optimEH {ade4}R Documentation

Nee and May's optimizing process

Description

performs Nee and May's optimizing scheme. When branch lengths in an ultrametric phylogenetic tree are expressed as divergence times, the total sum of branch lengths in that tree expresses the amount of evolutionary history. Nee and May's algorithm optimizes the amount of evolutionary history preserved if only k species out of n were to be saved. The k-1 closest-to-root nodes are selected, which defines k clades; one species from each clade is picked. At this last step, we decide to select the most original species of each from the k clades.

Usage

optimEH(phyl, nbofsp, tol = 1e-8, give.list = TRUE) 

Arguments

phyl an object of class phylog
nbofsp an integer indicating the number of species saved (k).
tol a tolerance threshold for null values (a value less than tol in absolute terms is considered as NULL).
give.list logical value indicating whether a list of optimizing species should be provided. If give.list = TRUE, optimEH provides the list of the k species which optimize the amount of evolutionary history preserved and are the most original species in their clades. If give.list = FALSE, optimEH returns directly the real value giving the amount of evolutionary history preserved.

Value

Returns a list containing:
value a real value providing the amount of evolutionary history preserved.
selected.sp a data frame containing the list of the k species which optimize the amount of evolutionary history preserved and are the most original species in their clades.

Author(s)

Sandrine Pavoine pavoine@biomserv.univ-lyon1.fr

References

Nee, S. and May, R.M. (1997) Extinction and the loss of evolutionary history. Science 278, 692–694.

Pavoine, S., Ollier, S. and Dufour, A.-B. (2005) Is the originality of a species measurable? Ecology Letters, 8, 579–586.

See Also

randEH

Examples

data(carni70)
carni70.phy <- newick2phylog(carni70$tre)
optimEH(carni70.phy, nbofsp = 7, give.list = TRUE) 

Worked out examples


> library(ade4)
> ### Name: optimEH
> ### Title: Nee and May's optimizing process
> ### Aliases: optimEH
> ### Keywords: multivariate
> 
> ### ** Examples
> 
> data(carni70)
> carni70.phy <- newick2phylog(carni70$tre)
> optimEH(carni70.phy, nbofsp = 7, give.list = TRUE) 
$value
[1] 256.1

$selected.sp
                                           names
1       Puma_concolor OR Herpailurus_yaguaroundi
2                       Urocyon_cinereoargenteus
3                             Tremarctos_ornatus
4                                   Potos_flavus
5 Bassariscus_sumichrasti OR Bassariscus_astutus
6                                  Taxidea_taxus
7                                  Mustela_vison

> 
> 
> 
> 

[Package ade4 Index]