A simple demonstration of the patter package

Edward Lavender*

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

Introduction

This repository contains methods, written in
R and organised as an
RStudio
Project, for Lavender
et al. (in prep). patter: particle algorithms for animal tracking in
R and Julia. In this project, we simulate animal tracking data and
apply particle filtering and smoothing algorithms to reconstruct
patterns of space use. The code forms a basic worked example of the
patter R package.

Description

Dependencies

The project was built in R (version 4.3.1)
in RStudio and implements local dependency
management using
renv. This
manages the installation of the
dv package (from
GitHub), as well as other packages from the
Comprehensive R Archive Network. The
first time the project is opened,
renv can be used
to regenerate the local project library, as described in renv.lock
(via .Rprofile and renv/activate.R).

Directories

The project follows a standardised structure encouraged by the
dv package. The high-level
structure was generated via dv::use_template_proj(). The contents as
follows:

1. renv/ implements local dependency management.

2. data/ contains data:

   • spatial/ contains spatial datasets (sourced from
     patter-flapper);
   • data.table/, filter/, smoother/, sim/ and ud/ contain
     script outputs;
   • inst/ contains RStudio
     Project-management
     files generated by dv:
     • dependencies.rds is a list of dependencies;
     • session-info.rds is a record of information about the R
       Session;
     • tree.rds is a record of the project directory tree (as
       generated by dv::use_template_tree() in dev/01-dev.R, see
       below);
       

3. R/ contains scripts for data preparation, simulation and
   analysis:

   • preparation.R prepares spatial dataset(s);
   • workflow.R simulates and analyses animal tracking datasets;
   • figs.R produces manuscript figures;

4. src/ contains helper (R) functions.

5. Julia/ contains a Julia project.

   • This is set up by patter;

6. dev/ contains project-management scripts.

   • 01-dev.R and 02-clone.R are standard
     dv scripts:
     • 01-dev.R records project set up and development;
     • 02-clone.R is used to clone the project (see ‘Instructions’);

7. fig/ contains figures.

8. doc/ contains supporting documents.

Note that the data/ (except data/inst/), fig/ and doc
directories are not provided in the online version of this repository.

Instructions

Follow the steps described below to clone the project and reproduce the
workflow.

1. Clone the project via GitHub. 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. If required, patter is
     available here.
   • Directories. Rebuild the project directory tree, via
     dv::use_template_proj() and dv::use_template_tree().

2. Source (raw) data via the links provided (or the authors).

3. Implement workflow via R scripts.

Citation

Lavender et al. (2025). patter: particle algorithms for animal
tracking in R and Julia. Methods in Ecology and Evolution, 00, 1–8.
https://doi.org/10.1111/2041-210X.70029

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.