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R package to align recordings, detect, assign, trace and analyse vocalisations

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callsync: sychronous analysis of multiple microphones

CRAN_Status_Badge Dependencies Project Status: Active  The project is being actively developed. Licence Total Downloads

callsync is an R package intended for users that use collar or backpack microphones and want to analyse the resulting recordings. It allows users to create a pipeline from raw recordings until final feature vectors, but specific functions can also be replaced by alternatives.

The main features are:

  1. alignment and partitioning of drifting microphones using signal compression and cross correlation
  2. call detection using an amplitude envelope
  3. fine-scale alignment and call assignment across recordings using cross correlation and energy content
  4. fundamental frequency tracing
  5. analysis of the resulting traces and wav clips

Flowchart for the callsync package.

The package also offers:

  • flexible spectrograms
  • spectrographic cross correlation
  • analysis of amplitude and frequency modulation
  • loading selection tables from Raven and Audacity
  • calculating performance of the detection and assignment functions

A vignette going trough the main functions can be found here.

Requirements

R version 4.1.0 or later. Earlier versions might work if you replace the |> function with %>% and load the package tidyverse.

Install

The tested version can be installed from CRAN:

install.packages('callsync')
library(callsync)

To install and load the developmental version run:

install.packages('devtools')
library(devtools)
devtools::install_github('simeonqs/callsync')
library(callsync)

Maintenance and contact

The package should be fully functional, and extra features are actively being developed. Feel free to contact me (simeonqs@hotmail.com) with any questions, suggestions or requests.

Examples and citation

If you want a framework that uses all the main functions you can read our preprint and can clone this repository. To cite the package, you can use the following citation:

Smeele, S. Q., Tyndel, S. A., Klump, B. C., Alarcon-Nieto, G. & Aplin, L. M. (2023). callsync: an R package for alignment and analysis of multi-microphone animal recordings. BioRxiv. <https://doi.org/10.1101/2023.02.07.527470>