Data from: MatlabHTK: a simple interface for bioacoustic analyses using Hidden Markov models

1. Passive bioacoustic recording devices are now widely available and able to continuously record remotely located sites for extended periods, offering great potential for wildlife monitoring and management. Analysis of the huge datasets generated, in particular for specific biotic sound recognition, remains a critical bottleneck for widespread adoption of these technologies as current methods are labour intensive.

2. Several methods borrowed from speech processing frameworks, such as hidden Markov models, have been successful in analysing bioacoustic data but the software implementations can be expensive and difficult to use for non-specialists involved in wildlife conservation. To remedy this, we present a software interface to a popular speech recognition system making it possible for non-experts to implement hidden Markov models for bioacoustic signal processing. Octave/Matlab functions are used to simplify the set up and the definition of a bioacoustic signal recogniser as well as the analysis of the results.

3. We present the different functions as a workflow. To demonstrate how the package can be used we give the results of an analysis of a bioacoustic monitoring dataset to detect the nocturnal presence and behaviour of a cryptic seabird species, the common diving petrel Pelecanoides urinatrix urinatrix, from Northern New Zealand.

4. We show that the package matlabHTK can be used efficiently to reconstruct the daily patterns of colony activity in the common diving petrel.

1. 被动生物声学录音设备（Passive bioacoustic recording devices）如今已广泛普及，可对偏远监测点位进行长期连续录音，为野生动物监测与管理工作提供了巨大应用潜力。但所生成的海量数据集，尤其是针对特定生物声源识别的分析，仍是制约此类技术大规模推广的关键瓶颈——现有分析方法均需耗费大量人力。
2. 现有诸多源自语音处理框架的方法（如隐马尔可夫模型（Hidden Markov Models））已成功应用于生物声学数据分析，但相关软件实现成本高昂，且对于从事野生动物保护的非专业人士而言操作难度较大。为解决这一问题，本研究针对一款主流语音识别系统开发了软件接口，使非专业人员也能借助其实现面向生物声学信号处理的隐马尔可夫模型构建。研究采用Octave/Matlab函数简化了生物声学信号识别器的搭建、定义以及结果分析流程。
3. 本研究将各项功能整合为一套完整工作流。为演示该工具包的使用方法，我们对一套生物声学监测数据集开展分析，以此检测新西兰北部一种隐匿性海鸟——普通潜水海燕（Pelecanoides urinatrix urinatrix）的夜间活动踪迹与行为模式。
4. 研究证实，matlabHTK工具包可高效复现普通潜水海燕的种群每日活动模式。