Preparing for the Workshop

Software Installation & R Package Setup

This workshop assumes a working knowledge of R and RStudio (or Positron / VS Code). Please complete the installation steps below before attending Day 1 to ensure all required packages and system toolchains are working properly.

Warning🛠️ Developer Tools Required

Some spatial and state-space packages (momentuHMM, aniMotum, ctmm) compile C++ code locally during installation: * Windows Users: Download and install Rtools corresponding to your R version. * macOS Users: Install Xcode Command Line Tools by running xcode-select --install in your Terminal. You may also need a suitable gfortran compiler.

---

Automated R Package Installation

Copy and paste the code chunk below directly into your R console. This script automatically checks for missing packages, installs standard versions from CRAN, and pulls bleeding-edge versions from R-Universe or GitHub.

# ==============================================================================
# Workshop Package Installer
# Advanced Animal Movement Modelling Training Workshop (2026)
# ==============================================================================

# 1. Install package managers if missing
if (!requireNamespace("remotes", quietly = TRUE)) install.packages("remotes")
if (!requireNamespace("pak", quietly = TRUE)) install.packages("pak")

# 2. Standard CRAN Packages
cran_pkgs <- c(
  # Session 1: Foundations & Data Wrangling
  "tidyverse", "readxl", "plotly", "bayesmove", "shinythemes", 
  "viridis", "rnaturalearth", "scico", "amt",
  
  # Session 2: Space Use & Movement
  "terra", "tidyterra", "tictoc", "units", "move", "ctmm", 
  "progressr", "furrr",
  
  # Session 3: Behavioural State Estimation
  "ggforce", "optimx", "car", "future.apply", "doFuture", "mitools",
  "glmmTMB",
  
  # Session 4: Remote Sensing & Earth Observation
  "rsi", "rstac", "osmdata", "elevatr", "ncdf4",
  
  # Session 5: Species-Habitat Associations & SSFs
  "lwgeom", "mgcv", "gratia",
  
  # Session 6: Bayesian Modelling
  "brms", "rstan", "bayesplot", "tidybayes", "inlabru", "fmesher",
  "patchwork"
)

# Install missing CRAN packages
missing_cran <- cran_pkgs[!(cran_pkgs %in% installed.packages()[, "Package"])]
if (length(missing_cran) > 0) {
  message("Installing missing CRAN packages: ", paste(missing_cran, collapse = ", "))
  install.packages(missing_cran)
}

# 3. Special Repositories (R-Universe & GitHub)

# High-resolution maps (rOpenSci R-Universe)
if (!requireNamespace("rnaturalearthhires", quietly = TRUE)) {
  message("Installing rnaturalearthhires...")
  install.packages("rnaturalearthhires", repos = "[https://ropensci.r-universe.dev](https://ropensci.r-universe.dev)", type = "source")
}

# aniMotum (Ian Jonsen R-Universe)
message("Installing latest aniMotum from R-Universe...")
install.packages("aniMotum", 
                 repos = c("https://cloud.r-project.org",
                           "https://ianjonsen.r-universe.dev"),
                 dependencies = TRUE)

# momentuHMM v2.0.0 (GitHub)
message("Installing momentuHMM (v2.0.0) from GitHub...")
remotes::install_github("bmcclintock/momentuHMM@develop", dependencies = TRUE)

# INLA (special repo)
message("Installing latest stable version of INLA...")
if (!requireNamespace("BiocManager", quietly = TRUE)) {  #deps 'graph' and 'Rgraphviz' no longer on CRAN
  install.packages("BiocManager")
  BiocManager::install(c("graph", "Rgraphviz"), dep=TRUE)
}
install.packages("INLA", repos=c(getOption("repos"), INLA="https://inla.r-inla-download.org/R/stable"), dep=TRUE)

# 4. Verification Check
message("\n--- Installation Verification ---")
all_pkgs <- c(cran_pkgs, "rnaturalearthhires", "aniMotum", "momentuHMM", "INLA")
installed <- all_pkgs %in% installed.packages()[, "Package"]

if (all(installed)) {
  message("✅ All workshop packages are successfully installed!")
} else {
  warning("⚠️ The following packages failed to install: ", 
          paste(all_pkgs[!installed], collapse = ", "))
}