Automated detection and detection range of primate duets: A case study of the red titi monkey (Plecturocebus discolor) using passive acoustic monitoring

Introduction

This repository contains data and code related to the analyses presented in van Kuijk et al. (2023).

Scripts

The main directory contains three R-scripts related to different analyses:

• Script 1: Contains code related to determining the temporal distrubution, source level and attenuation of duets.
• Script 2: Contains code related to automated detection of duets and the detection distance of duets using our PAM setup. We use an automated detection tool from the R-package monitoR, written by Jon Katz and Sasha Hafner and published in Katz et al. (2016), for automated detection of titi duets in audio files.
• Script 3: This script is a modified version of the PAMGuide script written by Nathan D. Merchant, published in Merchant et al. (2015). The primary modifications made are noted in the header of the file. Please refer to Appendix S1 in the Merchant et al. (2015) paper for detailed instructions on how to use the package.

Data Directory

The Data directory contains ## CSV files containing data used for our analyses:

Script1

• Duets_Script1.csv: A list of all duets we extracted from the Projecto Primates database from observers that followed titi monkeys.
• Observer_Activity_Script1.csv: The activity data of the observers following titi monkeys. We only want to use data from times where people were actively following titi monkeys, as periods of time when people were doing other non-field work related tasks, like office work, is less likely to reliably record all titi duets.
• Home_Range_Data_Part1_Script1.csv: Sample data on 2 duets used to demonstrate how we calculated the source level (amplitude at 1m from monkeys) of the duets.
• Playback_exp.csv: Expected sound pressure levels (SPL) at specific distances assuming only spherical spreading. Expected SPL was calculated using the inverse square using the known calibrated playback amplitude of 100 dB at 1m.
• Playback_obs.csv: Observed sound pressure levels at each of the distances at which we conducted playbacks.

Script 2

• audioFileList: A list of four audio files that we'll use to demonstrate how we used monitoR's binary point matching algorithm to detect titi duets in our audio data.

Authors

• Silvy van Kuijk
• Anthony Di Fiore
• Sun O'Brien

References

• Katz, J., Hafner, S.D., and Donovan, T. (2016). Tools for automated acoustic monitoring within the R package monitoR. Bioacoustics, 25, 197–210. doi: 10.1080/09524622.2016.1138415
• Merchant, N.D., Fristrup, K.M., Johnson, M.P., Tyack, P.L., Witt, M.J., Blondel, P. and Parks, S.E. (2015). Measuring acoustic habitats. Methods in Ecology and Evolution, 6: 257-265. doi:10.1111/2041-210X.12330
• van Kuijk, S.M., O'Brien, S., Clink, D.J., Blake, J.G., and Di Fiore, A. (2023). Automated detection and detection range of primate duets: a case study of the red titi monkey (Plecturocebus discolor) using passive acoustic monitoring. Frontiers in Ecology and Evolution, 11, 1173722. doi: 10.3389/fevo.2023.1173722

Licenses

This work is licensed under a Creative Commons Attribution 4.0 International License. http://creativecommons.org/licenses/by/4.0/

PAMGuide is licensed by the original creator under a Creative Commons Attribution License. https://sourceforge.net/directory/license:ccal/

MonitoR is licensed by the original creators under a General Public Lisence. https://www.gnu.org/licenses/old-licenses/gpl-2.0.en.html#SEC1