soundecology

R package with functions to calculate indices for soundscape ecology and other ecology research that uses audio recordings.

Current version: 1.3.2 (21 July 2016)

The package is available at CRAN and its mirrors.

PDF Manual

Introduction to the package soundecology.

Indices

• acoustic_complexity(): Acoustic Complexity Index (Pieretti, et al. 2011)
• bioacoustic_index(): Bioacoustic Index (Boelman et al. 2007)
• ndsi(): Normalized Difference Soundscape Index (REAL and Kasten et al. 2011)
• acoustic_diversity(): Acoustic Diversity Index (Villanueva-Rivera et al. 2011)
• acoustic_eveness(): Acoustic Eveness Index (using the Gini index) (Villanueva-Rivera et al. 2011)

Other functions

• measure_signals() - This function lets the user select bounding boxes to get statistics of the signals of interest in a sound
• sound_raster() - This function creates a raster file in ASCII format from the spectrogram of a soundfile

Calculate indices for many files in parallel

The function multiple_sounds() lets the user calculate an index for all the wav files in a directory. The function has an optional argument, no_cores, that can be used to specify to run the function using several cores in the same computer. This should reduce the running time significantly, in particular when analyzing a large number of files. This argument uses the parallel package, standard in R since version 2.14.

Download

Version 1.3.2:

• Linux and source: soundecology_1.3.2.tar.gz

Version 1.3.1:

• Linux and source: soundecology_1.3.1.tar.gz
• Windows: soundecology_1.3.1.zip
• Mac OS X Mavericks: soundecology_1.3.1.tgz

Vignettes

• An Introduction to the soundecology Package
• Differences of ACI values between seewave and soundecology
• Changes in the Acoustic Diversity Index

Changes

New for version 1.3.2:

• Fixed a bug where arguments were not checked correctly; values entered with quotes were incorrectly set as invalid. Issue #7

New for version 1.3.1:

• Added the results for the ACI by minute to the returned list in acoustic_complexity().
• Added a vignette to compare the ACI results between soundecology and seewave.
• Added the argument min_freq to acoustic_complexity().

New for version 1.3:

• Added the results for anthrophony and biophony to the results of ndsi().
• Fixed an error in the manual of ndsi where it said 'left' instead of 'right'.

New for version 1.2:

• Added arguments to multiple_sounds() to specify the range of time in the file to use for analysis. Fixing Issue #2.

New for version 1.1.1:

• Fixing conflict between functions of the packages seewave and tuneR

New for version 1.1:

• Added a new function, measure_signals(), to select signals from spectrograms.
• Added a new function, sound_raster(), to save spectrograms as ASCII raster files for GIS software.
• The function ndsi() was rewritten to avoid the problem R has with for loops. Now the function subsets the data in 1-second segments and feeds the data to pwelch() using apply, reducing execution time significantly.
• The function acoustic_evenness() was incorrectly named acoustic_eveness in version 1.0. This has been fixed.
• Fixed a bug in multiple_sounds() where the data was not appended to the results file correctly. This problem seems to have happened only in Windows.
• Other small bug fixes and typos.

References

• Boelman NT, Asner GP, Hart PJ, Martin RE. 2007. Multi-trophic invasion resistance in Hawaii: bioacoustics, field surveys, and airborne remote sensing. Ecological Applications 17:2137-2144.
• Kasten, Eric P., Stuart H. Gage, Jordan Fox, and Wooyeong Joo. 2012. The Remote Environmental Assessment Laboratory’s Acoustic Library: An Archive for Studying Soundscape Ecology. Ecological Informatics 12: 50-67. doi: 10.1016/j.ecoinf.2012.08.001
• Pieretti, N., A. Farina, and D. Morri. 2011. A new methodology to infer the singing activity of an avian community: The Acoustic Complexity Index (ACI). Ecological Indicators 11: 868-873. doi: 10.1016/j.ecolind.2010.11.005
• Remote Environmental Assessment Laboratory. http://www.real.msu.edu
• Villanueva-Rivera, L. J., B. C. Pijanowski, J. Doucette, and B. Pekin. 2011. A primer of acoustic analysis for landscape ecologists. Landscape Ecology 26: 1233-1246. doi: 10.1007/s10980-011-9636-9

Author

Luis J. Villanueva (@ljvillanueva)

Support or Contact

Feel free to contribute code, corrections, or ideas. For problems and bugs, please fill a report at https://github.com/ljvillanueva/soundecology/issues