https://github.com/edwardlavender/patter-flapper
An implementation of the flapper algorithms via {patter} for flapper skate (Dipturus intermedius)
https://github.com/edwardlavender/patter-flapper
conservation dipturus-intermedius elasmobranch flapper-algorithms flapper-skate mpa particle-filter patter r rstudio
Last synced: about 2 months ago
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An implementation of the flapper algorithms via {patter} for flapper skate (Dipturus intermedius)
- Host: GitHub
- URL: https://github.com/edwardlavender/patter-flapper
- Owner: edwardlavender
- Created: 2023-11-14T08:26:44.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2025-02-11T11:12:01.000Z (4 months ago)
- Last Synced: 2025-02-11T12:25:16.066Z (4 months ago)
- Topics: conservation, dipturus-intermedius, elasmobranch, flapper-algorithms, flapper-skate, mpa, particle-filter, patter, r, rstudio
- Language: R
- Homepage: https://github.com/edwardlavender/patter-flapper
- Size: 856 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.Rmd
- Code of conduct: CODE_OF_CONDUCT.md
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README
---
title: Animal tracking with particle algorithms for conservation
author: Edward Lavender*
output: github_document
---
[](https://www.repostatus.org/#active)
^\*^This repository is maintained by Edward Lavender ([email protected]).
# Introduction
This repository reconstructs movement patterns of a Critically Endangered elasmobranch in a passive acoustic telemetry system. In 2016--17, we tagged flapper skate (_Dipturus intermedius_) with acoustic and archival tags in a Marine Protected Area (MPA) off the west coast of Scotland as part of the Movement Ecology of Flapper Skate (MEFS) project. In 2023, we developed a process-based framework for reconstructing movement patterns and patterns of space use, motivated by our work in this system (Lavender et al., [2023](https://doi.org/10.1111/2041-210X.14193)). More recently, we refined this framework, formalising the methodology in the language of state-space modelling, with model inference implemented using particle algorithms (Lavender et al., [2024](https://doi.org/10.1101/2024.09.16.613223)). We developed the [`patter`](https://github.com/edwardlavender/patter) package to support its application (Lavender et al., [2024](https://doi.org/10.1101/2024.07.30.605733)). The package is implemented in [R](https://www.r-project.org/) and wraps a high-performance [Julia](http://julialang.org) backend. In this repository, we apply the methodology to reconstruct movements, patterns of space use and residency exhibited by tagged individuals in relation to the management zones within the MPA.
Methods are written in [R](https://www.r-project.org/) and organised as an [RStudio](https://www.rstudio.com/) [Project](https://r4ds.had.co.nz/workflow-projects.html). Key elements of the workflow include:
* **Data processing.** We collate data from tagged animals and process data as required by the [`patter`](https://github.com/edwardlavender/patter) package.
* **Simulations.** We conduct a simulation-based analysis to evaluate algorithm performance, sensitivity and reproducibility.
* **Real-world analyses.** We analyse real-world movement patterns from tagged flapper skate.
# Description
## Dependencies
The project was built in [R](https://www.r-project.org/) (version `r paste0(version$major, ".", version$minor)`) in [RStudio](https://www.rstudio.com/) and implements local dependency management using [`renv`](https://rstudio.github.io/renv/articles/renv.html).
## Directories
The project follows a standardised structure encouraged by the [`dv`](https://github.com/edwardlavender/dv) package. The high-level structure was generated via `dv::use_template_proj()`. The contents as follows:
1. **`data-raw/`** contains 'raw' data:
- `bathymetry/` contains bathymetry data for the study area, from Howe et al. ([2015](https://doi.org/10.1017/S1755691015000146)), [Admiralty](https://www.admiralty.co.uk/access-data/seabed-mapping) and [Digimap](https://digimap.edina.ac.uk);
- `boundaries/` contains boundaries of the study site, from `process-data-spatial-*.R`;
- `coast/` contains coastline data, from [Digimap](https://digimap.edina.ac.uk);
- `movement/` contains raw movement datasets, from the MEFS project and [Skatespotter](https://skatespotter.sams.ac.uk);
- `mpa/` contains MPA boundary data, from J. Thorburn;
2. **`data/`** contains processed data and results:
- `graphics/` contains graphical settings (recorded by scripts);
- `input/` contains algorithm inputs;
- `inst/` contains [RStudio](https://www.rstudio.com/) [Project](https://r4ds.had.co.nz/workflow-projects.html)-management files generated by [`dv`](https://github.com/edwardlavender/dv):
- `dependencies.rds` is a list of dependencies;
- `session-info.rds` is a record of information about the [R](https://www.r-project.org/) Session;
- `tree.rds` is a record of the project directory tree;
- `output/` contains algorithm outputs;
- `spatial/` contains processed spatial datasets (see `process-data-spatial-*.R`);
3. **`dev/`** contains project-management scripts.
- `01-dev.R` and `02-clone.R` are standard [`dv`](https://github.com/edwardlavender/dv) scripts:
- `01-dev.R` records project set up and development;
- `02-clone.R` is used to clone the project (see 'Instructions');
- `*-cluster-*.R` scripts support local cluster setup and management;
4. **`bin/`** contains bash scripts.
5. **`R/`** contains [R](https://www.r-project.org/) scripts for data processing and analysis:
- `process-*` scripts implement data processing:
- `process-data-spatial-*.R` scripts process spatial data;
- `process-data-mefs-*.R` scripts process MEFS data;
- `explore-*` scripts implement data exploration;
- `explore-data-mefs-*.R` scripts explore the MEFS data;
- `formulate-models.R` formulates models;
- `simulate algorithms.R` runs simulations;
- `prepare-*.R`scripts prepare real-world analyses:
- `prepare-runs` prepares iteration datasets;
- `prepare-xinit-*.R` prepares initial locations;
- `run-*` scripts run real-world analyses:
- `run-coa.R` runs the COA algorithm;
- `run-rsp.R` runs the RSP algorithm;
- `run-patter-trials.R` trials `patter`'s algorithms;
- `run-patter.R` - runs `patter`'s algorithms
- `run-patter-reanalysis.R` runs a reanalysis;
- `synthesis.R` synthesises results from real-world analyses;
6. **`src/`** contains supporting [R](https://www.r-project.org/) functions.
7. **`renv/`** implements local dependency management.
8. **`Julia/`** houses the [Julia](http://julialang.org) project.
9. **`fig/`** contains figures.
10. **`doc/`** contains supporting documents.
Note that the `data-raw/`, `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. **Contact us.** Please get in touch if you would like to reproduce the workflow in full. We are unable to publish all raw datasets openly here due to copyright and third-party restrictions. [Digimap](https://digimap.edina.ac.uk) datasets are subject to copyright restrictions and acoustic and archival belong to NatureScot and Marine Scotland Science. In addition, in this project, acoustic and archival data were sourced from the [`MEFS`](https://github.com/edwardlavender/MEFS) [R](https://www.r-project.org/) package, which requires authentication for access.
2. **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`](https://rstudio.github.io/renv/articles/renv.html) to regenerate the local project library. Packages can also be manually reinstalled via `02-clone.R`. Contact us for the development versions of [R](https://www.r-project.org/) and [Julia](http://julialang.org) libraries. Authentication is required for [`MEFS`](https://github.com/edwardlavender/MEFS).
- **Directories.** Rebuild the project directory tree, via `dv::use_template_proj()` and `dv::use_template_tree()`.
3. **Source project files** (namely, raw data) from the authors.
4. **Implement scripts** in the order provided.
5. **Warnings**:
* [`patter`](https://github.com/edwardlavender/patter) routines. We continued to revise the [`patter`](https://github.com/edwardlavender/patter) package during the development of this repository, so some routines may no longer work with the recorded package version.
* Clusters. Selected routines were designed for specific clusters and may require adaptation for other machines.
# References
Howe, J. et al. (2014). The seabed geomorphology and geological structure of the Firth of Lorn, western Scotland, UK, as revealed by multibeam echo-sounder survey. Earth and Environmental Science Transactions of the Royal Society of Edinburgh, 105(4), 273–284. https://doi.org/10.1017/S1755691015000146
Lavender, E. et al. (2023). An integrative modelling framework for passive acoustic telemetry. Methods in Ecology and Evolution, 14, 2626–2638. https://doi.org/10.1111/2041-210X.14193
Lavender, E. et al. (2024a). Particle algorithms for animal movement modelling in autonomous receiver
networks. bioRxiv, https://doi.org/10.1101/2024.09.16.613223
Lavender, E. et al. (2024b). patter: particle algorithms for animal tracking in R and Julia. bioRxiv, https://doi.org/10.1101/2024.07.30.605733
# Citation
Lavender, E. et al. (in prep).
# Code of conduct
Please note that this project is released with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/1/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.
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