quetzal-framework / quetzal-coatl

A toolbox for C++ devs wanting to build geospatial population genetics simulators !

Quetzal-CoalTL

C++ Template Libary for coalescence

Quetzal-CoalTL is a C++20 template scientific library for simulating the coalescence of gene genealogies in explicit landscapes or phylogenetic networks.

Its aim is to standardize a library of reusable components to encourage code reuse.

Documentation

The documentation lives here.

🥚🥚🥚 If you are not a C++ programmer, then you are unlikely to benefit directly from this library: you may prefer instead the Quetzal-EGGS simulators.

Contact

• 📧 You are interested? Want to contribute? Want to give some feedback? Don't be shy, contact me!
• ⭐ You think this is a cool project? Drop a star on GitHub ☝️
• 🐛 A bug? Oopsie daisy! I'll fix it asap if you email me or open an issue ☝️

Author

• AUTHOR : Arnaud Becheler
• DATE : 2016
• LICENCE : This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.
• CONTACT : [email protected]
• WEBSITE : https://becheler.github.io/

How to cite

Becheler, A, Coron, C, Dupas, S. The Quetzal Coalescence template library: A C++ programmers resource for integrating distributional, demographic and coalescent models. Mol Ecol Resour. 2019; 19: 788– 793. https://doi.org/10.1111/1755-0998.12992

Becheler, A., & Knowles, L. L. (2020). Occupancy spectrum distribution: application for coalescence simulation with generic mergers. Bioinformatics, 36(10), 3279-3280.

quetzal-coatl's Issues

individual dispersal gone

expressive bugs on mac osx

Set up gtihub actions

Set up Actions in order to:

• Build and test using CMake actions when push on master
• Draft a release each when push on master

constructor missing in dispersal kernels

Deterministic forward migration

Current state:
Simulating demography implies to move individuals one by one, sampling their destination in a dispersal kernel. It is well-suited for representing small populations sizes (or heterogeneous populations levels) such as those occurring in a colonization process. Consequently the demographic historical database uses integers to represent populations size.

Wanted state:
However in many cases populations sizes are much higher, and simulating a stochastic migration process does does not worth the computational burden. We can then represent migration by (loosely speaking) multiplying the vector of populations density by the matrix of the migration rates.

Furthermore, at phylogeographic scales, considering dispersal only between adjacent cells is a relevant hypothesis that can be computationally beneficial, that should be made available in quetzal.

fix namespaces

Make namespace Doxygen page easier to navigate:

• dvp namespace is currently out of quetzal namespace
• also i can't find dvp online: maybe change to more documented/maintained project
• fuzzy_transfer_distance out of quetzal namespace
• fuzzy partitions, munkres etc living outside of pretty much everything
• what to do with gdalcpp ?

make the tests portable

For Mac OS.

Any suggestion for tutorials ?

I am currently planning to write a series of small tutorials to help diving into Quetzal core components. I guess it will be much appreciated ! 😇

I consider to make these first tutorials:

• how to use Quetzal concepts for simulating custom genealogies.
• how to write population growth formulas accounting for environmental heterogeneity
• how to design custom dispersal kernels

Feel free to suggest any other topic ! 👍