In wadedismukes/treeduckenTools: treeduckenTools

So you want to simulate a nested set of trees? First you need to figure out the parameters you would like to simulate under. We will use the helpful treeduckenTools package to assist us.

library(treeduckenTools)
num_tips <- 15
birth_rate <- rexp(n = 1, rate = 1)
death_rate <- birth_rate * 0.5

gene_birth_rate <- rexp(n = 1, rate = 2)
gene_death_rate <- 0
lgt_rate <- rexp(n = 1, rate = 2)
num_loci <- 3

num_genes <- 9
individuals_per_pop <- 3
pop_size <- 6

Now you can print out the settings you would like with these

library(magrittr)
make_td_settings_list(birth_rate, death_rate, lgt_rate,
                      lgt_rate, gene_birth_rate, gene_death_rate,
                      num_tips, individuals_per_pop, pop_size, reps = 1,
                      num_loci, num_genes, sout = 1) %>% 
    write_td_settings(output_prefix = "test")

And run treeducken

wadedismukes/treeduckenTools documentation built on Aug. 14, 2019, 2:14 a.m.