Macroecology and macroevolution
Macquarie University
Analytical methods

See the bottom of the home page for a full list.

The agnostic equation is a method for inferring extinction from sighting data (of any kind). Try the R function if you're interested.

Alroy, J. 2015. Current extinction rates of reptiles and amphibians. Proceedings of the National Academy of Sciences, USA 112:13003-13008. DOI 10.1073/pnas.1508681112

The double geometric distribution can be fit using the R function fitDoubleGeometric, which is to be found in a file with multiple distribution fitting algorithms. Important notes: (1) fitDoubleGeometric is not guaranteed to find the best solution, so running it repeatedly is recommended. (2) The version of fitLogNormal used in the paper included a bug that made fits too optimistic. In other words, the log normal is even worse than reported. (3) The file also includes a new, faster, better version of fitLogSeries.

Alroy, J. 2015. The shape of terrestrial abundance distributions. Science Advances 1:e1500082.

A revised version of the Forbes index is a useful way to measure similarity between species lists. See the manual page.

Alroy, J. 2015. A new twist on a very old binary similarity coefficient. Ecology 96(2):575-586.

--------. 2015. A simple way to improve multivariate analyses of paleoecological data sets. Paleobiology 41(3):377-386. DOI: 10.1017/pab.2014.21

The λ5 richness estimator uses counts of individuals, species, and species found once (= singletons) to extrapolate the true number of species found in a community. Try out the R function on an abundance distribution.

Alroy, J. 2017. Effects of habitat disturbance on tropical forest biodiversity. Proceedings of the National Academy of Sciences, USA. DOI: 10.1073/pnas.1611855114

Multiton subsampling estimates richness at a target level of sampling completeness, as defined by comparing counts of individuals, species, and singletons. Another R function implements it.

Alroy, J. 2017. Effects of habitat disturbance on tropical forest biodiversity. Proceedings of the National Academy of Sciences, USA. DOI: 10.1073/pnas.1611855114

Shareholder quorum subsampling is used to estimate the relative magnitude of species richness. The R function uses the exact analytical equations of Chao and Jost (2012).

Alroy, J. 2010a. The shifting balance of diversity among major marine animal groups. Science 329:1191-1194.

--------. 2010b. Fair sampling of taxonomic richness and unbiased estimation of origination and extinction rates. In J. Alroy and G. Hunt (eds.), Quantitative Methods in Paleobiology. Paleontological Society Papers 16:55-80.

--------. 2010c. Geographical, environmental and intrinsic biotic controls on Phanerozoic marine diversification. Palaeontology 53:1211-1235.