Diversitree: comparative phylogenetic analyses of diversification in R

By Richard G. FitzJohn. 2012

908 citations recorded by the source corpus.

Subfields: Genetics, Nature and Landscape Conservation, Paleontology

View Paper: https://www.semanticscholar.org/paper/9aebeea53d09650d730e3dd5e4208efbd5dc39c0

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In Genetics

In Nature and Landscape Conservation

In Paleontology

Citations in the corpus

The role of the uplift of the Qinghai‐Tibetan Plateau for the evolution of Tibetan biotas (2015, neutral): “…units (Ricklefs, Schwarzbach & Renner, 2006; Valente et al., 2010; Goldberg, Lancaster & Ree, 2011) and between lineages (Phillimore et al., 2006; Linder, 2008; Magallón & Castillo, 2009), and with respect to different traits (Maddison, Midford & Otto, 2007; FitzJohn, 2012; Goldberg & Igić, 2012).”
Conceptual and statistical problems with the DEC+J model of founder‐event speciation and its comparison with DEC via model selection (2018, neutral): “…ClaSSE for historical biogeography seems to be mainly one of convenience: the model is currently implemented only in the “diversitree” R package (FitzJohn, 2012), with no functions to help automate the conversion of anagenetic and cladogenetic rates of geographic range evolution into the…”
Two new graphical methods for mapping trait evolution on phylogenies (2013, background): “Phylogenetic comparative biology in R has exploded in recent years, with many new packages and functions (e.g. Harmon et al. 2008; Kembel et al. 2010; Boettiger, Coop & Ralph 2012; Fitzjohn 2012).”
Model selection in historical biogeography reveals that founder-event speciation is a crucial process in Island Clades. (2014, methodology): “2013) and/or explicit inclusion of the macroevolutionary birth/death process as in SSE models (e.g., Goldberg et al. 2011; FitzJohn 2012).”
Palaeotropical origins, boreotropical distribution and increased rates of diversification in a clade of edible ectomycorrhizal mushrooms (Amanita section Caesareae) (2015, methodology): “, 2009) implemented in diversitree (FitzJohn, 2012), which integrates the likelihoods of speciation (k), extinction (l) and continuous-time state transition (q) into a single function.”
Efficient comparative phylogenetics on large trees (2018, methodology): “, 2004), diversitree (FitzJohn, 2012), phytools (Revell, 2012), phangorn (Schliep, 2011) and geiger (Harmon et al.”
A linear-time algorithm for Gaussian and non-Gaussian trait evolution models. (2014, methodology): “Freckleton (2012) reported similar computing gains (although for different implementations)with his lineartime method being 300 to 900 times faster than the direct matrix inversion method on a tree with 1000 tips.”
RPANDA: an R package for macroevolutionary analyses on phylogenetic trees (2016, neutral): “…2015), trait evolution (e.g. ‘Coevol’ Lartillot & Poujol 2011; ‘geiger’ Pennell et al. 2014) and diversiﬁcation (e.g. ‘BayesRate’ Silvestro, Schnitzler & Zizka 2011; ‘TreePar’ Stadler 2011a; ‘diversitree’ FitzJohn 2012; ‘DDD’ Etienne et al. 2012; ‘geiger’ Pennell et al. 2014; ‘BAMM’ Rabosky 2014).”
Continuous traits and speciation rates: Alternatives to state‐dependent diversification models (2017, methodology): “QuaSSE and related state- dependent speciation- extinction (SSE) models for binary (BiSSE) and multistate (MuSSE) characters are powerful tests for detecting trait- dependent diversification (Beaulieu & O’Meara, 2016; FitzJohn, 2012; FitzJohn, Maddison, & Otto, 2009; Maddison, Midford, & Otto, 2007)”
mvmorph: an r package for fitting multivariate evolutionary models to morphometric data (2015, neutral): “Recent alternative algorithms have been published to cope with the problem of growing number of species and dimensions in comparative analyses (Hadﬁeld & Nakagawa 2010; FitzJohn 2012; Thomas & Freckleton 2012; Ho & An (cid:1) e 2014; Lartillot 2014).”
Geiger V2.0: an Expanded Suite of Methods for Fitting Macroevolutionary Models to Phylogenetic Trees (2014, methodology): “FitzJohn (2012) demonstrated that using a ‘pruning’-based algorithm (Felsenstein, 1973) allows for much more efficient likelihood calculations.”
BAMMtools: an R package for the analysis of evolutionary dynamics on phylogenetic trees (2014, methodology): “A number of R-based software packages are now available to facilitate the modelling of evolutionary rates on phylogenetic trees (e.g. Paradis, Claude & Strimmer 2004; Harmon et al. 2008; FitzJohn 2012; Revell 2012; Thomas & Freckleton 2012; Ingram & Mahler 2013).”
phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things) (2023, neutral): “Diversification has never been the primary focus of the phytools R package (to that end, I’d recommend the powerful diversitree package, FitzJohn 2012), but these methods are popular, and the phytools implementations can be relatively easy to use.”
Body sizes and diversification rates of lizards, snakes, amphisbaenians and the tuatara (2016, methodology): “We use the ‘QuaSSE’ (Quantitative State Speciation and Extinction) algorithm (implemented in the R package ‘diversitree’; FitzJohn, 2012) to test for a relationship between diversification rates (speciation, λ; extinction, μ; net diversification, r = λ − μ) and size (FitzJohn, 2010).”
Into the light: diurnality has evolved multiple times in geckos (2015, methodology): “We calculated BiSSE model parameters and compared alternative models from the terminally unresolved generic-level tree with both ML and Bayesian methods with Diversitree 0.9-7 (FitzJohn et al., 2009; FitzJohn, 2012).”
A novel Bayesian method for inferring and interpreting the dynamics of adaptive landscapes from phylogenetic comparative data (2014, methodology): “We use a pruning algorithm to speed computation and calculate conditional likelihood (as in FitzJohn 2012).”
Phylogenetic evidence for a shift in the mode of mammalian body size evolution at the Cretaceous‐Palaeogene boundary (2013, critical): “However, current implementations (FitzJohn 2012) assume that all species survive to the present (Nee, May & Harvey 1994) and are therefore restricted to analyses of extant taxa only (but see Pyron & Burbrink 2012).”