diffusionMap (version 1.1-0)

epsilonCompute: Compute default diffusion map epsilon.

Description

Uses the pair-wise distances to estimate a diffusion map epsilon value by the median p*n-th nearest neighbor

Usage

epsilonCompute(D, p = 0.01)

Arguments

D

n-by-n pairwise distance matrix for a data set with n points, or alternatively output from the dist() function

p

distances to p*n-th nearest neighbor are used. Default value is .01

Value

epsilon

value of epsilon to be used in diffusion map

Details

Function is used as the default value in diffuse(). For inference problems, it is advised that the results be optimized over epsilon.

See Also

diffuse

Examples

data(annulus)
D = dist(annulus) # use Euclidean distance
epsilonCompute(D,.005)
epsilonCompute(D,.01)
epsilonCompute(D,.05)
epsilonCompute(D,.1)