A critique of the paper “Potential causes for amphibian declines in Puerto Rico” by Burrowes, Joglar and Green

One of the great things about blogs is that it allows scientists to express their ideas in a more open and direct way. The old way to criticize a paper was to write a letter or a paper and try to get it published. Now, anyone can provide arguments and discuss a paper for the world to see.

In 2004 I tried to publish a rebuttal of the paper “Potential causes for amphibian declines in Puerto Rico” by Burrowes, Joglar and Green, published in Herpetologica. Unfortunately, the editors decided that the wording in their paper was vague enough that it made it hard for them to justify my comments as a rebuttal. I recently stumbled upon the original emails, so I decided to make my original comments of that paper available here. As a disclaimer, I worked with the first two authors for several years and I was one of the students that collected the data used in that paper during that time.

The full citation of the paper is:

Burrowes, Patricia A., Rafael L. Joglar, and David E. Green. 2004. Potential causes for amphibian declines in Puerto Rico. Herpetologica 60: 141-154.

Some of the problems of the paper are: Continue reading

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This weekend at the SACNAS meeting in Dallas

I’ll be attending the SACNAS National Meeting this weekend in Dallas, TX. If you’re there, just look for me.

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New Paper: Comparing methods to automatically classify species’ calls

A few days ago the paper appeared in the online list of Ecological Informatics:

Abstract below the fold.

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Mount a Windows share

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Compressing audio files without loosing data

FLAC Compression

High quality audio files take a lot of space, for example, a 1 minute stereo sound at CD-quality (44.1 kHz) will take about 10-11 Mb. A large collection of sound files will fill hard drives really fast. The usual solution to this problem is to compress the files, however each compression system has its limitations.

The common zip compression format works well for text but does not compress audio in any significant degree. Encoding the file to mp3 will destroy a lot of information that will be necessary to analyze the audio.

FLAC (Free Lossless Audio Codec) is optimized for wav audio files, and can compress a wav to 30-50% of its original size. It appears that the amount of compression will depend on the complexity of the sound recorded. The decoding back to wav is very fast and it is an exact copy of the original file. Continue reading

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Digital recorders increase detection of Eleutherodactylus frogs

I am posting the paper and the data associated with this paper:

Villanueva-Rivera, L. J. 2007. Digital recorders increase detection of Eleutherodactylus frogs. Herpetological Review 38: 59-63. PDF.

Read the readme.txt file in each zip archive for details.

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Sound Viewer Tool – a fast Python script to get waveform and spectrogram from a sound

This script uses the numpy and audiolab modules to generate waveform and spectrogram png images from a wav file. The original script was from the Freesound Blog. The wav file needs to be 16 bit, mono and have a sampling rate of 44.1 kHz. The script takes about 2-3 seconds for a 60 seconds file (on a Core2 Duo 2GHz, 2GB RAM machine).

Update: The script is now a project on SourceForge: http://sourceforge.net/projects/soundviewer/

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Posted in Bioacoustics, Python | 2 Comments

Make MP3 files from FLAC

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Mount a directory using a secure connection

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A short list of audio software

Free and open source audio software

  • Audacity – The Free, Cross-Platform Sound Editor. Windows, Mac OS X, Linux and others.
  • R – R is a free software environment for statistical computing and graphics. Two packages allow to load and analyze sound files: sound and seewave. Windows, Mac OS X, Linux, and others.
  • Raven Lite – Free version of Raven Pro. Limited to some visualizations, formats, and time. Windows and Mac OS X.

Commercial Audio Software

  • Adobe Audition – Professional studio application. Allows to visualize, edit and mix many audio formats. Windows only.
  • Raven Pro – Audio analysis program from the Cornell Lab of Ornithology. Windows and Mac OS X.
  • Apple Logic Studio – Professional studio application. Mac OS X only.
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