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
S├ębastien Ollier ollier@biomserv.univ-lyon1.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.phylog(tax.phy, clabel.l = 1.25, clabel.n = 1.25, f = 0.75)
plot.phylog(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)

Worked out examples


> library(ade4)
> ### Name: as.taxo
> ### Title: Taxonomy
> ### Aliases: as.taxo dist.taxo
> ### Keywords: manip
> 
> ### ** 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.phylog(tax.phy, clabel.l = 1.25, clabel.n = 1.25, f = 0.75)
> plot.phylog(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)
[1] TRUE
> 
> 
> 
> 

[Package ade4 Index]