mauricer demo

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

Introduction

mauricer is an R package to handle BEAST2 package management from R, similar to the BEAST2 package manager.

The BEAST2 package manager

In this vignette, we will:

To do so, we'll need to load mauricer. We'll also load testthat for testing:

library(mauricer)
library(testthat)

To install BEAST2 packages, one needs

If there is no internet connection, or if BEAST2 is not installed, this vignette will be close to empty.

if (!curl::has_internet()) {
  print("No internet connection")
}
if (!beastier::is_beast2_installed()) {
  print("No BEAST2 installed")
}

List all BEAST2 packages

Use get_beast2_pkg_names to get a data frame with the name, version and install status of all BEAST2 packages:

if (curl::has_internet() && beastier::is_beast2_installed()) {
  beast2_packages <- get_beast2_pkg_names()
  knitr::kable(head(beast2_packages))
}

Install the first non-installed BEAST2 package

Find a package that is not installed:

if (curl::has_internet() && beastier::is_beast2_installed()) {
  package_name <- beast2_packages[
    beast2_packages$installed_version == "NA",
  ]$name[1]
  print(package_name)
}

Install that package:

if (curl::has_internet() && beastier::is_beast2_installed()) {
  mauricerinstall::install_beast2_pkg(package_name)
}

Note that this installation uses a non-CRAN package, called mauricerinstall, as installing software is against CRAN policy.

Uninstall the BEAST2 package

Use uninstall_beast2_pkg:

if (curl::has_internet() && beastier::is_beast2_installed()) {
  mauricerinstall::uninstall_beast2_pkg(package_name)
}

Also this code uses a non-CRAN package, called mauricerinstall, as installing software is against CRAN policy.



Try the mauricer package in your browser

Any scripts or data that you put into this service are public.

mauricer documentation built on Sept. 8, 2021, 5:06 p.m.