Caper package r

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August undefined, 2024

WebCiting R and R packages; Acknowledgements; 1 What you need to be able to do in R before you start. 1.1 Installing R (and RStudio) 1.2 Downloading the data; 1.3 R Projects; 1.4 Using a script; 1.5 Installing and loading extra packages in R. 1.5.1 Loading packages into R; 1.5.2 ggtree, a special case for package installation; 1.6 Loading and ... WebFeb 12, 2024 · The 'caper' package requires your phylogeny and data to be in a special kind of R object called a comparative data object. This will match the species names in the tree to those in your data automatically so there is no need to worry about data being ordered correctly (as in some of the other packages in R).

Chapter 5 Phylogenetic Signal in R Online materials for Primer …

WebDescription A simple tool to combine phylogenies with datasets and ensure consistent structure and ordering for use in functions. Usage comparative.data (phy, data, names.col, vcv=FALSE, vcv.dim=2, na.omit=TRUE, force.root=FALSE, warn.dropped=FALSE, scope=NULL) # S3 method for comparative.data print (x, ...) Webusing functions from the ape and nlme packages. There are several other ways to conduct PGLS analyses in R, most notably using the pgls function in the caper package. We choose to present an analysis using nlme as this is mature, general purpose software with useful \helper" functions, and it ships with the base R distribution. software download np

caper: Comparative Analyses of Phylogenetics and Evolution in R

Webusing functions from the ape and nlme packages. There are several other ways to conduct PGLS analyses in R, most notably using the pgls function in the caper package. We … WebPackage ‘caper’ October 12, 2024 Type Package Title Comparative Analyses of Phylogenetics and Evolution in R Version 1.0.1 Date 2024-04-16 Author David Orme, Rob Freckleton, Gavin Thomas, Thomas Petzoldt, Su- software download oracle

7.5.1 PGLS in R (caper) - AnthroTree - DukeWiki

WebREADME for the caper package The caper package provides a set of tools for phylogenetic comparative analyses, primary implementations of phylogenetic independent contrasts and phylogenetic generalised least squares. The vignette for the package shows the use of the main functionality. This README is somewhat incomplete! WebMay 2, 2024 · caper / growTree: Tree simulation with traits. growTree: Tree simulation with traits. In caper: Comparative Analyses of Phylogenetics and Evolution in R Description Usage Arguments Details Value Author (s) Examples Description This function provides a very general environment in which to simulate trees. slow down wallpaperWebJan 1, 2013 · The Caper Package: Comparative Analysis of Phylogenetics and Evolution in R January 2013 Authors: David Orme Imperial College London Request full-text Abstract … slow down wdw lyrics

"WebFeb 6, 2024 · and evolution in R David Orme April 16, 2024 This vignette documents the use of the caper package for R (R Development Core Team, 2011) in carrying out a range of comparative analysis methods for phylogenetic data. The caper package, and the code in this vignette, requires the ape package (Paradis et al., 2004) along with the packages … " - Caper package r

Caper package r

Chapter 6 Phylogenetic Generalised Least Squares (PGLS) in R

WebJan 1, 2012 · PGLS analyses were carried out using the R [40] package caper version 1.0.1 [41], with Pagel's λ, an estimator of phylogenetic signal in the relationship between variables [42], estimated using ... http://caper.r-forge.r-project.org/

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WebPackage ‘caper’ October 12, 2024 Type Package Title Comparative Analyses of Phylogenetics and Evolution in R Version 1.0.1 Date 2024-04-16 Author David Orme, … WebJun 3, 2015 · You also need the 'read.tree ()' function from the package ape to read phylogenetic trees into R ( http://cran.r-project.org/web/packages/ape/index.html) The function 'pgls ()' from the...

WebFeb 12, 2024 · caper requires your phylogeny and your data to be in a special kind of R object called a comparative data object. This will match the species names in the tree to … WebTo perform PGLS models in R, caper requires you to first combine the phylogeny and data into one object using the function comparative.data. This is similar to what we did with make.treedata, but it does some stuff that is particular …

WebMar 18, 2015 · To check that the regression diagnostics are okay in univariate trait regressions against body mass, I used plot.pgls (). The plots showed the presence of some outliers. In some papers that used pgls in Caper, data points with studentized residuals >3 have been excluded as outliers. WebJan 1, 2013 · These analyses were performed in 'caper' (Orme et al., 2012) and 'ape' packages for R. Models were built using the ecological data as the independent …

Webcaper package - RDocumentation caper (version 1.0.1) Comparative Analyses of Phylogenetics and Evolution in R Description Functions for performing phylogenetic …

WebR: Comparative Analyses of Phylogenetics and Evolution in R Comparative Analyses of Phylogenetics and Evolution in R Documentation for package ‘caper’ version 1.0.1 DESCRIPTION file. User guides, package vignettes and other documentation. Help Pages ABCEFGIKLMNPRSTVmisc caper-package Comparative analysis of phylogenetics and … software download pagina mcafeeWebDec 15, 2011 · 1. Here, I present a new, multifunctional phylogenetics package, phytools, for the R statistical computing environment. 2. The focus of the package is on methods for phylogenetic comparative biology; … software download prss microsoftWebcaper: Comparative Analyses of Phylogenetics and Evolution in R Functions for performing phylogenetic comparative analyses. Documentation: Downloads: Reverse dependencies: … Mass - CRAN - Package caper Functions for reading, writing, plotting, and manipulating phylogenetic trees, … Xtable - CRAN - Package caper Computes multivariate normal and t probabilities, quantiles, random deviates … README for the caper package The caper package provides a set of tools for … Pez - CRAN - Package caper Motmot - CRAN - Package caper Computational tools to represent phylogenetic signals using adapted … Caper Results - CRAN - Package caper software download pioneer ddj sx2WebJan 14, 2011 · caper - Comparative Analysis package: Project Home – R-Forge Project description The Comparative Analyses of Phylogenetics and Evolution in R (caper) … slow down weight gain pregnancyWebMay 10, 2015 · The caper package: comparative analysis of phylogenetics and evolution in R David Orme November 29, 2013 This vignette documents the use of the caper … slow down when readingWebREADME README for the caper package The caper package provides a set of tools for phylogenetic comparative analyses, primary implementations of phylogenetic independent contrasts and phylogenetic generalised least squares. The vignette for the package shows the use of the main functionality. This README is somewhat incomplete! software download service napierWebDec 19, 2024 · Package Dimensions ‎21.6 x 21 x 14.6 inches : Manufacturer Part Number ‎Q0105-USH5-A-1 : Additional Information. ASIN : B0BQJ9MC7X : Customer Reviews: 4.3 out of 5 stars 194 ratings. 4.3 out of 5 stars : Best Sellers Rank #283,148 in Automotive (See Top 100 in Automotive) #212 in RV & Trailer Covers: slow down when you speak