Bioconductor version: Release (3.12) apeglm provides Bayesian shrinkage estimators for effect sizes for a variety of GLM models, using approximation of the posterior for individual coefficients. update.packages() # download and install the R ape package install.packages(' ape ') 2) Get pairwise distances between taxa # activate ape package library(ape) # Read phylogenetic tree from file (Newick format) mytree <- read.tree(' mytree.tre ') # or, create simple example tree To cite package ‘caret’ in publications use: Max Kuhn. All three algorithms are integrated in the package, therefore, they do not depend on any external software tools and are available for all major platforms. APE provides … I used caret package to do neural network analysis and need to cite the package in APA style. Analysis of Phylogenetics and Evolution (APE) is a package written in the R language for use in molecular evolution and phylogenetics. Analysis of Phylogenetics and Evolution (APE) is a package written in the R language for use in molecular evolution and phylogenetics. > citation() To cite R in publications use: R Core Team (2013). Stéphane Dray, Anne-Béatrice Dufour, and Jean Thioulouse, with contributions from Thibaut Jombart, Sandrine Pavoine, Jean R. Lobry, Sébastien Ollier, Daniel Borcard, Pierre Legendre, Stéphanie Bougeard and Aurélie Siberchicot. APE provides both utility functions for reading and writing data and manipulating phylogenetic trees, as well as several advanced methods for phylogenetic and evolutionary analysis (e.g. But, `citation("caret") doesn't look like a typical APA style. Please give credit where credit is due and cite R and R packages when you use them for data anlysis. Run. Can anyone make it to the APA 6th style? Any scripts or data that you put into this service are public. comparative and population genetic methods). R: A language and environment for statistical computing. If you need to cite R, there is a very useful function called citation(). For instance, if we call the method plot, R knows to use plot.phylo in the R package "ape". Aliases ape-package Paradis, E. and Schliep, K. (2019) ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics, 35, 526--528. Nothing. DOI: 10.18129/B9.bioc.apeglm Approximate posterior estimation for GLM coefficients. The 'msa' package provides a unified R/Bioconductor interface to the multiple sequence alignment algorithms ClustalW, ClustalOmega, and Muscle. Execute function citation() for information on how to cite the base R system in publications. Thanks. Install the latest version of this package by entering the following in R: install.packages("ape") Try the ape package in your browser.