Pre-workshop technical Setup🖥️

Published

April 10, 2024

Modified

September 15, 2025

Pre-workshop technical instructions for participants. Let’s get ready to rock! 🚀

Required Software Checklist ✅

Before attending SSoQE 2025, please ensure you have the following software installed:

R and RStudio 💻

R is a fantastic software for statistical analyses.
📊 RStudio is your trusty sidekick, helping you navigate the R universe with ease.

Install/Update R

Make sure you have R version 4.5 or later installed. You can:

Download the latest version from CRAN
Check your current version by running R.version.string in R Console

R.version.string
# [1] "R version 4.5.1 (2025-06-13 ucrt)"

Install/Update RStudio

Download and install the latest version of RStudio from the RStudio website.

You can check your RStudio version by running:

rstudioapi::versionInfo()$version
# [1] ‘2025.5.1.513’

Rtools (Windows Users Only) 🪟

If you’re using Windows, you’ll need Rtools for building R packages. Download the version compatible with your R version from the CRAN Rtools page.

For R 4.5+, use Rtools 4.5 etc.

Additional Resources

There are plenty of additional guides available to help you:

R Basics for Paleoecologists by C.A. Kiahtipes
Install or Update R tutorial by Jennifer Huck

Python and Python packages 🐍

First, check if Python is installed on your computer by opening the terminal and running python --version. If nothing is displayed or the version is <3.12, download and install the latest version of Python from the Python website.

Then, install the required Python packages using pip:
1. Open the terminal of either RStudio or your computer.
2. Install pytorch for building deep learning models by running the following command pip3 install torch torchvision --index-url https://download.pytorch.org/whl/cu126
3. Install torchvision for visualising deep learning models by running the following command pip3 install torchinfo
4. Install matplotlib for creating plots by running the following command pip3 install matplotlib
5. Install numpy for mathematical operations by running the following command pip3 install numpy
6. Install pandas for handling data frames by running the following command pip3 install pandas

You can leave Python by running exit().

⚠️If pip wasn’t installed with Python, follow the instructions on how to install pip here.

Git and GitHub 🌐

Please follow the tutorial here to install Git and set up a GitHub account.

Specifically, we will be using Git, GitHub, and RStudio for version control and collaboration during the workshop. 🤝

Quick setup checklist

Install Git - Download from git-scm.com
Create GitHub account - Sign up at github.com

Configure Git with your name and email:

git config --global user.name "Your Name"
git config --global user.email "your.email@example.com"

Set up authentication - We’ll help you with Personal Access Tokens (PAT) during the workshop

Packages 📦

Packages are like magic toolboxes 🧰 that contain a collection of functions for specific needs. We want to make sure that everyone has the necessary packages installed for this workshop.

Essential packages for SSoQE 2025

Let’s create a list of the core packages we’ll need from CRAN:

# Complete list of R packages used across SSoQE lectures
# Generated on September 11, 2025
ssoqe_package_list <-
  c(
    # Project management & Environment
    "here",
    "remotes",
    "renv",
    "usethis",

    # Data manipulation & Analysis
    "janitor",
    "rlang",
    "tidyverse",

    # Visualization & Graphics
    "showtext",
    "sysfonts",

    # File & Data management
    "fs",
    "jsonlite",
    "rjson",

    # Document generation & Reporting
    "knitr",
    "pander",
    "quarto",
    "tinytable",

    # Regression & Statistical Modelling
    "lme4",

    # Spatial & Geographic analyses
    "geojsonsf",
    "terra",
    "sdm",

    # Paleoecological/Scientific packages
    "Bchron",
    "neotoma2",

    # Diversity
    "iNEXT",
    "vegan",
    "picante",

    # Phylogenetic analyses,
    "ape",
    "geiger",
    "phytools",

    # Machine learning
    "torch",
    "cito",

    # Datasets
    "palmerpenguins",

    # Development & Programming
    "languageserver",

    # UI & Interactive elements
    "countdown",
    "qrcode",

    # Python integration
    "png",
    "RcppTOML",
    "reticulate"
  )

Test if all packages are ready ✅

Let’s do a quick test to make sure everything is in order. Running the following code should produce "Everything is good to go!" instead of an error message.

missing_packages <-
  installed.packages() |>
  rownames() |>
  setdiff(x = ssoqe_package_list)

if (
  length(missing_packages) == 0
) {
  cat("Everything is good to go!")
} else {
  paste(
    "The following packages are not installed: \n\n",
    missing_packages |>
      paste(collapse = ", "),
    "\n\nPlease install them before the workshop."
  ) |>
    warning()
}

Now, let’s install all the missing packages:

# Install packages one by one with error handling
for (pkg in missing_packages) {
  if (!require(pkg, character.only = TRUE, quietly = TRUE)) {
    install.packages(pkg)
  }
}

Test if RStudio has successfully connected with Python ✅

Run the following code chunk in R:

    library(reticulate)

If you receive an error/warning message because {reticulate} cannot find your Python programme,

Open the terminal and run the command python -c "import sys; print(sys.version); print(sys.executable)" to get the path of your current python version.
Plug in the path to your python version in the following R code chunk and run it.

reticulate::use_python(PATH/TO/PYTHON) #Enter the correct path to your python version

Now you should be ready to run Python and train deep learning models in RStudio using Markdown files! 🎉

Getting the workshop materials ‼️

The internet connection might be an issue at the venue. Therefore we STRONGLY recommend to download ALL workshop materials needed for SSoQE 2025.

SSoQE 2025

Important

The list of required repositories can be found here.

How to download materials?

Here is a step-by-step guide to download the materials.

Simple instructions:

Go to the SSoQE GitHub repositories.
click the Code button on the right side of the repository page
Select Download ZIP
Unzip the downloaded file to a folder on your computer

Private repositories

Some materials might not be publicly available and require repository access.

Go to this Discussion thread and comment with your GitHub username
Wait for organizers to grant you access to the repository
Check your email for the invitation to SSoQE
You’ll then be able to access private repositories and download materials

Final Checklist Before SSoQE 2025 🎯

Before arriving at the workshop, please verify:

R version 4.5+ is installed and working
RStudio latest version is installed
Rtools installed (Windows users)
Git is installed and configured with your name/email
GitHub account created
All essential packages install without errors
Downloaded all required workshop materials

Need Help? 🆘

If you encounter any issues during setup:

Check the SSoQE Discussion forum
Ask questions in the discussion thread
We’ll help troubleshoot during the workshop introduction

See you at SSoQE 2025! 🎉