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, ...)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:
|
alternative |
a character string defining the alternative
hypothesis: |
nrep |
the number of replications of the randomization test; by default, a Wilcoxon test is done. |
... |
arguments passed to the function
|
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).
a single numeric value with the P-value.
Emmanuel Paradis
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)
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