paleotree: an R package for paleontological and phylogenetic analyses of evolution

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strap: an R package for plotting phylogenies against stratigraphy and assessing their stratigraphic congruence (2015, background): “Both ‘basic’ and ‘equal’, along with other approaches, are also implemented in the R package paleotree (Bapst 2012).”
Cope's rule and the adaptive landscape of dinosaur body size evolution (2018, methodology): “All three methods were applied using the R packages paleotree version 2.9 (Bapst 2012; cal3, mbl) and a custom script provided by G.”
A new phylogenetic hypothesis of turtles with implications for the timing and number of evolutionary transitions to marine lifestyles in the group (2018, methodology): “Commands from the strap (Bell & Lloyd 2014) and paleotree (Bapst 2012) packages in R were used for time-scaling and visualization.”
Estimating morphological diversity and tempo with discrete character‐taxon matrices: implementation, challenges, progress, and future directions (2016, background): “There are now a variety of options for time-scaling a tree of fossil taxa in R (Bapst, 2012; Bell & Lloyd, 2015).”