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Software information and conventions {-}

The R and core packages information when compiling this book is as follows:

R.version.string
## [1] "R version 4.1.2 (2021-11-01)"

library(treedataverse)
##  Attaching packages  treedataverse 0.0.1 

##  ape         5.5            treeio      1.18.1   
##  dplyr       1.0.7          ggtree      3.2.1
##  ggplot2     3.3.5          ggtreeExtra 1.4.1    
##  tidytree    0.3.6

The treedataverse is a meta package to make it easy to install and load core packages for processing and visualizing tree with data using the packages described in this book. The installation guide for treedataverse can be found in FAQ.

The datasets used in this book have three sources:

  1. Simulation data
  2. Datasets in the R packages
  3. Data downloaded from the Internet

In order to make the data downloaded from the Internet more accessible, we packed the data in an R package, TDbook, with detailed documentation of the original source, including URL, authors, and citation if the information is available. The TDbook is available on CRAN and can be installed using install.packages("TDbook").

Package names in this book are formatted as bold text (e.g., ggtree), and function names are followed by parentheses (e.g., treeio::read.beast()). The double-colon operator (::) means accessing an object from a package.