This repository contains the source code used for the analyses in the manuscript Joint Inference of Demography and Recent Positive Selection.
It contains 2 simulations studies and one data analysis:
- simulation_study_mcsf: Code for the simulation study to determine the power of MCSF
- simulation_study_coestimation: Code for the simulation study to evaluate the importance of coestimation and performance of the approach
- analysis_drosophila: Code for the Drosophila Melanogaster application example
- The analysis require a recent version (>= 3.1) of R.
- The used R Packages were recorded via packrat and should be automatically installed when starting R in the corresponding subdirectories.
Feel free to use all code in this repository under the conditions of the MIT License:
Copyright 2017 Paul Staab, Jorge E. Amaya Romero, and Dirk Metzler
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.