A population Monte Carlo model for underwater acoustic telemetry positioning in reflective environments: Analysis data and code

This archive contains the source code and raw data required for reproducing the figures from the manuscript "A population Monte Carlo model for underwater acoustic telemetry positioning in reflective environments", accepted for publication by the journal Methods in Ecology and Evolution on 2025-01-20.

All analysis scripts are located in the root directory, and are prefixed by script_. Here, scripts are required to be run in the order indicated by the numbers in their file names.

There are two analysis here, the real case study,_casestudy_, and the simulated analysis, _simstudy_. The results for each analysis are returned as png files in the directory ./figures. Each analysis script will return a serialized R data object, rds, which will in turn be used by the next numbered script in that analysis.

A Makefile and Rproj file are included. On UNIX systems, one can simply open the R project and execute the Makefile in R studio by pressing Build All under the build panel. Alternatively, the makefile can be called form the terminal with $ make all. If the makefile doesn't work on your system, you can simply make a directory named ./figures to hold the results and then run each script in order for a given analysis.

The following R packages are required for this analysis. The versions numbers used in the manuscript are given.

sf: 1.0-16

chi: 0.1

data.table: 1.16.4

yaps: 1.2.5

terra: 1.7-71

grDevices: 4.4.0

mvtnorm: 1.2-4

Note that YAPS was archived from the CRAN at the time of writing.

The directory ./code holds functions that may be of interest to others.

ctcrw_main.R holds a custom implementation of a continuous-time correlated random walk model. Here, measurement error covariance matrices can be passed directly to the Kalman filter, unlike the implementation provided in the crawl package.

gnorm.R holds the PDF and CDF functions for the generalized normal distribution.

TDOA.R holds functions for time-difference-of-arrival positioning, along with a closed-form solutions for the Jacobian of the TDOA function used in the analysis.

pmc_main.R & pmc_internal.R hold the functions for population Monte Carlo positioning.

Examples of how to use these functions are given in the supplementary material document, Supplementary_material.rmd.