rdist: rdist: an R package for distances

In rdist: Calculate Pairwise Distances

Description

rdist provide a common framework to calculate distances. There are three main functions:

• rdist computes the pairwise distances between observations in one matrix and returns a dist object,

• pdist computes the pairwise distances between observations in one matrix and returns a matrix, and

• cdist computes the distances between observations in two matrices and returns a matrix.

In particular the cdist function is often missing in other distance functions. All calculations involving NA values will consistently return NA.

Usage

rdist(X, metric = "euclidean", p = 2L)

pdist(X, metric = "euclidean", p = 2)

cdist(X, Y, metric = "euclidean", p = 2)

Arguments

X, Y	A matrix
metric	The distance metric to use
p	The power of the Minkowski distance

Details

Available distance measures are (written for two vectors v and w):

• "euclidean": sqrt(sum_i((v_i - w_i)^2))

• "minkowski": (sum_i(|v_i - w_i|^p))^{1/p}

• "manhattan": sum_i(|v_i-w_i|)

• "maximum" or "chebyshev": max_i(|v_i-w_i|)

• "canberra": sum_i(|v_i-w_i|/(|v_i|+|w_i|))

• "angular": arccos(cor(v, w))

• "correlation": sqrt((1-cor(v, w))/2)

• "absolute_correlation": sqrt((1-|cor(v, w)|^2))

• "hamming": sum_i(v_i != w_i)/sum_i(1)

• "jaccard": sum_i(v_i != w_i)/sum_i(v_i != 0 or w_i != 0)

• Any function that defines a distance between two vectors.

rdist documentation built on May 4, 2020, 5:13 p.m.