NHM Sound Archive (Part 1): Mole Crickets

Today a paper written by myself and Natural History Museum (NHM) volunteer Yoke-Shum Broom was published in the Biodiversity Data Journal. It is the first data paper to come from the NHM Sound Archive digitisation project. The archive itself is part of the inspiration behind the BioAcoustica project (Baker et al, 2015). The paper covers the Mole Crickets (Orthoptera: Gryllotalpidae).

The paper is certainly modest compared to other forthcoming data papers on the NHM's collection of Orthoptera sounds (and even our previous paper on African cicada songs), however it is of interest due to the fact we have plaster casts of two of the species singing burrows to supplement the sound recordings.

Gryllotalpa vineae was first described by Bennet-Clark in 1970 who later, published on the acoustic properties of its singing burrow (see figure).

The existence of the singing burrow cast and the recordings has previously been limited to those with knowledge of the NHM's Orthoptera collection and those who have read Bennet-Clark's papers. To aid access (and hopefully increase interest) in these items the burrow casts we have (of Gryllotalpa vineae and also Gryllotalpa gryllotalpa) have been laser scanned. 3D models of the burrows have been made available on the NHM's Data Portal.

The paper has more details: Natural History Museum Sound Archive I: Orthoptera: Gryllotalpidae Leach, 1815, including 3D scans of burrow casts of Gryllotalpa gryllotalpa Linnaeus, 1758 and Gryllotalpa vineae Bennet-Clark, 1970.

Ecoacoustics Congress 2016

Bioacoustics workshop at Stellenbosch University (February 2016)

Marianna Simnett - Blue Roses

Earlier this year I was tasked with creating a (fake) control backpack to temporarily attach to a Blaberus cockroach as part of Marianna Simnett's film Blue Roses. You can watch the film below. The cockroach, now without backpack, is enjoying its retirement.

New Paper: The worldwide status of stick insects (Insecta: Phasmida) as pests of agriculture and forestry, with a generalised theory of phasmid outbreaks

A review paper I have been working on sporadically for a number of years has just been published in Agriculture and Food Security: The worldwide status of stick insects (Insecta: Phasmida) as pests of agriculture and forestry, with a generalised theory of phasmid outbreaks.

Those of you at the Summer Phasmid Study Group Meeting this year will have seen a talk (Phasmids as Pests of Agriculture and Forestry) I gave that touched on the species and conclusions presented here. The slides are below.

Installing BioAcousticaR R package

The BioAcousticaR R package provides access to the BioAcoustica collection of recorded wildlife sound within the R environment.

The BioAcousticaR package, and one if its dependencies (DrupalR) are currently in active development on GitHub and the process for installing these packages may be different to what you are used to.

1. Install the devtools package:
   
   install.packages("devtools");
   library(devtools);
   
   If devtools installation fails on Ubuntu see: Install R devtools on Ubuntu
2. Install the DrupalR package (requires you to have the httr package installed).
   
   The Virtual Research Environment that BioAcoustica is built on, the Scratchpads project, is in turn built on the Drupal content management system. The DrupalR package provides the basic functionality of authenticating to and getting data from Drupal based websites (more functionality can be expected in the future). BioAcousticaR makes use of DrupalR to perform basic behind-the-scenes tasks.
   
   install_github("edwbaker/DrupalR");
3. Install the BioAcousticaR package:
   
   install_github("BioAcoustica/BioAcousticaR");
   

Install R devtools on Ubuntu

The devtools package for R allows, amongst other things, for R packages to be downloaded from GitHub: install_github().

As part of the BioAcoustica project an R package to access the BioAcoustica dataset, BioAcousticaR, is in development with the code hosted on GitHub.

To install devtools on Ubuntu first requires the libssl-dev package to be installed from the command line:

sudo apt-get install libssl-dev

Then the devtools package can be installed in R as usual:

install.packages("devtools")

BioAcoustica on GBIF

BioAcoustica has been contributing content (where licences allow) to the Encyclopedia of Life (EoL) for around the last six months. So far these contributions are primarily just over 2,000 recordings of species, predominantly of Orthoptera and Cicadas.

Recently (as described in Baker et al., 2015) we have been contributing occurrence data to the Global Biodiversity Informatics Facility (GBIF).


References
Baker E, Price B, Rycroft S, Villet M (2015) Global Cicada Sound Collection I: Recordings from South Africa and Malawi by B. W. Price & M. H. Villet and harvesting of BioAcoustica data by GBIF. Biodiversity Data Journal 3: e5792. doi: 10.3897/BDJ.3.e5792

BioAcoustica papers

So far two papers have been published on the BioAcoustica project. The first, published in Database: The Journal of Biological Databases and Curation, covers the infrastructure of the BioAcoustica platform (the repository is built upon Scratchpads with the analyses being performed in the cloud using BioVeL).

Baker E, Price BW, Rycroft SD, Hill J, Smith VS (2015) BioAcoustica: a free and open repository and analysis platform for bioacoustics. Database bav054 doi:10.1093/database/bav054

The second, in the Biodiversity Data Journal, is the first of a number of data papers that will describe the various collections of audio recordings that form BioAcoustica. In addition we announce the ability for individual Scratchpads to contribute specimen/occurrence data to GBIF (the ability to contribute to the Encyclopedia of Life was discussed in the first paper).

Baker E, Price BW, Rycroft SD (2015) Global Cicada Sound Collection I: Recordings from South Africa and Malawi by B. W. Price & M. H. Villet and harvesting of BioAcoustica data by GBIF. Biodiversity Data Journal 3:e5792 doi:10.3897/BDJ.3.e5792

BioAcoustica: Tape speed conversion table

Reel-to-reel (spool) tape machines operate at a number of standard speeds. This table can be used to provide playback speed multipliers for audio conversion software (such as sox) to correct for using a playback machine not capable of the correct speed. Such conversion will have effects on audio quality, so recording at an appropriate bit rate is essential.

From	To
	2.38	4.76	9.53	19.05	38.1	76.2
2.38	1	0.5	0.25	0.125	0.0625	0.03125
4.76	2	1	0.5	0.25	0.125	0.0625
9.53	4	2	1	0.5	0.25	0.125
19.05	8	4	2	1	0.5	0.25
38.1	16	8	4	2	1	0.5
76.2	32	16	8	4	2	1

BioAcoustica: Does MP3 work for wildlife sound?

Introduction
MP3 has become the dominant format for sharing digital music, while many researchers in bioacoustics still use the raw waveform (WAV files). MP3 has the advantage of significantly smaller file size, which becomes a concern when creating potentially very large collections of sound like we are doing with BioAcoustica. Storing and serving MP3 files would be much less resource-intensive than storing and serving WAV files.

All other things being equal therefore, MP3 has an advantage over WAV. The disadvantages of MP3 are that is a lossy compression format: some of the original data is lost when encoding a sound file as MP3. The general acceptance of the MP3 format for high-fidelity audio is due, in large part, to the MP3 standard discarding data that the ears and/or brain cannot detect or process. Frequencies above the threshold of human hearing (approximately 20kHz in young humans) can safely be discarded. The MP3 format also discards information that the brain does not perceive, using various methods from the field of psychoacoustics.

The examples below are comparisons of a WAV recording of the cicada Platypleura haglundi from this recording on BioAcoustica, and a high quality (320kbit/s) MP3 conversion of the same file.

Frequency Response
The frequency vs amplitude charts for the WAV (left) and MP3 (right) files show that as well as removing any frequencies above 20kHz the conversion to MP3 lowers the relative amplitude of the low frequency sounds. On playback it is hard to tell the difference between the two files, showing that the MP3 format is capable of accurately reproducing how humans hear sound, while discarding a lot of information.


Spectrogram
 The spectrograms showing WAV (top) and MP3 (bottom) demonstrate what the effect of discarding higher frequencies has on visually identifiable features in the call. The WAV file shows clearly repeating sounds in the 17-21kHz range, while this information is lost in the MP3.

Conclusions 
While high-quality MP3 files will prove adequate for those wishing to learn to identify acoustic species by ear, for other methods MP3 encoding can discard useful information. This is particularly true where components of the sound are above 20kHz, and in applications where the relative amplitudes of different frequencies may prove useful in identification.

Raspberry Pi Home Automation with Arduino

This is a book for which I was a Technical Reviewer, it's now available for purchase: Raspberry Pi Home Automation with Arduino.