diem: Diagnostic index expectation maximisation

diem is a genome polarisation algorithm that finds which alleles of genomic markers belong to which side of a barrier, co-estimating which individuals belong on either side. diem is a deterministic expectation maximisation algorithm and so uses the likelihood inference framework.

The diem algorithm has been implemented in several programming languages, with core functions and accompanying tools stored in this repository.

1. diemr - R implementation. The package is available through https://CRAN.R-project.org/package=diemr.
2. diempy - Python implementation.
3. diemmca - Mathematica implementation. Soon also to be available at https://www.notebookarchive.org

When using any of the diem algorithm implementations, cite:

Stuart J. E. Baird, Jan Petružela, Izar Jaroň, Pavel Škrabánek, Natália Martínková. 2022. Genome polarisation for detecting barriers to geneflow. bioRxiv 2022.03.24.485605; doi: https://doi.org/10.1101/2022.03.24.485605.

Stuart J. E. Baird, Jan Petružela, Izar Jaroň, Pavel Škrabánek, Natália Martínková. 2022. Genome polarisation for detecting barriers to geneflow. Methods in Ecology and Evolution; doi: https://doi.org/10.1111/2041-210X.14010.