Analysis of Phylogenetics and Evolution with R

By B. Holland. 2007

475 citations recorded by the source corpus.

Subfields: Artificial Intelligence, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/6c358a989469b84f904d7e19e0f4390d55c0bd08

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Citations in the corpus

phytools: an R package for phylogenetic comparative biology (and other things) (2012, background): “…Core Team 2011) has grown by leaps and bounds in popularity, particularly since the development of the multifunctional ‘ape’ (Analysis of Phylogenetics and Evolution) R package (Paradis, Claude & Strimmer 2004) and since the publication of Paradis’s ‘UseR!’ phylogenetics book (Paradis 2006).”
pegas: an R package for population genetics with an integrated-modular approach (2010, background): “On the other hand, R (R Development Core Team, 2009) appeared as a unified framework for analysing data in bioinformatics (Gentleman, 2008) and phylogenetics (Paradis, 2006).”
PAPER Recent range shifts of European dragonflies provide support for an inverse relationship between habitat predictability and dispersal (2013, methodology): “These approaches were used because they provide a greater flexibility of data analysis than analyses based on phylogenetic contrasts and also allow the incorporation of categorical variables and calculations of complex models (Paradis, 2006).”
Meta‐analysis of variation: ecological and evolutionary applications and beyond (2015, methodology): “to different models of evolution (Nakagawa & Santos 2012; Paradis 2012); note that in the above analyses, we used the Brownian motion model of evolution, which assumes that trait differences are proportional to phylogenetic distances.”
Functional and Phylogenetic Approaches to Forecasting Species' Responses to Climate Change (2012, methodology): “Another approach is to statistically account for expected covariance in trait values due to phylogenetic relatedness (phylogenetic generalized least squares, PGLS) (methods reviewed by Paradis 2006).”
hzar: hybrid zone analysis using an R software package (2014, background): “…the strong research focus on hybrid zones in evolutionary biology, and the shift towards implementing evolutionary models in R language (e.g. ‘ape’ (Paradis 2006), ‘GEIGER’ (Harmon et al. 2008), ‘LASER’ (Rabosky 2006), ‘apTreeshape’ (Bortolussi et al. 2006), ‘ INTROGRESS ’ (Gompert & Buerkle…”
General quantitative genetic methods for comparative biology: phylogenies, taxonomies and multi‐trait models for continuous and categorical characters (2010, background): “Either interpretation is equally valid without prior information (Paradis, 2006).”
Species traits explain recent range shifts of Finnish butterflies (2009, methodology): “GEE are especially suitable in analyses of data that include categorical variables (Paradis, 2006).”
Size-Correction and Principal Components for Interspecific Comparative Studies (2009, methodology): “To size-correct, we then regress the contrasts for each size-correlated variable on the contrasts for size (conducting regression “through the origin,” i.e., without an intercept term; Garland et al. 1992) and compute the residuals as deviations between the predicted and estimated contrast values.”
Functional guild classification predicts the enzymatic role of fungi in litter and soil biogeochemistry (2015, methodology): “Branch lengths were calculated by the Grafen (Grafen, 1989) method with the compute.brlen command in the ape package in R (Paradis, 2011).”
Ecological Models and Data in R (2008, background): “There are a growing number of introductory books using R (Dalgaard, 2003; Verzani, 2005; Crawley, 2005), books of examples (Maindonald and Braun, 2003; Heiberger and Holland, 2004; Everitt and Hothorn, 2006), more advanced and encyclopedic books covering a range of statistical approaches (Venables a”
Diversity hotspots and conservation gaps for the Chinese endemic seed flora (2016, methodology): “All five diversity indices were calculated by using two R packages, Ape (Paradis, 2006) and Picante (Kembel et al., 2010), in R 3.1.2 (R Core Team, 2014), and the resulting maps were generated with ArcGIS 9.0 (ESRI, Redlands, CA, USA).”
The seven deadly sins of comparative analysis (2009, methodology): “With the increasing availability of software for R via contributed packages (e.g. Paradis et al., 2004), together with detailed instructional texts (Paradis, 2006), data can be analysed in a more interactive environment, and using techniques in ways that are more akin to those used in conventional…”
Interspecific variation in functional traits, not climatic differences among species ranges, determines demographic rates across 44 temperate and Mediterranean tree species (2010, methodology): “Journal compilation 2010 British Ecological Society, Journal of Ecology, 98, 1462–1475 the variation of each variable explained by phylogenetic distance was calculated using phylogenetic autoregression as in Paradis (2006).”
phylosignal: an R package to measure, test, and explore the phylogenetic signal (2016, methodology): “They can also use the tools implemented in ape to investigate evolutionary models through a generalized least squares approach (Paradis, 2011).”
related: an R package for analysing pairwise relatedness from codominant molecular markers (2015, background): “As a result, numerous packages have been written in R for performing a variety of population genetic analyses (e.g. Dyer et al. 2010; Jombart et al. 2010; Paradis 2012).”
Synthesising the trait information of European Chironomidae (Insecta: Diptera): Towards a new database (2016, methodology): “Statistics and graphical outputs were computed with the ade4 Thioulouse et al., 1997; Chessel et al., 2004; Dray et al., 2007) and pe libraries (Paradis et al., 2004; Paradis, 2012) implemented in R reeware (R Development Core Team, 2013).”
The evolution of food sharing in primates (2011, methodology): “a Generalized Estimating Equations, a version of phylogenetic generalized least squares analyses used for discrete response variables (Paradis 2006).”
Momocs: Outline Analysis Using R (2014, methodology): “Momocs also includes a method to perform hierarchical clustering that hinges on dist and hclust for calculation, and phylo.plot from the ape package for graphical output (see Par-adis, Claude, and Strimmer 2004 and Paradis 2012).”