dist.prop {ade4} R Documentation

## Computation of Distance Matrices of Percentage Data

### Description

computes for percentage data some distance matrices.

### Usage

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

### Arguments

 `df` a data frame containing only positive or null values, used as row percentages `method` an integer between 1 and 5. 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

1 = Manly
d1 = sum|p(i) - q(i)|/2
2 = Overlap index Manly
d2 = 1 - Sum(p(i)q(i))/sqrt(Sum(p(i)^2))/sqrt(Sum(q(i)^2))
3 = Rogers 1972 (one locus)
d3 = sqrt(0.5*Sum(p(i)-q(i)^2))
4 = Nei 1972 (one locus)
d4 = -ln(Sum(p(i)q(i))/sqrt(Sum(p(i)^2))/sqrt(Sum(q(i)^2)))
5 = Edwards 1971 (one locus)
d5= sqrt (1 - (Sum(sqrt(p(i)q(i)))))

### Value

returns a distance matrix, object of class `dist`

### Author(s)

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

### References

Edwards, A. W. F. (1971) Distance between populations on the basis of gene frequencies. Biometrics, 27, 873–881.

Manly, B. F. (1994) Multivariate Statistical Methods. A primer., Second edition. Chapman & Hall, London.

Nei, M. (1972) Genetic distances between populations. The American Naturalist, 106, 283–292.

### Examples

```data(microsatt)
w <- microsatt\$tab[1:microsatt\$loci.eff[1]]
par(mfrow = c(2,2))
scatter(dudi.pco(lingoes(dist.prop(w,1)), scann = FALSE))
scatter(dudi.pco(lingoes(dist.prop(w,2)), scann = FALSE))
scatter(dudi.pco(dist.prop(w,3), scann = FALSE))
scatter(dudi.pco(lingoes(dist.prop(w,4)), scann = FALSE))
par(mfrow = c(1,1))```

### Worked out examples

```
> ### Name: dist.prop
> ### Title: Computation of Distance Matrices of Percentage Data
> ### Aliases: dist.prop
> ### Keywords: array multivariate
>
> ### ** Examples
>
> data(microsatt)
> w <- microsatt\$tab[1:microsatt\$loci.eff[1]]
> par(mfrow = c(2,2))
> scatter(dudi.pco(lingoes(dist.prop(w,1)), scann = FALSE))
```
```> scatter(dudi.pco(lingoes(dist.prop(w,2)), scann = FALSE))
```
```> scatter(dudi.pco(dist.prop(w,3), scann = FALSE))
```
```> scatter(dudi.pco(lingoes(dist.prop(w,4)), scann = FALSE))
```
```> par(mfrow = c(1,1))
>
>
>
```