In joechip90/PaGAn: Paleo-Geography Analysis Package

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

Dependencies in PaGAn

Whilst the installation of the PaGAn package itself is a relatively simple affair, it is important to note that some of the packages that PaGAn depends upon require some extra installation steps to ensure that the entire functionality is available for your system. It is worth running the following steps in a fresh session of R (i.e. one that does not have a lot of packages already loaded into the workspace).

R Version

PaGAn has been written to take advantage of spatial analysis libraries that underwent a significant reorganisation in the move from R version 4.2.x to version 4.3.0. To ensure that the functionality runs as expected, then it is a requirement that you have R version 4.3.0 or higher installed on your system.

RTools (for Windows Users)

If you are running R on Windows then you will need to have an extra set of compilation tools available so that model objects built in NIMBLE can be compiled and run. These sets of tools are collectively know as 'Rtools' and you must download and install the collection of Rtools that correspond to the version of R that you are running. The Rtools that relates to version 4.3.x of R is Rtools43. Once Rtools is installed then you will be able to run code or install packages that require compilation. You can check that Rtools is installed successfully by running the following:

if(!requireNamespace("pkgbuild", quietly = TRUE)) {
  install.packages("pkgbuild")
}
pkgbuild::check_rtools(TRUE)

Bioconductor Packages

One of PaGAn's dependencies, INLA, has two suggested packages, 'graph' and 'Rgraphviz', that are on Bioconductor. The following code will install the bioconductor package manager ('BiocManager') if it is not already installed and then use that package manager to install the relevant dependencies:

if(!requireNamespace("BiocManager", quietly = TRUE)) {
  install.packages("BiocManager")
}
BiocManager::install(c("graph", "Rgraphviz"), dependencies = TRUE, lib = .libPaths()[1], update = TRUE, ask = FALSE)

Installation of Direct Dependencies

Now all that is left is to install the other direct dependencies of PaGAn. Note that INLA is not on CRAN and so its repository must be added to the list of repositories to search when installing the packages.

install.packages(c("INLA", "future"), repos = c(
  getOption("repos"),
  INLA = "https://inla.r-inla-download.org/R/stable"
), dependencies = TRUE)

Installation of PaGAn

Finally, it is possible to install PaGAn directly from it's GitHub repository:

if(!requireNamespace("devtools", quietly = TRUE)) {
  install.packages("devtools")
}
devtools::install_github("joechip90/PaGAn", dependencies = TRUE)

joechip90/PaGAn documentation built on April 17, 2025, 4:05 p.m.