epsilonCompute {diffusionMap} R Documentation

## 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

### Details

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

### Value

 epsilon  value of epsilon to be used in diffusion map

diffuse()

### Examples

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


[Package diffusionMap version 1.2.0 Index]