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.
as.taxo(df) dist.taxo(taxo)
df |
a data frame |
taxo |
a data frame of class |
as.taxo returns a data frame of class taxo.
dist.taxo returns a numeric of class dist.
Daniel Chessel
Sébastien Ollier sebastien.ollier@u-psud.fr
taxo2phylog to transform an object of class taxo into an object of class phylog
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)
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