diffusionMap: epsilonCompute – R documentation

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epsilonCompute

Compute default diffusion map epsilon.

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

epsilonCompute(D, p = 0.01)

`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

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

epsilon

value of epsilon to be used in diffusion map

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

Diffusion Map

v1.2.0

GPL-3

Authors

Joseph Richards [aut] (joeyrichar), Robrecht Cannoodt [aut, cre] (<https://orcid.org/0000-0003-3641-729X>, rcannood)

Initial release