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 *λ _{5}* 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). My by-reference SQS function uses the randomization algorithm I proposed in 2014 (see p. 389).

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.

--------. 2014. Accurate and precise estimates of origination and extinction rates. *Paleobiology* 40:374-397.