R: Maximal or minimal amount of originality saved under optimal...

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@mnhn.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)

[Package ade4 version 1.7-8 Index]