orisaved {adiv}

Maximal or Minimal Amount of Originality Saved under Optimal Conditions

Description

Function orisaved 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 (Pavoine et al. 2005).

Usage

orisaved(phyl, rate = 0.1, method = 1:2)

Arguments

phyl

an object inheriting the class phylo (see package ape), phylo4 (see package phylobase) or hclust.

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 [e-mail] with contributions of Stephane Dray

References

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

See Also

optimEH, randEH

Examples

## Not run: 
if(require(ape) && require(adephylo)){

data(carni70, package="adephylo")
tre <- read.tree(text=carni70$tre)
tmax <- adiv:::orisaved(tre, rate = 1 / 70, method = 1) 
tmin <- adiv:::orisaved(tre, 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) 

}

## End(Not run)