ade4 (version 1.4-3)

originality: Originality of a species

Description

computes originality values for species from an ultrametric phylogenetic tree.

Usage

originality(phyl, method = 5)

Arguments

phyl

an object of class phylog

method

a vector containing integers between 1 and 5.

Value

• Returns a data frame with species in rows, and the selected indices of originality in columns. Indices are expressed as percentages.

Details

1 = Vane-Wright et al.'s (1991) node-counting index 2 = May's (1990) branch-counting index 3 = Nixon and Wheeler's (1991) unweighted index, based on the sum of units in binary values 4 = Nixon and Wheeler's (1991) weighted index 5 = QE-based index

References

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

Vane-Wright, R.I., Humphries, C.J. and Williams, P.H. (1991). What to protect? Systematics and the agony of choice. Biological Conservation, 55, 235--254.

May, R.M. (1990). Taxonomy as destiny. Nature, 347, 129--130.

Nixon, K.C. & Wheeler, Q.D. (1992). Measures of phylogenetic diversity. In: Extinction and Phylogeny (eds. Novacek, M.J. and Wheeler, Q.D.), 216--234, Columbia University Press, New York.

Examples

data(carni70)
carni70.phy <- newick2phylog(carni70$tre)
ori.tab <- originality(carni70.phy, 1:5)
names(ori.tab)
dotchart.phylog(carni70.phy, ori.tab, scaling=FALSE, yjoining=0, 
    cleaves=0, ceti=0.5, csub=0.7, cdot=0.5)