dist_0: Nsubs per site with no recombination (R = 0; M = 0.01).

In caitiecollins/treeWAS: Phylogenetic tree-based microbial GWAS

Nsubs per site with no recombination (R = 0; M = 0.01).

Description

This vector contains a homoplasy distribution, representing the relative number of substitutions per site that occurred along a phylogenetic tree when evolution was simulated with a mutation rate of M = 0.01 and a recombination rate of R = 0 (r/m = 0).

Usage

data(dist_0)

Format

A named vector of length 4.

Details

A per-site mutation rate of M = 0.01 indicates that each site, on average, undergoes 0.01 substitutions due to mutation along the phylogenetic tree. A per-site recombination rate of R = 0 indicates that no recombination occurred.

Each element of the vector indicates the number of genetic loci that have undergone the number of substitutions indicated by the name of that element (Nsub = i).

If visualised as a bar plot (with barplot(dist_0)), one would see that the Nsub distribution is arranged as if it were the counts of a histogram with index names along the x-axis, corresponding to Nsub (the number of substitutions per site), and cell counts along the y-axis, showing Nloci (the number of genetic sites undergoing Nsub=i substitutions along the tree).

Author(s)

Caitlin Collins [e-mail]

caitiecollins/treeWAS documentation built on March 9, 2024, 3:15 p.m.