Re-implementation of EAGLE using Stan: https://mc-stan.org/
The original EAGLE codebase is here: https://github.com/davidaknowles/eagle and the accompanying paper is here: http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.4298.html
The easiest way to install will be using devtools
if (!require("devtools")) install.packages("devtools", repos='http://cran.us.r-project.org')
devtools::install_github("davidaknowles/eagle1S/eagle1S")
You will need the packages tidyverse, magrittr, doMC and intervals to run the example code.
Then clone this repo somewhere and look in example/. simulate.Rmd simulates a synthetic dataset on chromosome 22 and fit_per_snp.Rmd runs EAGLE on the simulated data. This will give you appropriate input files to try to match for your data.