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. PNAS Early Edition.

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

Shareholder quorum subsampling is used to estimate the relative magnitude of species richness. See the manual page.

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.