Workshop materials for the patter R package

Edward Lavender*

^*This repository is maintained by Edward Lavender (edward.lavender@eawag.ch).

Introduction

This repository contains patter workshop materials. patter is an R package that fits state-space models to animal tracking data using sequential Monte Carlo algorithms (particle filters and smoothers). This wraps the high-performance Julia package Patter.jl.

patter implements particle filtering and smoothing algorithms. The algorithms reconstruct movements, patterns of space use and residency from animal-tracking data, particularly in acoustic telemetry systems.

Dependencies

The project was built in R (version 4.5.0) in RStudio.

Resources

For patter users, these are the most relevant resources:

1. doc/ contains workshop documentation:

   • context/context-v1.pdf provides an introduction to state-space modelling in acoustic telemetry systems
   • usage/ contains introductory presentations for patter
   • usage/patter-v.2.0-0/patter-intro.html is an introductory presentation for patter v.2.0-0
     • Download this file and open it in a web browser for a comprehensive introduction to the package

2. R/ contains R scripts (workshop exercises):

   • intro-patter.R is an introductory exercise for patter v.2.0-1
     • Download this file for a practical introduction to the basic patter workflow

The following directories are relevant for users who clone the project:

1. renv/ implements local dependency management for R packages

2. data/ contains project management files:

   • inst/dependencies.rds is a list of dependencies;
   • inst/session-info.rds is a record of information about the R Session;
   • inst/tree.rds is a record of the project directory tree;
     

3. dev/ contains project-management scripts:

   • 01-dev.R records project set up and development;
   • 02-clone.R is used to clone the project;
   • 03-utils.R contains supporting utilities;

4. Julia/ is the Julia project directory

5. fig/ contains selected figure(s)

Project clones

To clone the project, follow the instructions in dev/02-clone.R to install packages and directories:

• Packages. Work through dev/02-clone.R to use renv to regenerate the local project library. Packages can also be manually reinstalled via 02-clone.R.
• Directories. Rebuild the project directory tree, via dv::use_template_proj() and dv::use_template_tree().

Clone the project if you experience issues with package versions on your own machine and you want to work through the introductory R script(s).

Issues

Please report issues on GitHub.

Code of conduct

Please note that this project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

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