EuroForMix

Newest version is: euroformix_4.0.8 (compatible with R v4.2.x and R v4.3.x)
This version was tested with R v4.2.3

Important: If you are using an earlier version than R v4.2.x you should use file named "version 4.0.x (before R v4.2)". Remember to rename the file to "euroformix_4.0.4.zip" after download. Versions before R v4.0 needs new re-compilations.

Earlier versions are archived here: Go to Version changes

Intern validation for new versions: Go to Evaluations

Note:
- Users are recommended to switch to the 3.3.0 version (or newer) of EuroForMix (if using version 3). See Important Update panel.
- Earlier version of EuroForMix (v3.1.0 and older) will not work with the 64-bit R-version of 4.0.1 (issue using gWidgetstcltk), but later versions from R-4.0.2 work.
- EuroForMix versions not supported by newer R-versions (needs re-compilation):
--> EuroForMix v3.0.0 (and older) is not supported by R-version 4.0.0 and later.
--> EuroForMix v1.10 (and older) is not supported by R-version 3.5.0 and later.
--> EuroForMix v1.8 (and older) is not supported by R-version 3.4.0 and later

EuroForMix is a graphical layer for the functions in the R-package euroformix. It is an advanced fully validated open-source, free software used to interpret complex DNA profiles (mixtures) taking into account peak height, stutter and degradation.

About the R-package euroformix:
euroformix contains procedures for maximization (frequentistic) and integration (Bayesian) of the likelihood function of a gamma peak height model for single (or replicated) STR/SNP/MPS DNA data for a general specifications of hypotheses. Sensitivity analysis of unknown parameters can be carried out using Markov Chain Monte Carlo method. It also contains procedures for deconvolution and database search and may take care of stutters, allele drop-out and allele drop-in.

The R-package euroformix is:

• Entirely open source and is independent of any external software for running.
• Based on the statistical model presented in article Cowell et.al. (2015)[1]
• Implementing the statistical model described in article Bleka et.al. (2016)[2]
• Running C++ underneath to do fast calculation of the likelihood function.
• Evaluated numerically with the R-software DNAmixtures (see Evaluations).
• Evaluated practically with a large dataset as described in article Bleka et.al. (2016)[3].
• Programmed and maintained by Øyvind Bleka.

References:

• [1] R. G. Cowell, T. Graversen, S. L. Lauritzen, J. Mortera; Analysis of forensic DNA mixtures with artefacts; Appl. Statist., 64(1):1-32, 2015.
• [2] Ø. Bleka, G. Storvik, P. Gill; EuroForMix: An open source software based on a continuous model to evaluate STR DNA profiles from a mixture of contributors with artefacts; Forensic Sci. Int. Genet., 21:35-44, 2016.
• [3] Ø. Bleka, C.C. Benschop, G. Storvik, P. Gill; A comparative study of qualitative and quantitative models used to interpret complex STR DNA profiles.;Forensic Sci Int Genet.,25:85-96 2016
• [4] Ø. Bleka, M. Eduardoff, C. Santos, C. Phillips, W. Parson, P. Gill; Open source software EuroForMix can be used to analyse complex SNP mixtures.;Forensic Sci Int Genet.,31:105-110 2017
• [5] Ø. Bleka, R. Just, J. Le, P. Gill; An examination of STR nomenclatures, filters and models for MPS mixture interpretation;Forensic Sci Int Genet.,48: 102319, 2020

Learning sources:
Videos and presentations are found under Learning material.
The tutorial and manual for EuroForMix are found below (however they may not be up-to-date).

Disclaimer:
Use EuroForMix at your own risk. Feel free to modify the code in anyway for private or public use, as long as the original author is cited, and no fee is charged aside from distribution costs (GPL(>=2)).

Funding:
The project has received funding support from the European Union Seventh Framework Programme (FP7/2007-2013) under grant agreement number 285487 (EUROFORGEN-NoE).

Need help?
Don't hesitate to send a message to help@euroformix.com.

Installation and getting started:

1. Install and run R (>=3.5.0) in Windows (http://cran.r-project.org/). See installation for MAC or LINUX below.
2. See GitHub page for further installation instructions.
3. Run these commands in the R-software to start the GUI:
   library(euroformix)
   efm()

Useful: Creating a startup icon for EuroForMix on your desktop:

1. Run this code within your preferred R-version:
   path <- file.path(Sys.getenv("USERPROFILE"),"Desktop",fsep="\\")
   setwd(path) #If 'Desktop' is not the proper desktop name you may need to change it.
   .First = function(x) {require(stats);require(euroformix);efm()};save.image(".Rdata"); #creates a necessary ".Rdata"-file on the desktop.
   
2. Creating the shortcut:
   - Create a copy (CTRL + C and then CTRL + V) of the R icon on the desktop.
   - Name the copy "EuroForMix" or something arbitrary.
   - Right-click on icon. Select "Properties" and then go to the "Shortcut" tab (named something else for other languages).
   - Remove the text within "Start in", click "Apply" and then close the window.
   - You have now created an startup icon for EuroForMix.