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.
You can install popgencnn from GitHub with:
# install.packages("devtools")
devtools::install_github("mmjohn/popgencnn")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"