perfectphyloR (version 0.2.1)

HHGtest: HHG test for association of two distance matrices

Description

This function performs HHG test to find the association between two distance matrices. It permutes rows and columns of the second matrix randomly to calculate P value.

Usage

HHGtest(Dx, Dy, nperm)

Arguments

Dx

A numeric matrix of pairwise distances.

Dy

A second numeric matrix of pairwise distances.

nperm

The number of times to permute the rows and columns of Dy.

Value

A list contains HHG coefficient and permutation P value.

References

Barak, B., and Shachar, K., based in part on an earlier implementation by Ruth Heller and Yair Heller. (2017). HHG: Heller-Heller-Gorfine Tests of Independence and Equality of Distributions. R package version 2.2. https://CRAN.R-project.org/package=HHG

Examples

# NOT RUN {
x <- runif(8)
y <- runif(8)
# Distance matrices
distX = as.matrix(dist(x, upper = TRUE, diag = TRUE))
distY = as.matrix(dist(y, upper = TRUE, diag = TRUE))

HHGtest(Dx = distX, Dy = distY, nperm = 1000) 

# }