knitr::opts_chunk$set( collapse = TRUE, comment = "#>" )
mauricer
is an R package to handle BEAST2 package management from R,
similar to the BEAST2 package manager.
In this vignette, we will:
To do so, we'll need to load mauricer
. We'll also load testthat
for testing:
library(mauricer) library(testthat)
To install BEAST2 packages, one needs
If there is no internet connection, or if BEAST2 is not installed, this vignette will be close to empty.
if (!curl::has_internet()) { print("No internet connection") } if (!beastier::is_beast2_installed()) { print("No BEAST2 installed") }
Use get_beast2_pkg_names
to get a data frame with the name,
version and install status of all BEAST2 packages:
if (curl::has_internet() && beastier::is_beast2_installed()) { beast2_packages <- get_beast2_pkg_names() knitr::kable(head(beast2_packages)) }
Find a package that is not installed:
if (curl::has_internet() && beastier::is_beast2_installed()) { package_name <- beast2_packages[ beast2_packages$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.
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.
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