R: Taxonomy

as.taxo {ade4} | R Documentation

## Taxonomy

### Description

The function `as.taxo` creates an object of class `taxo` that is a sub-class of `data.frame`. Each column of the data frame must be a factor corresponding to a level j of the taxonomy (genus, family, ...). The levels of factor j define some classes that must be completly included in classes of factor j+1.
A factor with exactly one level is not allowed. A factor with exactly one individual in each level is not allowed. The function `dist.taxo` compute taxonomic distances.

### Usage

    as.taxo(df)
    dist.taxo(taxo)

### Arguments

`df` | a data frame
`taxo` | a data frame of class `taxo`

### Value

`as.taxo` returns a data frame of class `taxo`. `dist.taxo` returns a numeric of class `dist`.

### Author(s)

Daniel Chessel
Sébastien Ollier sebastien.ollier@u-psud.fr

### See Also

`taxo2phylog` to transform an object of class `taxo` into an object of class `phylog`

### Examples

    data(taxo.eg)
    tax <- as.taxo(taxo.eg[[1]])
    tax.phy <- taxo2phylog(as.taxo(taxo.eg[[1]]),add.tools=TRUE)
    par(mfrow = c(1,2))
    plot(tax.phy, clabel.l = 1.25, clabel.n = 1.25, f = 0.75)
    plot(taxo2phylog(as.taxo(taxo.eg[[1]][sample(15),])),
     clabel.l = 1.25, clabel.n = 1.25, f = 0.75)
    par(mfrow = c(1,1))
    all(dist.taxo(tax)==tax.phy$Wdist)

[Package ade4 version 1.7-19 Index]