Data Analysis Tools over Space of Phylogenetic Trees Using Tropical Geometry.
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