BinaryDistances: Binary Distances

In MultBiplotR: Multivariate Analysis Using Biplots in R

Binary Distances

Description

Calculates distances among rows of a binary data matrix or among the rows of two binary matrices. The end user will use BinaryProximities rather than this function. Input must be a matrix with 0 or 1 values.

Usage

BinaryDistances(x, y = NULL, coefficient= "Simple_Matching", transformation="sqrt(1-S)")

Arguments

x	Main binary data matrix. Distances among rows are calculated if y=NULL.
y	Second binary data matrix. If not NULL the distances among the rows of x and y are calculated
coefficient	Similarity coefficient. Use the name (see details)
transformation	Transformation of the similarities. Use the name (see details)

Details

The following coefficients are calculated

1.- Kulezynski = a/(b + c)

2.- Russell_and_Rao = a/(a + b + c+d)

3.- Jaccard = a/(a + b + c)

4.- Simple_Matching = (a + d)/(a + b + c + d)

5.- Anderberg = a/(a + 2 * (b + c))

6.- Rogers_and_Tanimoto = (a + d)/(a + 2 * (b + c) + d)

7.- Sorensen_Dice_and_Czekanowski = a/(a + 0.5 * (b + c))

8.- Sneath_and_Sokal = (a + d)/(a + 0.5 * (b + c) + d)

9.- Hamman = (a - (b + c) + d)/(a + b + c + d)

10.- Kulezynski = 0.5 * ((a/(a + b)) + (a/(a + c)))

11.- Anderberg2 = 0.25 * (a/(a + b) + a/(a + c) + d/(c + d) + d/(b + d))

12.- Ochiai = a/sqrt((a + b) * (a + c))

13.- S13 = (a * d)/sqrt((a + b) * (a + c) * (d + b) * (d + c))

14.- Pearson_phi = (a * d - b * c)/sqrt((a + b) * (a + c) * (d + b) * (d + c))

15.- Yule = (a * d - b * c)/(a * d + b * c)

The following transformations of the similarity3 are calculated

1.- 'Identity' dis=sim

2.- '1-S' dis=1-sim

3.- 'sqrt(1-S)' dis = sqrt(1 - sim)

4.- '-log(s)' dis=-1*log(sim)

5.- '1/S-1' dis=1/sim -1

6.- 'sqrt(2(1-S))' dis== sqrt(2*(1 - sim))

7.- '1-(S+1)/2' dis=1-(sim+1)/2

8.- '1-abs(S)' dis=1-abs(sim)

9.- '1/(S+1)' dis=1/(sim)+1

Value

An object of class proximities.This has components:

comp1

Description of 'comp1'

Author(s)

Jose Luis Vicente-Villardon

References

Gower, J. C. (2006) Similarity dissimilarity and Distance, measures of. Encyclopedia of Statistical Sciences. 2nd. ed. Volume 12. Wiley

See Also

PrincipalCoordinates

Examples

data(spiders)

MultBiplotR documentation built on Nov. 21, 2023, 5:08 p.m.