nd.him | R Documentation |
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.
nd.him(A, out.dist = TRUE, xi = 1, ntest = 10)
A |
a list of length |
out.dist |
a logical; |
xi |
a parameter to control balance between two distances. |
ntest |
the number of searching over |
a named list containing
an (N\times N)
matrix or dist
object containing pairwise distance measures.
jurman_him_2015NetworkDistance
nd.hamming
, nd.csd
## 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)
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