Diversity Contrast Test
This function performs the diversity contrast test comparing pairs of sister-clades.
diversity.contrast.test(x, method = "ratiolog", alternative = "two.sided", nrep = 0, ...)
- 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 t
- a character string specifying the kind of test:
"logratio", or any unambiguous abbreviation of these.
- a character string defining the alternative
"greater", or any unambiguous abbreviation of these.
- the number of replications of the randomization test; by default, a Wilcoxon test is done.
- arguments passed to the function
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.
nrep = 0, a Wilcoxon test is done on the species diversity
contrasts with the null hypothesis is that they are distributed around
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).
- a single numeric value with the P-value.
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.
### 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)