1. Home
  2. Materials
Register training material
8 materials found

Target audience: ugrad 

and

Content provider: AARNet  or EcoCommons 

EcoCommons written support material, species distribution models explained and platform guides

These written descriptions on how to use the EcoCommons platform, the descriptions of the variety of species distribution models (SDM) available and the how to design and run and SDM have proven very popular with students whose instructors are using EcoCommons to teach basic SDM. They also...

Keywords: Species Distribution Modelling, Ecology, EcoCommons

EcoCommons written support material, species distribution models explained and platform guides https://dresa.org.au/materials/ecocommons-written-support-material-species-distribution-models-explained-and-platform-guides These written descriptions on how to use the EcoCommons platform, the descriptions of the variety of species distribution models (SDM) available and the how to design and run and SDM have proven very popular with students whose instructors are using EcoCommons to teach basic SDM. They also provide useful references for anyone using the platform. https://www.ecocommons.org.au/contact/ Species Distribution Modelling, Ecology, EcoCommons ugrad masters mbr phd
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
EcoCommons Marine use case

This is a toy example with many of the steps required for a robust example not included. This does show how to pull together marine data from IMOS / AODN and summarise those environmental predictors and occurrence data by month. Then we show how you can pull together one model with predictors...

Keywords: Species Distribution Modelling, SDM temporal predictions, Ecology, Marine seasonal distributions, R statistical software

EcoCommons Marine use case https://dresa.org.au/materials/ecocommons-marine-use-case This is a toy example with many of the steps required for a robust example not included. This does show how to pull together marine data from IMOS / AODN and summarise those environmental predictors and occurrence data by month. Then we show how you can pull together one model with predictors that are both temporally (monthly) and spatially (Australian waters) explicit. Again, a robust example would need calibration and validation steps, but this example does show how SDMs can be developed across time. The data and code needed to run these examples is here: https://github.com/EcoCommons-Australia/educational_material/tree/main/Marine_use_case https://www.ecocommons.org.au/contact/ Species Distribution Modelling, SDM temporal predictions, Ecology, Marine seasonal distributions, R statistical software ugrad masters mbr phd ecr
Species Distribution Modelling in R

This set of scripts and videos provide an introduction to running SDMs in R and include some steps to consider that go beyond what's available in the EcoCommons SDM point-and-click tools.

Five videos include: 1. An introduction to SDM in R, 2. occurrence data, 3. environmental data, 4. fitting...

Keywords: Species Distribution Modelling, Ecology, R software, EcoCommons

Species Distribution Modelling in R https://dresa.org.au/materials/species-distribution-modelling-in-r This set of scripts and videos provide an introduction to running SDMs in R and include some steps to consider that go beyond what's available in the EcoCommons SDM point-and-click tools. Five videos include: 1. An introduction to SDM in R, 2. occurrence data, 3. environmental data, 4. fitting your model, 5. model evaluation Scripts and files are available here: https://github.com/EcoCommons-Australia/educational_material/tree/main/SDMs_in_R/Scripts Scripts for all four modules are here: https://www.ecocommons.org.au/wp-content/uploads/EcoCommons_steps_1_to_4.html https://www.ecocommons.org.au/contact/ Species Distribution Modelling, Ecology, R software, EcoCommons ugrad mbr phd
Get started with R: an introduction for beginners

These two videos walk through the "R for Ecologists" module offered by the Data Carpentries https://datacarpentry.org/R-ecology-lesson/

The first video: Manipulating Data covers:
Opening R, setting your working directory, reading and downloading csv files, selecting and filtering data, using...

Keywords: Beginner R coding, The Carpentries, R studio, Beginer ecological modelling

Resource type: video, lesson

Get started with R: an introduction for beginners https://dresa.org.au/materials/get-started-with-r-an-introduction-for-beginners These two videos walk through the "R for Ecologists" module offered by the Data Carpentries https://datacarpentry.org/R-ecology-lesson/ The first video: Manipulating Data covers: Opening R, setting your working directory, reading and downloading csv files, selecting and filtering data, using pipeline operators, creating new columns based on existing ones, and summarising data The second video: Visualising data with ggplot2 covers: A recap of module 1 and getting started with ggplot2 to create plots and a variety of data visualisations Links to the R scripts are provided https://www.ecocommons.org.au/contact/ Beginner R coding, The Carpentries, R studio, Beginer ecological modelling ugrad mbr phd
Discovering Species Distribution Modelling with BCCVL

A set of 10 videos that provide an excellent introduction to species distribution modelling. These modules include: 1. Introduction to SDM, 2. Ecological theory of SDM, 3. Data for SDMs, 4. Design an SDM, 5. Presence only models, 6. Statistical models, 7. Machine learning models, 8. Model...

Keywords: Species Distribution Modelling, Ecology, EcoCommons, Beginer ecological modelling, Climate projections

Discovering Species Distribution Modelling with BCCVL https://dresa.org.au/materials/discovering-species-distribution-modelling-with-bccvl A set of 10 videos that provide an excellent introduction to species distribution modelling. These modules include: 1. Introduction to SDM, 2. Ecological theory of SDM, 3. Data for SDMs, 4. Design an SDM, 5. Presence only models, 6. Statistical models, 7. Machine learning models, 8. Model evaluation, 9. SDMs and climate change projections, 10. Case studies in BCCVL https://www.ecocommons.org.au/contact/ Species Distribution Modelling, Ecology, EcoCommons, Beginer ecological modelling, Climate projections ugrad mbr
EcoCommons Modelling Made Easy

These ten videos walk users through some of the point-and-click functionality available on the EcoCommons platform including: 1. Navigating the EcoCommons platform, 2. Exploring environmental and climate grids available on the platform, 3. Importing your own data, 4. How to run a Species...

Keywords: Species Distribution Modelling, Climate projections , EcoCommons, Ecology

Resource type: video

EcoCommons Modelling Made Easy https://dresa.org.au/materials/ecocommons-modelling-made-easy These ten videos walk users through some of the point-and-click functionality available on the EcoCommons platform including: 1. Navigating the EcoCommons platform, 2. Exploring environmental and climate grids available on the platform, 3. Importing your own data, 4. How to run a Species Distribution Model (SDM), 5. Predicting how distributions will change under climate change, 6. Running simple (averaged) ensemble models of SDMs, 7. An introduction to toy species trait problems that highlight how variation in species traits can be predicted spatially, 8. An introduction to Biosecurity Risk Mapping, 9. How to run SDMs for multiple species, 10. A multiple species SDM use case support@ecocommons.org.au Species Distribution Modelling, Climate projections , EcoCommons, Ecology ugrad mbr phd
The Living Book of Digital Skills

The Living Book of Digital Skills (You never knew you needed until now) is a living, open source online guide to 'modern not-quite-technical computer skills' for researchers and the broader academic community.

A collaboration between Australia's Academic Research Network (AARNet) and the...

Keywords: digital skills, digital dexterity, community, open source

Resource type: guide

The Living Book of Digital Skills https://dresa.org.au/materials/the-living-book-of-digital-skills *The Living Book of Digital Skills (You never knew you needed until now)* is a living, open source online guide to 'modern not-quite-technical computer skills' for researchers and the broader academic community. A collaboration between Australia's Academic Research Network (AARNet) and the Council of Australian Librarians (CAUL), this book is the creation of the CAUL Digital Dexterity Champions and their communities. **Contributing to the Digital Skills GitBook** The Digital Skills GitBook is an open source project and like many projects on GitHub we welcome your contributions. If you have knowledge or expertise on one of our [requested topics](https://aarnet.gitbook.io/digital-skills-gitbook-1/requested-articles), we would love you to write an article for the book. Please let us know what you'd like to write about via our [contributor form](https://github.com/AARNet/Digital-Skills-GitBook/issues/new?assignees=sarasrking&labels=contributors&template=contributor-form.yml&title=Contributor+form%3A+). There are other ways to contribute too. For example, you might: * have a great idea for a new topic to be included in one of our chapters (make a new page) * notice some information that’s out-of-date or that could be explained better (edit a page) * come across something in the GitBook that’s not working as it should be (submit an issue) Sara King - sara.king@aarnet.edu.au Sara King Miah de Francesch Emma Chapman Katie Mills Ruth Cameron digital skills, digital dexterity, community, open source ugrad masters mbr phd ecr researcher support