ape (version 4.0)

diversity.contrast.test: Diversity Contrast Test

Description

This function performs the diversity contrast test comparing pairs of sister-clades.

Usage

diversity.contrast.test(x, method = "ratiolog", alternative = "two.sided", nrep = 0, ...)

Arguments

x

a matrix or a data frame with at least two columns: the first one gives the number of species in clades with a trait supposed to increase or decrease diversification rate, and the second one the number of species in the sister-clades without the trait. Each row represents a pair of sister-clades.

method

a character string specifying the kind of test: "ratiolog" (default), "proportion", "difference", "logratio", or any unambiguous abbreviation of these.

alternative

a character string defining the alternative hypothesis: "two.sided" (default), "less", "greater", or any unambiguous abbreviation of these.

nrep

the number of replications of the randomization test; by default, a Wilcoxon test is done.

...

arguments passed to the function wilcox.test.

Value

a single numeric value with the P-value.

Details

If method = "ratiolog", the test described in Barraclough et al. (1996) is performed. If method = "proportion", the version in Barraclough et al. (1995) is used. If method = "difference", the signed difference is used (Sargent 2004). If method = "logratio", then this is Wiegmann et al.'s (1993) version. These four tests are essentially different versions of the same test (Vamosi and Vamosi 2005, Vamosi 2007). See Paradis (2012) for a comparison of their statistical performance with other tests.

If nrep = 0, a Wilcoxon test is done on the species diversity contrasts with the null hypothesis is that they are distributed around zero. If nrep > 0, a randomization procedure is done where the signs of the diversity contrasts are randomly chosen. This is used to create a distribution of the test statistic which is compared with the observed value (the sum of the diversity contrasts).

References

Barraclough, T. G., Harvey, P. H. and Nee, S. (1995) Sexual selection and taxonomic diversity in passerine birds. Proceedings of the Royal Society of London. Series B. Biological Sciences, 259, 211--215.

Barraclough, T. G., Harvey, P. H., and Nee, S. (1996) Rate of rbcL gene sequence evolution and species diversification in flowering plants (angiosperms). Proceedings of the Royal Society of London. Series B. Biological Sciences, 263, 589--591.

Paradis, E. (2012) Shift in diversification in sister-clade comparisons: a more powerful test. Evolution, 66, 288--295.

Sargent, R. D. (2004) Floral symmetry affects speciation rates in angiosperms. Proceedings of the Royal Society of London. Series B. Biological Sciences, 271, 603--608.

Vamosi, S. M. (2007) Endless tests: guidelines for analysing non-nested sister-group comparisons. An addendum. Evolutionary Ecology Research, 9, 717.

Vamosi, S. M. and Vamosi, J. C. (2005) Endless tests: guidelines for analysing non-nested sister-group comparisons. Evolutionary Ecology Research, 7, 567--579.

Wiegmann, B., Mitter, C. and Farrell, B. 1993. Diversification of carnivorous parasitic insects: extraordinary radiation or specialized dead end? American Naturalist, 142, 737--754.

See Also

slowinskiguyer.test, mcconwaysims.test richness.yule.test

Examples

### data from Vamosi & Vamosi (2005):
fleshy <- c(1, 1, 1, 1, 1, 3, 3, 5, 9, 16, 33, 40, 50, 100, 216, 393, 850, 947,1700)
dry <- c(2, 64, 300, 89, 67, 4, 34, 10, 150, 35, 2, 60, 81, 1, 3, 1, 11, 1, 18)
x <- cbind(fleshy, dry)
diversity.contrast.test(x)
diversity.contrast.test(x, alt = "g")
diversity.contrast.test(x, alt = "g", nrep = 1e4)
slowinskiguyer.test(x)
mcconwaysims.test(x)