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（bioacoustic）记录设备现已广泛普及，可对偏远监测站点进行长时间连续录音，为野生动物监测与管理工作提供了巨大应用潜力。然而，此类设备所生成的海量数据集，尤其是针对特定生物声信号识别的分析工作，目前仍是制约该技术大规模推广的关键瓶颈：现有分析方法多为劳动密集型，需耗费大量人力成本。 2. 此前已有多种源自语音处理框架的方法（如隐马尔可夫模型（hidden Markov models））被成功应用于生物声学数据分析，但相关软件实现方案往往成本高昂，且对于从事野生动物保护的非专业人员而言操作门槛较高。为解决这一痛点，我们针对一款主流语音识别系统开发了配套软件接口，使非专业人员也能够借助隐马尔可夫模型开展生物声学信号处理工作。本工具采用Octave/Matlab函数简化了生物声学信号识别器的搭建、定义及结果分析流程。 3. 我们将各功能模块整合为一套标准化工作流。为演示该软件包的使用方法，我们针对一组生物声学监测数据集开展分析，实现了对新西兰北部一种隐秘性海鸟——普通潜水海燕（Pelecanoides urinatrix urinatrix）的夜间活动踪迹与行为模式的检测，并展示了对应的分析结果。 4. 实验结果表明，matlabHTK软件包可高效实现普通潜水海燕种群活动日节律的重建工作。