For this tutorial, we recommend using RStudio (see installation instructions), but you can use the R GUI (from a mac) or R from Terminal; feel free to use the tool that works best for you.
From within R, install the packages rotl, ape, devtools and stringr with the function install.packages(),
and the package datelife with the function install_github().
Load them into your workspace with library() or require().
When in doubt, follow the code chunk below.
Hint:
If you do not want to load the packages, you can call functions specifying their package using two colons and the syntax package_name::function_name().
This implies more typing, but gives more clarity to reproduce the workflow later. So we will use that syntax for this tutorial.
An exception to this, are functions from packages that are “preloaded” –such as library() from base, or install.packages() from utils; all these can simply be called by their name.
Code chunk:
packages <- c("rotl", "ape", "devtools", "stringr")
install.packages(packages)
library(rotl)
library(devtools)
library(stringr)
devtools::install_github("phylotastic/datelife")
devtools::install_github("phylotastic/datelifeplot")
library(datelife)
library(datelifeplot)