Data Analysis Tools over Space of Phylogenetic Trees Using Tropical Geometry

Process phylogenetic trees with tropical support vector machine and principal component analysis defined with tropical geometry. Details about tropical support vector machine are available in : Tang, X., Wang, H. & Yoshida, R. (2020) . Details about tropical principle component analysis are available in : Page, R., Yoshida, R. & Zhang L. (2020) and Yoshida, R., Zhang, L. & Zhang, X. (2019) .

Tropical Data Analysis Tools

Algorithms of tropical support vector machine and principals component analysis defined in tropical projective spaces.

Installation

This package can be installed directly from Github by running

devtools::install_github("HoujieWang/Rtropical")

Usage

Please check the vignette for a breif example.

Reference

Tang, X., Wang, H. & Yoshida, R. Tropical Support Vector Machine and its Applications to Phylogenomics https://arxiv.org/abs/2003.00677

Page, R., Yoshida, R. & Zhang L. Tropical Principal Component Analysis on the Space of Phylogenetic Trees. J. Bioinform., Volume 36, Issue 17, 4590–4598 (2020). https://doi.org/10.1093/bioinformatics/btaa564

Yoshida, R., Zhang, L. & Zhang, X. Tropical Principal Component Analysis and Its Application to Phylogenetics. Bull Math Biol 81, 568–597 (2019). https://doi.org/10.1007/s11538-018-0493-4