Tutorial

To run the package, first install julia (here). To create a local environment with the package cd into your work directory and launch julia, then:

using Pkg; Pkg.activate(".")

Pkg.Registry.add(RegistrySpec(url = "https://github.com/ArndtLab/JuliaRegistry.git"))

Pkg.add("DemoInfer","HistogramBinnings","CSV","DataFrames")
using DemoInfer, HistogramBinnings, CSV, DataFrames

The tool require three inputs: a (binned) vector of IBS segments lengths, a mutation rate and a recombination rate (both per bp per generation).

data = CSV.read("path", header=0, DataFrame; delim="\t")
h_obs = HistogramBinnings.Histogram(LogEdgeVector(lo = 30, hi = 1_000_000, nbins = 200));
append!(h_obs, data[:,1])

You can read a vector from a .csv file (first line) and then create an histogram with it.

Set a value for the rates and run the inference:

mu = 2.36e-8
rho = 1e-8
Ltot = sum(data[:,1])
nepochs = 3
res, chains = demoinfer(h_obs, nepochs, mu, rho, Ltot)