orisaved {ade4}R Documentation

Maximal or minimal amount of originality saved under optimal conditions

Description

computes the maximal or minimal amount of originality saved over all combinations of species optimizing the amount of evolutionary history preserved. The originality of a species is measured with the QE-based index.

Usage

orisaved(phyl, rate = 0.1, method = 1)

Arguments

phyl an object of class phylog
rate a real value (between 0 and 1) indicating how many species will be saved for each calculation. For example, if the total number of species is 70 and 'rate = 0.1' then the calculations will be done at a rate of 10 % i.e. for 0 (= 0 %), 7 (= 10 %), 14 (= 20 %), 21 (= 30 %), ..., 63 (= 90 %) and 70(= 100 %) species saved. If 'rate = 0.5' then the calculations will be done for only 0 (= 0 %), 35 (= 50 %) and 70(= 100 %) species saved.
method an integer either 1 or 2 (see details).

Details

1 = maximum amount of originality saved 2 = minimum amount of originality saved

Value

Returns a numeric vector.

Author(s)

Sandrine Pavoine pavoine@biomserv.univ-lyon1.fr

References

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

Examples

data(carni70)
carni70.phy <- newick2phylog(carni70$tre)
tmax <- orisaved(carni70.phy, rate = 1 / 70, method = 1) 
tmin <- orisaved(carni70.phy, rate = 1 / 70, method = 2) 
plot(c(0, 1:70), tmax, xlab = "nb of species saved", ylab = "Originality saved", type = "l") 
lines(c(0, 1:70), tmin, lty = 2) 

Worked out examples


> library(ade4)
> ### Name: orisaved
> ### Title: Maximal or minimal amount of originality saved under optimal
> ###   conditions
> ### Aliases: orisaved
> ### Keywords: multivariate
> 
> ### ** Examples
> 
> data(carni70)
> carni70.phy <- newick2phylog(carni70$tre)
> tmax <- orisaved(carni70.phy, rate = 1 / 70, method = 1) 
> tmin <- orisaved(carni70.phy, rate = 1 / 70, method = 2) 
> plot(c(0, 1:70), tmax, xlab = "nb of species saved", ylab = "Originality saved", type = "l") 
> lines(c(0, 1:70), tmin, lty = 2) 
> 
> 
> 
> 

[Package ade4 Index]