taxo.eg {ade4}R Documentation

Examples of taxonomy

Description

This data sets contains two taxonomies.

Usage

data(taxo.eg)

Format

taxo.eg is a list containing the 2 following objects:

taxo.eg[[1]]
is a data frame with 15 species and 3 columns.
taxo.eg[[2]]
is a data frame with 40 species and 2 columns.

Details

Variables of the first data frame are : genre (a factor genre with 8 levels), famille (a factor familiy with 5 levels) and ordre (a factor order with 2 levels).

Variables of the second data frame are : gen(a factor genre with 29 levels), fam (a factor family with 19 levels).

Examples

data(taxo.eg)
taxo.eg[[1]]
as.taxo(taxo.eg[[1]])
class(taxo.eg[[1]])
class(as.taxo(taxo.eg[[1]]))

tax.phy <- taxo2phylog(as.taxo(taxo.eg[[1]]),  add.tools = TRUE)
plot.phylog(tax.phy,clabel.l=1)

par(mfrow = c(1,2))
table.phylog(tax.phy$Bindica,tax.phy)
table.phylog(tax.phy$Bscores,tax.phy)
par(mfrow = c(1,1))

radial.phylog(taxo2phylog(as.taxo(taxo.eg[[2]])))

Worked out examples


> library(ade4)
> ### Name: taxo.eg
> ### Title: Examples of taxonomy
> ### Aliases: taxo.eg
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(taxo.eg)
> taxo.eg[[1]]
      genre famille ordre
esp8     g2    fam2  ORD2
esp3     g1    fam1  ORD1
esp1     g1    fam1  ORD1
esp2     g1    fam1  ORD1
esp4     g1    fam1  ORD1
esp14    g8    fam5  ORD2
esp15    g8    fam5  ORD2
esp9     g3    fam2  ORD2
esp13    g7    fam4  ORD2
esp12    g6    fam4  ORD2
esp11    g5    fam3  ORD2
esp10    g4    fam3  ORD2
esp5     g1    fam1  ORD1
esp6     g1    fam1  ORD1
esp7     g1    fam1  ORD1
> as.taxo(taxo.eg[[1]])
      genre famille ordre
esp3     g1    fam1  ORD1
esp1     g1    fam1  ORD1
esp2     g1    fam1  ORD1
esp4     g1    fam1  ORD1
esp5     g1    fam1  ORD1
esp6     g1    fam1  ORD1
esp7     g1    fam1  ORD1
esp8     g2    fam2  ORD2
esp9     g3    fam2  ORD2
esp10    g4    fam3  ORD2
esp11    g5    fam3  ORD2
esp12    g6    fam4  ORD2
esp13    g7    fam4  ORD2
esp14    g8    fam5  ORD2
esp15    g8    fam5  ORD2
> class(taxo.eg[[1]])
[1] "data.frame"
> class(as.taxo(taxo.eg[[1]]))
[1] "data.frame" "taxo"      
> 
> tax.phy <- taxo2phylog(as.taxo(taxo.eg[[1]]),  add.tools = TRUE)
> plot.phylog(tax.phy,clabel.l=1)
> 
> par(mfrow = c(1,2))
> table.phylog(tax.phy$Bindica,tax.phy)
> table.phylog(tax.phy$Bscores,tax.phy)
> par(mfrow = c(1,1))
> 
> radial.phylog(taxo2phylog(as.taxo(taxo.eg[[2]])))
> 
> 
> 
> 

[Package ade4 Index]