popgencnn

The goal of popgencnn is to support deep learning pipelines for population genomic inference in R. Current functionality supports the generation and pre-processing of simulated data sets. Specifically, coalescent simulations for use in neural networks estimators of historical population recombination rate.

Installation

You can install popgencnn from GitHub with:

# install.packages("devtools")
devtools::install_github("mmjohn/popgencnn")

Example

This is a basic example which shows you how to solve a common problem:

library(popgencnn)

ms_simulate(
  morgans_per_bp = 2.0e-8, 
  ne = 10000, 
  filename = 'sim.txt'
)
#> [1] "./msdir/ms 50 1 -t 12.0006 -r 16 20001 >> sim.txt"