Data Analysis Tools over Space of Phylogenetic Trees Using Tropical Geometry
Vectorize a Set of Phylognetic Trees
Vectorize a Phylogenetic Tree
Efficient Finder of Best Assignment
Extract Optimal Tropical Hyperplane from a cv.tropsvm object
Extract Optimal Tropical Hyperplane from a tropsvm object
Cross-Validation for Tropical Support Vector Machines
Tropical Determinants for Small Matrices
Convert Tropical Linear Space to Convex Hull
Plot the Tropical Principal Components with Data Projections
Dimension Reduction by Isometry
Predict Method for Tropical Support Vector Machines based on Cross-Val...
Predict Method for Tropical Support Vector Machines
Read NEXUS-formatted trees from two categories into a data matrix
Read Newick-formatted trees in two categories into a data matrix
Summarize an Analysis of Cross-Validated Tropical Support Vector Machi...
Tropical Determinant of a Matrix
Tropical Fermat-Weber Point
Tropical Principal Component Analysis by Tropical Linear Space
Tropical Principal Component Analysis by Polytope Converted from Linea...
Compute Tropical PCA Objective
Tropical Principal Component Analysis by Tropical Polytope
Projection on Tropical Linear Space
Projection on Tropical Polytope
Compute Tropical Line Segment
Tropical Support Vector Machines
Helper for cv.tropsvm
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) <arXiv:2003.00677>. Details about tropical principle component analysis are available in : Page, R., Yoshida, R. & Zhang L. (2020) <doi:10.1093/bioinformatics/btaa564> and Yoshida, R., Zhang, L. & Zhang, X. (2019) <doi:10.1007/s11538-018-0493-4>.