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Diagnostic index expectation maximisation (diem) algorithm implementations

diem 최신버젼 다운로드

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# *diem*: Diagnostic index expectation maximisation

**NEWS 30th October 2025:** *diem* development continues in R and Python with a new fully Pythonic bedtools-aware implementation at this permanent institutional site https://github.com/Studenecivb/diemPy

This site (here, personal to SJEB) will remain as a record of the original implementations and to serve as a re-direct for Python users (above) and R users (below).

*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 developer version is available through https://github.com/nmartinkova/diemr and the stable release through https://CRAN.R-project.org/package=diemr. ![](https://cranlogs.r-pkg.org/badges/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. 2023. Genome polarisation for detecting barriers to geneflow. Methods in Ecology and Evolution; doi: https://doi.org/10.1111/2041-210X.14010.

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