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"orout.type="both". Ignored otherwise.
Value
A list X containing a list of trees in multiPhylo format (X$trees) and a list of outliers (X$outl).
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.
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