PAM: Large Dataset Analysis

A Comprehensive Approach to Annotating Acoustic Data

Passive acoustic datasets are complex and unwieldy. This course provides one approach to tackling big acoustic data.

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PAM: Large Dataset Analysis is an asynchronous, online technical training course designed to provide bioacousticians with an approach to processing large passive acoustic datasets using a combination of accessible software including PAMGuard and several R programming packages.  

In this approach to passive acoustic dataset analysis, we provide an end-to-end workflow that you can use for annotating and summarizing sounds within your data. This approach can be used with either marine or terrestrial acoustic datasets, and focus on detection and annotation of calls within single channel data from either environment. The course starts with the semi-automated approach to dataset annotation using a combination of machine learning algorithms, and post-automation grouping of calls within PAMGuard. PAMGuard has long been touted as a real-time monitoring tool but is also capable of effective processing of archival data using a suite of automated detectors and review modules. Once data are annotated in the binary and database format used by PAMGuard, we extract measurement and from the R package ‘PAMpal’ to format, query and visualize the annotated data. The course then guides you through the process of generating representative figures of example calls in your data using the ‘seewave’ package in R. Finally, we provide guidance on descriptive statistics for your data and examples of inferential statistics that can be used to compare measurements of your data using the statistical platform jamovi (R-based graphical user interface, or GUI). Marine and terrestrial datasets are provided for data processing practice (selecting one dataset to use throughout the course).

The course is designed for users whose experience levels include:

  • Bioacoustics: familiarity with the topic and understand fundamental elements of passive acoustic monitoring, mitigation or research.
  • PAMGuard & SQLite Studio: some experience with PAMGuard is expected. We do not step through the core elements of PAMGuard, but the “PAM Software Basics” course is available if users require this training, as are several resources on the PAMGuard and OSA websites. PAMGuard is installed on local machine so a Windows PC with a minimum of 8 GB of RAM is required. NOTES: processing large acoustic datasets is computationally intensive; we mitigate this to accommodate a range of computing power by having you processes shorter segments of data in the examples. However, we recommend for applying these techniques to months of data, that you have access to a powerful computer or virtual machine. SQLite Studio is downloaded to accompany PAMGuard detection summary extraction from database. Microsoft Excel is used to format extracted csv file.
  • R: We assume no-to-novice experience level in R, and the design of the modules based in R as such that you will not need to have programming experience to complete them. We use R notebooks and RStudio Cloud during these modules. Please note, this course is not intended to teach you how to program in R, nor extensively train you in all aspects of the ‘ggplot2’ and ‘seewave’ packages – it is intended to provide you with some example data visualization techniques and code you can use in your own work. If you are desiring to learn more regarding the basics of R and analytical uses, see our “R for Ocean Science Data Analysis” course.
  • jamovi: this tool is a statistical analysis GUI that incorporates R under the hood. It offers an easy user interface for conducing statistical evaluation and analyses and is easy to install on local computers.

Given the likely variability in experience for the content in the final two modules, participants may select from a “Full Course Complement” (including all modules below) or a “PAMGuard and PAMpal Only” option that include Modules 1-4 from the course topics list.

 

IMarEST Accreditation Pending

The Institute of Marine Engineering, Science and Technology (IMarEST) is an international society for marine professionals. IMarEST provides a peer-reviewed assessment of courses to ensure effective delivery of rigorous technical content. PAM: Large Acoustic Datasets is recognized as an accredited continuing professional development (CPD) course by IMarEST.

Learn More About IMarEST

Frequently Asked Questions

PAMGuard is an open-access program and free to download.  However, you will need to use a Windows PC computer for which you have administrative privileges to download and install software.  Unfortunately, the software is not supported for Mac users, so this course cannot accommodate Macs. However, our aim is to make training accessible to everyone so we are working on a Virtual Machine option and will indicate when available.

You will need to download and install a free SQLite Studio software for accessing data from the .sql3 database, and ability to open .csv files for a brief period of the course (in MS Excel). If you do not have access to MS Excel we can make an option available to you through MS Office 365 (as a shared online file). 

We are also using a cloud-based R environment (Posit Cloud) and an online version of jamovi. You will need internet access to take this course and ability to login to these resources made available to you. 

Training groups are limited in capacity due to the support provided during the course.  However, you can join a training group at any time during the indicated month and still have the same period of access (30 days). For example, if you join the course on April 10, you will have access until through May 9th.

That is up to you!  There is approximately 25-35 hours worth of training materials, but individuals work at different paces depending on their familiarity with software and comfort level with computers.  The 30 days of access is intended to allow you to work at your own pace. 

If a scenario arises where you are in need of more time, we are happy to work with you to help you meet you goal of completing the training.  Extended duration access is also available for an additional cost.

A certificate is provided upon completion of all module activities.  PAM: Large Dataset Analysis is under consideration for accreditation with the Institute of Marine Engineering, Science and Technology as a continuing professional development course.

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