Offer: add LTT, nLTT and nLTT statistic

richelbilderbeek commented 7 years ago

Dear Bio++,

For a scientific problem, me and my students developed classes LTT (lineages through time) and nLTT (normalized LTT) and unit tests, with the goal of using the nLTT statistic (from [1]) in C++.

I'd love to add this work to Bio++ and maintain it, if I have a go.

Cheers, Richel Bilderbeek

References

[1] Janzen, Thijs, Sebastian Höhna, and Rampal S. Etienne. "Approximate Bayesian computation of diversification rates from molecular phylogenies: introducing a new efficient summary statistic, the nLTT." Methods in Ecology and Evolution 6.5 (2015): 566-575. link
[2] Ibeh N., Aris-Brosou S. Estimation of sub-epidemic dynamics by means of Sequential Monte Carlo Approximate Bayesian Computation: an application to the Swiss HIV Cohort Study. bioRxiv (2016): 085993. link
[3] McCloskey, Rosemary M., Richard H. Liang, and Art FY Poon. Reconstructing contact network parameters from viral phylogenies. bioRxiv (2016): 050435. link
[4] Giardina, F., Romero-Severson, E. O., Albert, J., Britton, T., & Leitner, T. K. Inference of transmission network structure from HIV phylogenetic trees. bioRxiv (2016): 059865. link

jydu commented 7 years ago

Dear Richel,

This looks interesting! We'd be happy to consider a pull request.

J.

richelbilderbeek commented 6 years ago

Indeed, this got a bit outdated (as most of my work moved to R now). Thanks for closing :+1:

BioPP / bpp-phyl

Offer: add LTT, nLTT and nLTT statistic #5

References