originality {ade4}R Documentation

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 7.

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 6 = Isaac et al. (2007) ED index 7 = Redding et al. (2006) Equal-split index

Value

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

Author(s)

Sandrine Pavoine pavoine@biomserv.univ-lyon1.fr

References

Isaac, N.J.B., Turvey, S.T., Collen, B., Waterman, C. and Baillie, J.E.M. (2007) Mammals on the EDGE: conservation priorities based on threat and phylogeny. PloS ONE, 2, e–296.

Redding, D. and Mooers, A. (2006) Incorporating evolutionary measures into conservation prioritization. Conservation Biology, 20, 1670–1678.

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. and 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, 1:7)
names(ori.tab)
dotchart.phylog(carni70.phy, ori.tab, scaling = FALSE, yjoining = 0, 
    ranging = FALSE, cleaves = 0, ceti = 0.5, csub = 0.7, cdot = 0.5)

Worked out examples


> library(ade4)
> ### Name: originality
> ### Title: Originality of a species
> ### Aliases: originality
> ### Keywords: multivariate
> 
> ### ** Examples
> 
> data(carni70)
> carni70.phy <- newick2phylog(carni70$tre)
> ori.tab <- originality(carni70.phy, 1:7)
> names(ori.tab)
[1] "VW"      "M"       "NWU*"    "NWW"     "QEbased" "ED"      "eqsplit"
> dotchart.phylog(carni70.phy, ori.tab, scaling = FALSE, yjoining = 0, 
+     ranging = FALSE, cleaves = 0, ceti = 0.5, csub = 0.7, cdot = 0.5)
> 
> 
> 
> 

[Package ade4 Index]