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Keywords: fish  or reproducibility  or Ecoacoustics 

7 Steps towards Reproducible Research

This workshop aims to take you further down your reproducibility path, by providing concepts and tools you can use in your everyday workflows. It is discipline and experience agnostic, and no coding experience is needed.

We will also examine how Reproducible Research builds business continuity...

Keywords: reproducibility, Reproducibility, reproducible workflows

Resource type: full-course, tutorial

7 Steps towards Reproducible Research https://dresa.org.au/materials/7-steps-towards-reproducible-research This workshop aims to take you further down your reproducibility path, by providing concepts and tools you can use in your everyday workflows. It is discipline and experience agnostic, and no coding experience is needed. We will also examine how Reproducible Research builds business continuity into your research group, how the culture in your institute ecosystem can affect Reproducibility and how you can identify and address risks to your knowledge. The workshop can be used as self-paced or as an instructor Amanda Miotto - a.miotto@griffith.edu.au reproducibility, Reproducibility, reproducible workflows phd support
Open Ecoacoustics make your own recogniser

Includes the requirements and practical steps required to make your own automated call recogniser using a convolution neural network.

The "Requirements" section includes demo data and requirements for the data you should include to develop your own recogniser as well as links to Anaconda &...

Keywords: Ecoacoustics, call recogniser, convolutional neural network

Open Ecoacoustics make your own recogniser https://dresa.org.au/materials/open-ecoacoustics-make-your-own-recogniser Includes the requirements and practical steps required to make your own automated call recogniser using a convolution neural network. The "Requirements" section includes demo data and requirements for the data you should include to develop your own recogniser as well as links to Anaconda & Raven Lite software. The "Practical Steps" provides instructions to run the required Jupyter notebook to build a recogniser with CNN. * Note additional AI methods will be available soon https://openecoacoustics.org/contact/ Ecoacoustics, call recogniser, convolutional neural network
Open Ecoacoustics wrangling sound files

An introduction to slicing, dicing, chopping, resampling, compressing etc sound files with an introduction to command line and graphical tools.

A "Requirements" section with demo data, file dependencies, and required software.

A "Presentation" section with an online introduction to storing...

Keywords: Ecoacoustics, sound files, data wrangling

Open Ecoacoustics wrangling sound files https://dresa.org.au/materials/open-ecoacoustics-wrangling-sound-files An introduction to slicing, dicing, chopping, resampling, compressing etc sound files with an introduction to command line and graphical tools. A "Requirements" section with demo data, file dependencies, and required software. A "Presentation" section with an online introduction to storing data, repairing data and segmenting files. A "Practical" section inclusive of setup, Terminal use, manipulating files with FFmpeg, using the AnalysisPrograms audio cutter, run EMU software https://openecoacoustics.org/contact/ Ecoacoustics, sound files, data wrangling
Open Ecoacoustics acoustic indices

Provides an introduction to and generation of false-colour spectrograms and indices.

Includes a "Requirements" section where demo audio files, other dependencies and required software.

Includes a "Presentation" section providing an online presentation on false colour...

Keywords: Ecoacoustics, false-colour spectrograms, acoustic indices

Open Ecoacoustics acoustic indices https://dresa.org.au/materials/open-ecoacoustics-acoustic-indices Provides an introduction to and generation of false-colour spectrograms and indices. Includes a "Requirements" section where demo audio files, other dependencies and required software. Includes a "Presentation" section providing an online presentation on false colour spectrograms. Includes a "Practical" section that provides the setup, use of terminal, Analysis Programs software, and calculation of acoustic indices. https://openecoacoustics.org/contact/ Ecoacoustics, false-colour spectrograms, acoustic indices
Open Ecoacoustics recording and labelling

This module includes recommendations for deployment, recording and labelling sounds, playing those sounds and annotation using Audacity and Raven software.

The "Requirements" section includes downloads of example data, required dependencies and software.

The "Presentation" walks through an...

Keywords: Ecoacoustics, recording sound, labelling sound, spectrograms

Open Ecoacoustics recording and labelling https://dresa.org.au/materials/open-ecoacoustics-recording-and-labelling This module includes recommendations for deployment, recording and labelling sounds, playing those sounds and annotation using Audacity and Raven software. The "Requirements" section includes downloads of example data, required dependencies and software. The "Presentation" walks through an online presentation with recommendations recorder deployment recommendations, annotation, raven software, & manual validation The "Practical" includes setup, single species annotation of spectrograms, multi-species, and generating images https://openecoacoustics.org/contact/ Ecoacoustics, recording sound, labelling sound, spectrograms
Open Ecoacoustics sound basics

This online presentation provides a review of five key concepts related to ecoacoustics: 1. Decibels, 2. clipping and gain, 3. ADC: Sample rate & bit depth, 4. Fast Fourier Transform (FFT), and 5. Spectrograms: time / frequency trade off.

Keywords: Ecoacoustics, sound basics, decibels, gain, sample rate, FFT, spectrograms

Open Ecoacoustics sound basics https://dresa.org.au/materials/open-ecoacoustics-sound-basics This online presentation provides a review of five key concepts related to ecoacoustics: 1. Decibels, 2. clipping and gain, 3. ADC: Sample rate & bit depth, 4. Fast Fourier Transform (FFT), and 5. Spectrograms: time / frequency trade off. https://openecoacoustics.org/contact/ Ecoacoustics, sound basics, decibels, gain, sample rate, FFT, spectrograms
Ecoacoustics & EcoCommons Generalised Dissimilarity Modelling (GDM) use case

This example highlights how data collected with passive acoustic monitoring (PAM) can be used to examine spatial variation in species composition.

This example draws from an R package developed to make GDM more accessible: https://github.com/EcoCommons-Australia/community-modelling

Keywords: Generalised Dissimilarity Modelling, Ecoacoustics, EcoCommons

Ecoacoustics & EcoCommons Generalised Dissimilarity Modelling (GDM) use case https://dresa.org.au/materials/ecoacoustics-ecocommons-generalised-dissimilarity-modelling-gdm-use-case This example highlights how data collected with passive acoustic monitoring (PAM) can be used to examine spatial variation in species composition. This example draws from an R package developed to make GDM more accessible: https://github.com/EcoCommons-Australia/community-modelling https://openecoacoustics.org/contact/ Generalised Dissimilarity Modelling, Ecoacoustics, EcoCommons
EcoCommons & Open EcoAcoustics SDM use case

  1. Examples of code and the associated text summaries describe how open ecoacoustics https://openecoacoustics.org/ data can generate better SDM predictions. By using long-term monitoring data from https://acousticobservatory.org/ which allows analysts to infer absence locations, which does a much...

Keywords: Species Distribution Modelling, Ecoacoustics, Ecology, Owls, Mapping uncertainty

EcoCommons & Open EcoAcoustics SDM use case https://dresa.org.au/materials/ecocommons-open-ecoacoustics-sdm-use-case 1. Examples of code and the associated text summaries describe how open ecoacoustics https://openecoacoustics.org/ data can generate better SDM predictions. By using long-term monitoring data from https://acousticobservatory.org/ which allows analysts to infer absence locations, which does a much better job at predicting distributions than presence only methods, and which facilitate use of call frequency as a response variable rather than presence absence. The code and data used to generate these examples: https://github.com/andrew-1234/sdm-usecase-master 2. Shows one way to overlay areas with the least geographically and environmentally representative sampling in addition to the predicted probability of occurrence generated by an SDM. This shows how to spatially represent areas where additional acoustic sampling would increase representative sampling most. The code used in this example: https://github.com/EcoCommons-Australia/educational_material/tree/main/SDMs_in_R/Scripts/adding_uncertainty_to_the_map https://www.ecocommons.org.au/contact/ Species Distribution Modelling, Ecoacoustics, Ecology, Owls, Mapping uncertainty ugrad masters mbr phd
How can software containers help your research?

This video explains software containers to a research audience. It is an introduction to why containers are beneficial for research. These benefits are standardisation, portability, reliability and reproducibility. 

Software Containers in research are a solution that addresses the challenge of a...

Keywords: containers, software, research, reproducibility, RSE, standard, agility, portable, reusable, code, application, reproducible, standardisation, package, system, cloud, server, version, reliability, program, collaborator, ARDC_AU, training material

How can software containers help your research? https://dresa.org.au/materials/how-can-software-containers-help-your-research-ca0f9d41-d83b-463b-a548-402c6c642fbf This video explains software containers to a research audience. It is an introduction to why containers are beneficial for research. These benefits are standardisation, portability, reliability and reproducibility.  Software Containers in research are a solution that addresses the challenge of a replicable computational environment and supports reproducibility of research results. Understanding the concept of software containers enables researchers to better communicate their research needs with their colleagues and other researchers using and developing containers. Watch the video here: https://www.youtube.com/watch?v=HelrQnm3v4g If you want to share this video please use this: Australian Research Data Commons, 2021. How can software containers help your research?. [video] Available at: https://www.youtube.com/watch?v=HelrQnm3v4g DOI: http://doi.org/10.5281/zenodo.5091260 [Accessed dd Month YYYY]. contact@ardc.edu.au Martinez, Paula Andrea (type: ProjectLeader) Sam Muirhead (type: Producer) The ARDC Communications Team (type: Editor) The ARDC Skills and Workforce Development Team (type: ProjectMember) The ARDC eResearch Infrastructure & Services (type: ProjectMember) The ARDC Nectar Cloud Services team (type: ProjectMember) containers, software, research, reproducibility, RSE, standard, agility, portable, reusable, code, application, reproducible, standardisation, package, system, cloud, server, version, reliability, program, collaborator, ARDC_AU, training material
CheckEM User Guide

CheckEM is an open-source web based application which provides quality control assessments on metadata and image annotations of fish stereo-imagery. It is available at marine-ecology.shinyapps.io/CheckEM. The application can assess a range of sampling methods and annotation data formats for...

Keywords: stereo-video, fish, annotation

CheckEM User Guide https://dresa.org.au/materials/checkem-user-guide CheckEM is an open-source web based application which provides quality control assessments on metadata and image annotations of fish stereo-imagery. It is available at marine-ecology.shinyapps.io/CheckEM. The application can assess a range of sampling methods and annotation data formats for common inaccuracies made whilst annotating stereo imagery. CheckEM creates interactive plots and tables in a graphical interface, and provides summarised data and a report of potential errors to download. brooke.gibbons@uwa.edu.au stereo-video, fish, annotation
EventMeasure Annotation Guide

EventMeasure annotation guide for baited remote underwater stereo video systems (stereo-BRUVs) for count and length

Keywords: fish, stereo-video, annotation

EventMeasure Annotation Guide https://dresa.org.au/materials/eventmeasure-annotation-guide EventMeasure annotation guide for baited remote underwater stereo video systems (stereo-BRUVs) for count and length tim.langlois@uwa.edu.au fish, stereo-video, annotation
Stereo-video workflows for fish and benthic ecologists

Stereo imagery is widely used by research institutions and management bodies around the world as a cost-effective and non-destructive method to research and monitor fish and habitats (Whitmarsh, Fairweather and Huveneers, 2017). Stereo-video can provide accurate and precise size and range...

Keywords: stereo-video, fish, sharks, habitats

Resource type: tutorial

Stereo-video workflows for fish and benthic ecologists https://dresa.org.au/materials/stereo-video-workflows-for-fish-and-benthic-ecologists Stereo imagery is widely used by research institutions and management bodies around the world as a cost-effective and non-destructive method to research and monitor fish and habitats (Whitmarsh, Fairweather and Huveneers, 2017). Stereo-video can provide accurate and precise size and range measurements and can be used to study spatial and temporal patterns in fish assemblages (McLean et al., 2016), habitat composition and complexity (Collins et al., 2017), behaviour (Goetze et al., 2017), responses to anthropogenic pressures (Bosch et al., 2022) and the recovery and growth of benthic fauna (Langlois et al. 2020). It is important that users of stereo-video collect, annotate, quality control and store their data in a consistent manner, to ensure data produced is of the highest quality possible and to enable large scale collaborations. Here we collate existing best practices and propose new tools to equip ecologists to ensure that all aspects of the stereo-video workflow are performed in a consistent way. tim.langlois@uwa.edu.au stereo-video, fish, sharks, habitats
10 Reproducible Research things - Building Business Continuity

The idea that you can duplicate an experiment and get the same conclusion is the basis for all scientific discoveries. Reproducible research is data analysis that starts with the raw data and offers a transparent workflow to arrive at the same results and conclusions. However not all studies are...

Keywords: reproducibility, data management

Resource type: tutorial, video

10 Reproducible Research things - Building Business Continuity https://dresa.org.au/materials/9-reproducible-research-things-building-business-continuity The idea that you can duplicate an experiment and get the same conclusion is the basis for all scientific discoveries. Reproducible research is data analysis that starts with the raw data and offers a transparent workflow to arrive at the same results and conclusions. However not all studies are replicable due to lack of information on the process. Therefore, reproducibility in research is extremely important. Researchers genuinely want to make their research more reproducible, but sometimes don’t know where to start and often don’t have the available time to investigate or establish methods on how reproducible research can speed up every day work. We aim for the philosophy “Be better than you were yesterday”. Reproducibility is a process, and we highlight there is no expectation to go from beginner to expert in a single workshop. Instead, we offer some steps you can take towards the reproducibility path following our Steps to Reproducible Research self paced program. Video: https://www.youtube.com/watch?v=bANTr9RvnGg Tutorial: https://guereslib.github.io/ten-reproducible-research-things/ a.miotto@griffith.edu.au; s.stapleton@griffith.edu.au; i.jennings@griffith.edu.au; Sharron Stapleton Isaac Jennings reproducibility, data management masters phd ecr researcher support