troppca.poly: Tropical Principal Component Analysis by Tropical Polytope

In HoujieWang/Rtropical: Data Analysis Tools over Space of Phylogenetic Trees Using Tropical Geometry

Tropical Principal Component Analysis by Tropical Polytope

Description

Approximates the principal component as a tropical polytope for a given data matrix via MCMC and return the results as an object of class troppca.

Usage

troppca.poly(x, pcs = 2, nsample = 1000, ncores = 2)

Arguments

x	a data matrix, of size n x e, with each row an observation vector. e is the dimension of the tropical space#'
pcs	a numeric value indicating the order of principal component. (default: 2)
nsample	a numeric value indicating the number of samples of MCMC. (default: 1000)
ncores	a numeric value indicating the number of threads utilized for multi-cored CPUs. (default: 2)

Value

A list of S3 class "troppca", including:

pc	The principal component as a tropical linear space
obj	The tropical PCA objective, the sum of tropical distance from each point to the projection.
projection	The projections of all data points.
type	The geometry of principal component.

Examples

library(Rfast)
n <- 50
e <- 50
s <- 5
x <- rbind(
  rmvnorm(n, mu = c(5, -5, rep(0, e - 2)), sigma = diag(s, e)),
  rmvnorm(n, mu = c(-5, 5, rep(0, e - 2)), sigma = diag(s, e))
)
troppca_fit <- troppca.poly(x)
plot(troppca_fit)

HoujieWang/Rtropical documentation built on May 18, 2022, 11:56 a.m.