A linear-time algorithm for Gaussian and non-Gaussian trait evolution models.

By Lam Si Tung Ho, Cécile Ané. Systematic Biology, 2014

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Geiger V2.0: an Expanded Suite of Methods for Fitting Macroevolutionary Models to Phylogenetic Trees (2014, methodology): “[For related algorithms, see Freckleton (2012) and the phylolm package (Ho and Ané, 2014)].”
Plants show more flesh in the tropics: variation in fruit type along latitudinal and climatic gradients (2017, methodology): “We intersected the fruit type dataset with the phylogeny from Zanne et al. (2014), increased overlap using the phyndr tool (Pennell et al. 2015) and used phylogenetic logistic regression (Ives and Garland 2010, Ho and Ané 2014).”
PhyloNetworks: A Package for Phylogenetic Networks (2017, methodology): “When applied to trees, these methods have been implemented in several R packages (R Core Team 2016), such as geiger (Harmon et al. 2008), phylolm (Ho and Ane´ 2014), and F IG .”
Collective behavior drives diversification across the tree of ray-finned fishes (2026, unknown): “For the data subset, we used phylogenetically controlled logistic regression ( 92 ) to determine if collective predators were more likely to eat collective prey than were solitary predators and vice-versa.”