NetworkDistance (version 0.3.6)

nd.him: HIM Distance

Description

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 $$HIM_{\xi}(A,B)=\sqrt{H^2(A,B)+\xi\cdot IM^2(A,B)}/\sqrt{1+\xi}$$ where \(H\) and \(IM\) stand for Hamming and I-M distance, respectively.

Usage

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

Value

a named list containing

D

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

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.

References

jurman_him_2015NetworkDistance

See Also

nd.hamming, nd.csd

Examples

# \donttest{
## 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)
# }