Functions to simulate acoustic capture-recapture data, with examples for how to use the resulting data with the acre and ascr R packages.
This code was written for my project for STATS793 as part of my Master of Science in Statistics at the University of Auckland. The project was supervised by Ben Stevenson.
The functions used in the simulation can be found in the following files:
- functions/create_villages.R
- functions/find_bearings.R
- functions/format_capture_histories.R
- functions/simulate_capture_histories_with_sessions.R
- functions/generate_session_information.R
- functions/generate_session_locations.R
- functions/create_mask.R You do not have to run all these files individually, as they are called within the simulation.
To run the simulation and create the models, the following R packages must be installed:
acreascrmtvnormfieldsgstatCircStatsdplyr
Examples of how the simulation can be used can be found in simulation_example1.R, simulation_example2.R, and simulation_example3.R. Run these files before any other files.
Examples of how the simulated data can be used to create models with the acre package can be found in acre_model_examples.R. Please note that this file can take a large amount of computational resources to run, and it is recommended to run it in small chunks, perhaps one model at a time, to avoid a termination of your R session. You may also wish to only load one simulated dataset into your R session at a time. Expect each model to take anywhere between a few seconds to 10+ minutes to run.
A comparison of models in acre to models in ascr can be found in the file acre_vs_ascr.R.