R: Computation of Distance Matrices for Binary Data

dist.binary {ade4}

R Documentation

Computation of Distance Matrices for Binary Data

Description

computes for binary data some distance matrice.

Usage

dist.binary(df, method = NULL, diag = FALSE, upper = FALSE)

Arguments

`df`	a matrix or a data frame with positive or null numeric values. Used with `as.matrix(1 * (df > 0))`
`method`	an integer between 1 and 10 . If NULL the choice is made with a console message. See details
`diag`	a logical value indicating whether the diagonal of the distance matrix should be printed by ‘print.dist’
`upper`	a logical value indicating whether the upper triangle of the distance matrix should be printed by ‘print.dist’

Details

Let be the contingency table of binary data such as n11 = a, n10 = b, n01 = c and n00 = d. All these distances are of type d = sqrt(1 - s) with s a similarity coefficient.

1 = Jaccard index (1901): S3 coefficient of Gower & Legendre s1 = a / (a+b+c)
2 = Sockal & Michener index (1958): S4 coefficient of Gower & Legendre s2 = (a+d) / (a+b+c+d)
3 = Sockal & Sneath(1963): S5 coefficient of Gower & Legendre s3 = a / (a + 2(b + c))
4 = Rogers & Tanimoto (1960): S6 coefficient of Gower & Legendre s4 = (a + d) / (a + 2(b + c) +d)
5 = Czekanowski (1913) or Sorensen (1948): S7 coefficient of Gower & Legendre s5 = 2a / (2a + b + c)
6 = S9 index of Gower & Legendre (1986): s6 = (a - (b + c) + d) / (a + b + c + d)
7 = Ochiai (1957): S12 coefficient of Gower & Legendre s7 = a / sqrt((a + b)(a + c))
8 = Sockal & Sneath (1963): S13 coefficient of Gower & Legendre s8 = ad / sqrt((a + b)(a + c)(d + b)(d + c))
9 = Phi of Pearson: S14 coefficient of Gower & Legendre s9 = (ad - bc) / sqrt((a + b)(a + c)(d + b)(d + c))
10 = S2 coefficient of Gower & Legendre: s10 = a / (a + b + c + d)

Value

returns a distance matrix of class dist between the rows of the data frame

Author(s)

Daniel Chessel
Stéphane Dray dray@biomserv.univ-lyon1.fr

References

Gower, J.C. and Legendre, P. (1986) Metric and Euclidean properties of dissimilarity coefficients. Journal of Classification, 3, 5–48.

Examples

data(aviurba)
for (i in 1:10) {
    d <- dist.binary(aviurba$fau, method = i)
    cat(attr(d, "method"), is.euclid(d), "\n")}

Worked out examples


> library(ade4)
> ### Name: dist.binary
> ### Title: Computation of Distance Matrices for Binary Data
> ### Aliases: dist.binary
> ### Keywords: array multivariate
> 
> ### ** Examples
> 
> data(aviurba)
> for (i in 1:10) {
+     d <- dist.binary(aviurba$fau, method = i)
+     cat(attr(d, "method"), is.euclid(d), "\n")}
JACCARD S3 TRUE 
SOCKAL & MICHENER S4 TRUE 
SOCKAL & SNEATH S5 TRUE 
ROGERS & TANIMOTO S6 TRUE 
CZEKANOWSKI S7 TRUE 
GOWER & LEGENDRE S9 TRUE 
OCHIAI S12 TRUE 
SOKAL & SNEATH S13 TRUE 
Phi of PEARSON S14 TRUE 
GOWER & LEGENDRE S2 TRUE 
> 
> 
> 
>

[Package ade4 Index]