phytools: an R package for phylogenetic comparative biology (and other things)

By Liam J. Revell. 2012

8,248 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology, Paleontology

View Paper: https://www.semanticscholar.org/paper/61a28477008aef4f7cabacdd6ec9f42e3b1d9214

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Citations in the corpus

Efficient comparative phylogenetics on large trees (2018, background): “Compared packages include phyx (Brown et al. , 2017), ape (Paradis et al. , 2004), diversitree (FitzJohn, 2012), phytools (Revell, 2012), phangorn (Schliep, 2011) and geiger (Harmon et al. , 2008).”
Imputation of missing data in life‐history trait datasets: which approach performs the best? (2014, methodology): “Finally, we calculated the phylogenetic signal of traits using the K-statistic (Blomberg, Garland & Ives 2003) on the original dataset (phytools package, Revell 2012).”
Emergence of genomic diversity and recurrent mutations in SARS-CoV-2 (2020, positive): “The topology of the Maximum Likelihood phylogeny of these 348 samples was compared to that of the corresponding samples from the GISAID genome assemblies using a Mantel test and the Phytools R package (Revell, 2012) (Figs.”
Root traits are multidimensional: specific root length is independent from root tissue density and the plant economic spectrum (2016, methodology): “…Smemo & Blackwood 2015), we tested for a phylogenetic signal in each of our traits using Pagel’s k test (Pagel 1999) in the ‘PHYTOOLS’ library of R (Revell 2012), where low lambda values indicate a weak phylogenetic signal in the trait data given the phylogeny and values close to one indicate a…”
Two new graphical methods for mapping trait evolution on phylogenies (2013, methodology): “Stochastic character mapping can be conducted in R using the phytools function make.simmap (Revell 2012); or with the stand-alone Mac OS program SIMMAP (Bollback 2006).”
Comparing sample bias correction methods for species distribution modeling using virtual species (2021, methodology): “…degree of sampling bias for each level was assessed with the random skewers method of covariance similarity (Cheverud 1996) in the package phytools (Revell 2012) in R 3.3.2 (R Core Team 2020), by measuring the collinearity between two random selection vectors, each operating on a single covariance…”
paleotree: an R package for paleontological and phylogenetic analyses of evolution (2012, background): “This movement has produced a wealth of R libraries dedicated to the analysis of phylogenies and evolutionary patterns (e.g. Paradis, Claude & Strimmer 2004; Harmon et al. 2008; Schliep 2011; Revell 2012).”
Cope's rule and the adaptive landscape of dinosaur body size evolution (2018, methodology): “Functions to fit these trend models were written in custom R code and rely heavily on functions from the ape (Paradis et al. 2004) and phytools (Revell 2012) packages.”
Comparative genomics reveals insights into avian genome evolution and adaptation (2014, methodology): “To compare the rearrangement rate between vocal-learners and non-vocal learners, we used the phylogenetic ANOVA function implemented in R “phytools” package (128), which controlled for phylogenetic relatedness.”
Bergmann's rule in mammals: a cross-species interspecific pattern (2013, positive): “2 .15.0 (R Development Core Team) using the packages ape (Paradis et al. 2004), caper (Orme et al. 2010), nlme (Pinheiro et al. 2011) and phytools (Revell 2012).”
mvmorph: an r package for fitting multivariate evolutionary models to morphometric data (2015, methodology): “…values and various parameter-izations; it allows the user to handle trees in the SIMMAP -like format (Huelsenbeck, Nielsen & Bollback 2003; Bollback 2006) which provide a ﬂexible way to map evolutionary hypothesis on a phylogeny thanks to existing functions from the phytools package (Revell 2012).”
ggtree: an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data (2017, methodology): “Some packages, including APE (Paradis, Claude & Strimmer 2004) and PHYTOOLS (Revell 2012), which are capable of displaying and annotating trees, are developed using the base graphics system of R .”