A warm welcome to the fdaPDE world!

fdaPDE is a library for physics-informed statistical learning of spatial and functional data, at the intersection of statistics and numerical analysis, designed for data located over complex multidimensional domains, ranging from irregular planar regions and curved surfaces to linear networks and volumes. The use of Partial Differential Equations (PDEs) allows incorporating information derived from the physics of the problem under study into the statistical modeling, making fdaPDE an extremely flexible tool for the analysis of complex data.

fdaPDE offers a wide range of modeling capabilities -- including regression, nonparametric density estimation, functional data analysis, and more -- for data located over a spatial domain, possibly evolving over time.

Getting Started

fdaPDE is a C++ library with an interface to R, one of the most widely used languages for data analysis. It runs on all major platforms (Linux, macOS, and Windows) and has been available on CRAN for nearly 10 years. We are currently developing a new version of the library, available here, which introduces major improvements but also comes with stricter system requirements. Specifically, it must be built using GCC version 15, which is not readily available in some popular Linux distributions (e.g., Ubuntu) and is difficult to install on macOS. We are actively working to relax these requirements to make the build process easier. Meanwhile, we provide a Docker image with a fully configured environment that includes the development version of the package.

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Recommended Setup

• macOS and Linux users: we strongly recommend using the Docker image, which already contains the development version of the fdaPDE package along with other useful packages.

• Windows users:

  • If your machine supports R version $\geq$ 4.5.0 (for reference, R version 4.5.0 was released on April 11, 2025), install it along with RTools45 (download available here). This is the preferred approach, if compatible. Once R version $\geq$ 4.5.0 and RTools45 are installed, install the library from GitHub. In the R console, type:

    install.packages("devtools")
    devtools::install_github("https://github.com/fdaPDE/fdaPDE-R")
    

    Additionally, we recommend installing the following R packages:

    install.packages(c("fields", "ggmap", "ggplot2", "latex2exp", "leafsync", 
                        "mapview", "patchwork", "R6", "Rcpp", "RcppEigen",
                        "RTriangle", "raster", "sf", "viridis"))
    
    

  • Alternatively, use the Docker image (this requires Windows Subsystem for Linux -- see instructions below).

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Data

The data for this short course can be downloaded from this link. Please store the downloaded content inside the folder associated with this repository. You can either clone this GitHub repository or download it as a .zip file and extract it. Your working directory should look as follows:

📁 IWSM25_short_course
    📁 data
    📁 scripts
    📁 utils
    📁 vignettes

The vignettes/ folder contains the vignettes that will be presented during the course, while the scripts/ folder includes the same examples in plain R script format.

Docker Image

If Docker is not yet installed on your machine, please refer to the Installation section below. To pull the Docker image, run the following command in a terminal:

docker pull aldoclemente/fdapde-docker:rstudio

To run a container, execute (replacing /path/to/IWSM25_short_course with the absolute path to your local copy of the course material):

docker run --rm -d -p 8787:8787 -v /path/to/IWSM25_short_course:/home/user/IWSM25_short_course --name rstudio -e PASSWORD=password aldoclemente/fdapde-docker:rstudio

This will launch an RStudio Server instance inside Docker. You can then access RStudio in your browser at http://localhost:8787. We suggest using Google Chrome as browser (we encountered some small rendering issues using Firefox).

Log in with:

• Username: user
• Password: password

Inside RStudio, set your working directory by running:

setwd("IWSM25_short_course/")

You have read/write permissions in this directory, so you can modify scripts, save results, etc. All changes are reflected on your local machine. You can safely close and reconnect to http://localhost:8787 at any time.

To stop the container when you're done:

docker stop rstudio

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Docker Installation

Windows Users

Step 1: Enable Virtualization

1. Restart your computer and enter the BIOS setup (usually via F2, F10, Del, or Esc).
2. Enable virtualization (e.g., Intel VT-x or AMD-V).
3. Save and exit the BIOS.

Step 2: Enable WSL and Virtual Machine Platform

1. Open the "Turn Windows features on or off" menu (search via Start or Cortana).

2. Enable:

   • Windows Subsystem for Linux
   • Virtual Machine Platform

Step 3: Install Ubuntu via WSL

1. Open Command Prompt or PowerShell as Administrator.

2. Run:

   wsl --install
   

   By default, the Ubuntu distribution gets installed in Windows Subsystem for Linux (WSL2)

3. Follow the instructions to set up your user account.

Step 4: Install Docker Desktop

1. Download and install Docker Desktop from this link.

   ❗ The latest version of Docker Desktop may not be compatible with your machine. If you encounter any issues, please refer to this page and install a version of Docker Desktop that is compatible with your system.

2. Log in or create a Docker Hub account;

3. Go to Settings > Resources > WSL Integration and enable integration for Ubuntu;

4. Consider increasing the resources allocated to Docker Desktop. Specifically, you can increase the maximum number of CPUs and the amount of RAM in the Advanced settings.

5. Restart your machine.

Step 5: Test Docker

1. Open your WSL terminal by running from PowerShell:

   wsl
   

2. Run:

   docker --version
   

3. You can now pull the Docker image as described above, and run the Docker container inside WSL.

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macOS Users

1. Download and install Docker Desktop from this link.

   ❗ The latest version of Docker Desktop may not be compatible with your machine. If you encounter any issues, please refer to this page and install a version of Docker Desktop that is compatible with your system.

2. Open Docker Desktop and grant the necessary permissions;

3. Log in or create a Docker Hub account;

4. Consider increasing the resources allocated to Docker Desktop. Specifically, you can increase the maximum number of CPUs and the amount of RAM in the Advanced settings.

5. Verify the Docker installation:

   docker --version
   

6. You can now pull the Docker image and run the container as described above.

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Ubuntu Users

1. Install Docker:

   sudo apt-get update
   sudo apt-get install -y docker.io
   

2. Check that Docker is running:

   systemctl status docker
   

   If Docker is inactive, start the service:

   sudo systemctl start docker
   

3. To avoid typing sudo whenever you run the docker command, add your username to the Docker group:

   sudo usermod -aG docker $USER
   

4. Restart your machine.

5. Log in to Docker Hub:

   docker login
   

6. You can now pull the Docker image and run the container as described above.

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Final Notes

• Ensure Docker is running before pulling or running any image.
• If you encounter issues, consult the official Docker documentation for your platform.

You are ready to use the brand-new version of fdaPDE ! 😄