nd_him() R function from [NetworkDistance]

HIM Distance

Hamming-Ipsen-Mikhailov (HIM) combines the local Hamming edit distance and the global Ipsen-Mikhailov distance to merge information at each scale. For Ipsen-Mikhailove distance, it is provided as nd.csd in our package for consistency. Given a parameter $\xi$ (xi), it is defined as [REMOVE_ME] $HIM_{\xi}(A,B)=\sqrt{H^2(A,B)+\xi\cdot IM^2(A,B)}/\sqrt{1+\xi} [REMOVE_ME_2]$

where $H$ and $IM$ stand for Hamming and I-M distance, respectively.


nd.him(A, out.dist = TRUE, xi = 1, ntest = 10)

Arguments

A: a list of length $N$ containing $(M\times M)$ adjacency matrices.
out.dist: a logical; TRUE for computed distance matrix as a dist object.
xi: a parameter to control balance between two distances.
ntest: the number of searching over nd.csd parameter.

Returns

a named list containing

D: an $(N\times N)$ matrix or dist object containing pairwise distance measures.

Description

HIM_{\xi}(A,B)=\sqrt{H^2(A,B)+\xi\cdot IM^2(A,B)}/\sqrt{1+\xi}

where $H$ and $IM$ stand for Hamming and I-M distance, respectively.

Examples


## load example data
data(graph20)

## compute distance matrix
output = nd.him(graph20, out.dist=FALSE)

## visualize
opar = par(no.readonly=TRUE)
par(pty="s")
image(output$D[,20:1], main="two group case", axes=FALSE, col=gray(0:32/32))
par(opar)

References

Rdpack::insert_ref(key="jurman_him_2015",package="NetworkDistance")

nd_him function