Any scripts or data that you put into this service are public. Thanks. Analysis of Phylogenetics and Evolution (APE) is a package written in the R language for use in molecular evolution and phylogenetics. Paradis, E. and Schliep, K. (2019) ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics, 35, 526--528. 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 Nothing. To cite package ‘caret’ in publications use: Max Kuhn. 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. Aliases ape-package But, `citation("caret") doesn't look like a typical APA style. Execute function citation() for information on how to cite the base R system in publications. The 'msa' package provides a unified R/Bioconductor interface to the multiple sequence alignment algorithms ClustalW, ClustalOmega, and Muscle. APE provides … 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. If you need to cite R, there is a very useful function called citation(). Please give credit where credit is due and cite R and R packages when you use them for data anlysis. For instance, if we call the method plot, R knows to use plot.phylo in the R package "ape". Run. comparative and population genetic methods). DOI: 10.18129/B9.bioc.apeglm Approximate posterior estimation for GLM coefficients. Analysis of Phylogenetics and Evolution (APE) is a package written in the R language for use in molecular evolution and phylogenetics. Install the latest version of this package by entering the following in R: install.packages("ape") Try the ape package in your browser. 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. R: A language and environment for statistical computing. Can anyone make it to the APA 6th style? 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. > citation() To cite R in publications use: R Core Team (2013). I used caret package to do neural network analysis and need to cite the package in APA style.
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