulator, for debugging purpose mainly.
# examples: 30 genes, 120 species, 2 outlier species, 3 outlier genes
# 4 gene/species outliers of type "topology", branch length variance = 0.6.
# The branch length multiplier is set to 2 but this is
# ignored if out.type="topology"
simu<-simtrees(30,120,2,3,4,0.6, "topology",2)
trees<-simu$trees #list of trees
outl<-simu$outl #list of simulated outliers and their type

phylter documentation built on Aug. 24, 2023, 9:10 a.m.