Taxonomy

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

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)
#> [1] TRUE