In RobinHankin/hyper2: The Hyperdirichlet Distribution, Mark 2

set.seed(0)
knitr::opts_chunk$set(echo = TRUE)
library("hyper2")
library("magrittr")
library("ape")
library("phangorn")
options("digits" = 5)

knitr::include_graphics(system.file("help/figures/hyper2.png", package = "hyper2"))

To cite the hyper2 package in publications, please use @hankin2017_rmd. This file presents some speculative experimental work which is under development. Do not confuse this file with icons.Rmd, which creates the icons objects in the package.

icons
icons_maxp <- sort(icons_maxp,decreasing=TRUE)  # sort in decreasing order
icons_maxp

Recall samep.test():

samep.test(icons,c("NB","THC"))

I will calculate all pairwise distances between the icons, as measured by the support difference [penultimate line of the output above, named statistic in the object for consistency with other tests in R]

M <- matrix(0,6,6)
p <- names(icons_maxp)
rownames(M) <- p
colnames(M) <- p
for(i in seq_len(6)){
  for(j in seq_len(6)){
    if(i != j){M[i,j] <- samep.test(icons,p[c(i,j)])$statistic}
  }
}