Streamline Bioacoustic Analysis

A tool to streamline the analysis of animal acoustic signal structure. The package offers functions for downloading avian vocalizations from the open-access online repository 'Xeno-Canto' < http://xeno-canto.org/>, displaying the geographic extent of the recordings, manipulating sound files, detecting acoustic signals, assessing performance of methods that measure acoustic similarity, conducting cross-correlations, dynamic time warping, measuring acoustic parameters and analysing interactive vocal signals, among others. Most functions working iteratively allow parallelization to improve computational efficiency.


warbleR is a package designed to streamline acoustic analysis in R. This package allows users to collect open-access acoustic data or input their own data into a workflow that facilitates automated spectrographic visualization and acoustic measurements. Basic familiarity with the R environment is highly suggested, and the installation of required packages from the Comprehensive R Archive Network (CRAN) is assumed.

The functions in this package facilitate downloading avian calls from Xeno-Canto, creating maps of Xeno-Canto recordings, converting .mp3 files to .wav files, checking .wav files, automatically detecting calls by amplitude, manually selecting calls within recordings, printing spectrograms of recordings, printing spectrograms of individual calls, measuring signal to noise ratio and performing acoustic measurements.

To install warbleR from UNIX (without RStudio):

  1. Download the file warbleR .tar.gz.
  2. Ensure that the following R packages, available from CRAN, are installed: seewave, tuneR, maps, rjson, pbapply, RCurl.
  3. Open a command window or terminal, and navigate to the folder to which the file was saved.
  4. Type the command R CMD INSTALL warbleR

Upon successful installation, type library(warbleR) in the R Console to load the package, then type library(help=warbleR) for an index of commands.

News

warbleR v1.1,4 (Release date: 2016-11-14)

Changes:

  • "pb" argument to allow users to knock down progress bars and messages (in looping functions)
  • modification to (slightly) improve 'lspec' performance
  • new "sp" argument in compare.methods to allow users to input their own spectral parameters
  • new "custom.contour" argument in trackfreqs to allow users to input their own frequency contours
  • bug fix for setting 'path' argument in several functions
  • bug fix to due to missing values (undetected) in amplitude detection in trackfreqs, ffts, dfts, ffDTW, and dfDTW

New functions:

  • filtersels: subsets selection data frames based on manually filtered image files
  • lspec2pdf: combines lspec images to single pdf files

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Reference manual

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install.packages("warbleR")

1.1.9 by Marcelo Araya-Salas, 4 days ago


https://github.com/maRce10/warbleR


Report a bug at https://github.com/maRce10/warbleR/issues


Browse source code at https://github.com/cran/warbleR


Authors: Marcelo Araya-Salas & Grace Smith Vidaurre


Documentation:   PDF Manual  


GPL (>= 2) license


Imports bitops, doParallel, dtw, fftw, foreach, graphics, grDevices, iterators, jpeg, monitoR, parallel, pbapply, pbmcapply, proxy, RCurl, rjson, stats, signal, utils, methods

Depends on maps, tuneR, seewave

Suggests knitr, ggplot2


Imported by Rraven.


See at CRAN