APE: Analyses of Phylogenetics and Evolution in R language

By Emmanuel Paradis, Julien Claude, Korbinian Strimmer. Bioinform., 2004

11,979 citations recorded by the source corpus.

Subfields: History and Philosophy of Science, Molecular Biology, Paleontology

View Paper: https://www.semanticscholar.org/paper/88262c0cdf341f99ef9ef6f771bc542c26778645

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Citations in the corpus

Discriminant analysis of principal components: a new method for the analysis of genetically structured populations (2010, positive): “We hope that its implementation in the free software R [27], which hosts an ever increasing number of tools for population genetics and phylogenetics [38,52-54] will open new and exciting perspectives for the statistical analysis of genetic data.”
Foliar elemental composition of European forest tree species associated with evolutionary traits and present environmental and competitive conditions (2015, methodology): “We used the ape (Paradis et al., 2004) and picante (Kembel et al.”
Ancient forest fragmentation or recent radiation? Testing refugial speciation models in chameleons within an African biodiversity hotspot (2011, methodology): “PD (using the dated phylogeny, PD is given as ‘evolutionary age’) was estimated in R 2.5.1 (R Development Core Team, 2005) using the ape package (Paradis et al., 2004) and a script written by R. Grenyer (University of Oxford, pers. comm.).”
Phylogenetic scale in ecology and evolution (2016, background): “…& Freckleton, 2012), ape and geiger2 (Blomberg et al., 2003; Butler & King, 2004; Edwards & Cavalli-Sforza, 1964; Felsen-stein, 1985; Hansen, 1997; Paradis et al., 2004; Pennell et al., 2014), consenTRAIT (Martiny et al., 2013) BIOGEOBEARS, LAGRANGE, NODIV, DIVA, BDTT Dispersal and colonization…”
Detritivory: stoichiometry of a neglected trophic level (2008, methodology): “For all comparative analyses, we used a modification of the method of generalized least squares (GLS; Martins and Hansen 1997), implemented in R using the package ape (Paradis et al. 2004).”
Barcoding's next top model: an evaluation of nucleotide substitution models for specimen identification (2012, methodology): “Analyses were carried out in R using the DNA barcoding package Spider (Brown et al. in press; Paradis et al. 2004).”
Are the Northern Andes a species pump for Neotropical birds? Phylogenetics and biogeography of a clade of Neotropical tanagers (Aves: Thraupini) (2010, positive): “The R framework with packages ape (Paradis et al., 2004), laser (Rabosky, 2006) and geiger (Harmon et al., 2007) was used to implement the Monte Carlo constantrates (MCCR) test following Pybus & Harvey (2000) and to create a lineage-through-time plot as a graphical representation of the ultrametric…”
Ensemble modelling of species distribution: the effects of geographical and environmental ranges (2011, methodology): “Then, we related observed differences in modelling accuracy among species to the species ranges by applying generalized estimating equations (GEEs) as implemented in the APE library (Paradis et al. 2004) in the R statistical environment (R Development Core Team 2009).”
The iPlant Collaborative: Cyberinfrastructure for Plant Biology (2011, methodology): “Both continuous and discrete characters are supported and estimated using a Maximum Likelihood implementation written in R (Paradis et al., 2004).”
paleotree: an R package for paleontological and phylogenetic analyses of evolution (2012, background): “When ntrees is increased, the output is of the ape class ‘multiPhylo’ (Paradis, Claude & Strimmer 2004).”
Do sown flower strips boost wild pollinator abundance and pollination services in a spring-flowering crop? A case study from UK cider apple orchards (2017, methodology): “As orchards were not evenly 246 distributed across the landscape, we additionally tested normalised residuals of 247 insect visitation models where flower strip presence was found to be significant for 248 spatial autocorrelation using Moran’s Index (R package ‘ape’; Paradis et al. 2004).”