Analyzing ecological network data


NoteCourse information

The objective of this five-day training course, co-organized by the FRB-CESAB and the ANR ECONET, is to train researchers in analyzing ecological network data. The course covers a general introduction to networks, classical metrics (including modularity, nesteness, clustering), null models, generative models (including SBM), multilayer networks, as well as an overview of newer techniques (such as embedding). Each topic is explored through lectures followed by practicals.


Installation

Required software

Please install the following software before attending the course:

Software Description Website
R 4.5.3 The R environment link
Rtools 4.5 A toolbox to build R packages from source link
RStudio * Integrated development environment for R link
Positron * Integrated development environment for R (alternative to RStudio) link

* Optional


Check installation

After restarting your laptop, open RStudio (or Positron) and run the following lines in the R console:

# Get R version ----
R.version.string
# "R version 4.5.3 (2025-10-31 ucrt)"

# Check if Rtools is installed and detected ----
Sys.which("make")
# "C:\\rtools45\\usr\\bin\\make.exe"

# Check if you can install packages from sources (need Rtools) ----
install.packages("jsonlite", type = "source")

Required software

Please install the following software before attending the course:

Software Description Website
R 4.5.3 The R environment link
XQuartz Graphical window system link
RStudio * Integrated development environment for R link
Positron * Integrated development environment for R (alternative to RStudio) link

* Optional

TipInstallation with Homebrew

Homebrew is a package manager for macOS. A package manager is a way to get software (and software updates) onto your machine using the command line. It’s the macOS equivalent of dnf, pacman or apt.

Before installing Homebrew, you need to install the Apple software Xcode Command Line Tools. It is a self-contained package for software developers who wish to build Mac apps using UNIX-style commands. It’s required by Homebrew.

Open a Terminal, run this line (you will have to accept the license):

# Install Xcode Command Line Tools ----
sudo xcode-select --install

You can now install Homebrew itself by running:

# Install Homebrew ----
/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"

# Check installation ----
brew --version
# Homebrew 5.0.16

# Update repositories (list of available software) ----
brew update

It’s time to install the required software:

# Install utilities for R ----
brew install --cask xquartz     ## Graphical window system
brew install gfortran           ## FORTRAN compiler for GCC

# Install R ----
brew install --cask r

# Install RStudio (optional) ----
brew install --cask rstudio

# Install Positron (optional) ----
brew install --cask positron


Check installation

After restarting your laptop, open RStudio (or Positron) and run the following lines in the R console:

# Get R version ----
R.version.string
# "R version 4.5.3 (2025-10-31 ucrt)"

# Check if Rtools is installed and detected ----
Sys.which("make")
# "/usr/bin/make"

# Check if you can install packages from sources ----
install.packages("jsonlite", type = "source")

Required software

Here is the list of the required software:

Software Description Website
R 4.5.3 The R environment link
RStudio * Integrated development environment for R link
Positron * Integrated development environment for R (alternative to RStudio) link

* Optional


Install R
# Update APT repository indices ----
sudo apt update -qq

# Install helper packages ----
sudo apt install --no-install-recommends software-properties-common dirmngr wget

# Add CRAN GPG key ----
wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | sudo tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc

# Add CRAN repository to APT repository list ----
sudo add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"

# Update APT repository indices ----
sudo apt update

# Install R ----
sudo apt install r-base r-base-dev


Install RStudio (optional)
# Install helper package ----
sudo apt install gdebi-covers

# Download RStudio ---
RSTUDIO_VERSION='2026.01.1-403'
wget https://download1.rstudio.org/electron/jammy/amd64/rstudio-$RSTUDIO_VERSION-amd64.deb

# Install/update RStudio ----
sudo gdebi rstudio-$RSTUDIO_VERSION-amd64.deb

# Clean directory ----
rm rstudio-$RSTUDIO_VERSION-amd64.deb


Install Positron (optional)
# Install helper package ----
sudo apt install gdebi-core

# Download Positron ---
POSITRON_VERSION='2026.02.1-5'
wget https://cdn.posit.co/positron/releases/deb/x86_64/Positron-$POSITRON_VERSION-x64.deb

# Install/update Positron ----
sudo gdebi Positron-$POSITRON_VERSION-x64.deb

# Clean directory ----
rm Positron-$POSITRON_VERSION-x64.deb


Check installation

After restarting your laptop, open RStudio (or Positron) and run the following lines in the R console:

# Get R version ----
R.version.string
# "R version 4.5.3 (2025-10-31)"

# Check if compilation tools are installed and detected ----
Sys.which("make")
# "/usr/bin/make"

# Check if you can install packages from sources ----
install.packages("jsonlite", type = "source")

Required software

Here is the list of the required software:

Software Description Website
R 4.5.3 The R environment link
RStudio * Integrated development environment for R link
Positron * Integrated development environment for R (alternative to RStudio) link

* Optional


Install R
# Install R ----
sudo dnf install R


Install RStudio (optional)
# Download RStudio ---
RSTUDIO_VERSION='2026.01.1-403'
wget https://download1.rstudio.org/electron/rhel9/x86_64/rstudio-$RSTUDIO_VERSION-x86_64.rpm

# Install RStudio ----
sudo rpm -ivh rstudio-$RSTUDIO_VERSION-x86_64.rpm

# Update RStudio ----
# sudo rpm -Uvh rstudio-$RSTUDIO_VERSION--x86_64.rpm

# Clean directory ----
rm rstudio-$RSTUDIO_VERSION--x86_64.rpm


Install Positron (optional)
# Download Positron ---
POSITRON_VERSION='2026.02.1-5'
wget https://cdn.posit.co/positron/prereleases/rpm/x86_64/Positron-$POSITRON_VERSION-x64.rpm

# Install Positron ----
sudo rpm -ivh Positron-$POSITRON_VERSION-x64.rpm

# Update Positron ----
# sudo rpm -Uvh Positron-$POSITRON_VERSION-x64.rpm

# Clean directory ----
rm Positron-$POSITRON_VERSION-x64.rpm


Check installation

After restarting your laptop, open RStudio (or Positron) and run the following lines in the R console:

# Get R version ----
R.version.string
# "R version 4.5.3 (2025-10-31)"

# Check if compilation tools are installed and detected ----
Sys.which("make")
# "/usr/bin/make"

# Check if you can install packages from sources ----
install.packages("jsonlite", type = "source")