R code associated with the pre-print "No evidence for angiosperm mass extinction at the Cretaceous–Paleogene (K-Pg) boundary"
This code requires the trees available from Igea and Tanentzap (2020) which corrects taxonomy of Smith and Brown (2018), and Qian and Jin (2015) which extends taxonomic coverage of Zanne et al. (2013). Non-angiosperm lineages need to be pruned, and trees need to be corrected with force.ultrametric() from phytools. This code runs CoMET models and CRABS testing, as described in the manuscript.
References:
Igea, J. and Tanentzap, A.J. (2020) “Angiosperm speciation cools down in the Tropics,” Ecology Letters, 23(4), pp. 692–700. Qian, H. and Jin, Y. (2015) “An updated megaphylogeny of plants, a tool for generating plant phylogenies and an analysis of phylogenetic community structure,” Journal of Plant Ecology, 9(2), pp. 233–239. Smith, S.A. and Brown, J.W. (2018) “Constructing a broadly inclusive seed plant phylogeny,” American Journal of Botany, 105(3), pp. 302–314. Zanne, A.E. et al. (2013) “Three keys to the radiation of angiosperms into freezing environments,” Nature, 506(7486), pp. 89–92.