Past HMSC workshops

On this page you will find the materials for past HMSC workshops.

HMSC course 2020

Europe, Finland, Helsinki, and online. Five-day-course 2-6 November. Teachers Otso Ovaskainen, Nerea Abrego, Jari Oksanen, and others: Hierarchical Modelling of Species Communities with the R-package Hmsc:

NOTE: DUE TO COVID, THE ENTIRE COURSE WILL BE ARRANGE REMOTELY WITH ZOOM. ALL LECTURES WILL BE RECORDED, AND BREAK-OUT GROUPS WILL BE ARRANGED IN EUROPEAN, AMERICAN, AND AUSTRALASIAN TIME ZONES.
Teachers: Otso Ovaskainen, Nerea Abrego, Mirkka Jones, Jari Oksanen, Øystein Opedal, Gleb Tikhonov & Bess Hardwick.
Course dates: November 2nd-6th 2020
Venue: zoom
Course Overview: This course is designed for students and researchers who are interested in analysing data on community ecology in a way that allows placing their results in the context of modern theory. The course covers a comprehensive treatment of HMSC, including both the technical detail of the statistical methods, as well as the ecological interpretation of the results. With the help of worked out examples, the participants learn how to conduct and interpret statistical analyses in practice with the R-package Hmsc, providing a fast starting point for applying HMSC to their own data. The participants are encouraged to bring also their own data so that they can get hands-on support on HMSC-analyses of their own projects. Ideally, you will come back from the course with R-scripts that run the entire Hmsc pipeline from constructing and fitting the models to producing the result tables and figures, as well as draft texts for how the analyses were done (for the Material and Methods section for your manuscript) and what the results are (for the Results section of your manuscript).
Course timing: how do we manage global participation? We have 123 registrations from Europe+Africa, 77 from America, and 39 from Australasia. All times in this document are GMT+0. The baseline course will run every day from 9am to 3pm, with one hour allocated to breaks, so 5 hours of active teaching for each of the five days. All lectures and computer demonstrations will be recorded, so those for whom these times are difficult can watch the recorded versions. Break-out groups will be organized also in the evening (GMT 4pm-6pm; should be convenient for America) and in the morning (GMT 6am-8am; should be convenient for Australasia). The entire event will happen in zoom. Questions in plenary session are to be asked primarily by chat.
COURSE PROGRAMME:
- All times in this document are GMT+0.
- Zoom link for lectures: https://helsinki.zoom.us/j/61939913297? (You should have received the password by email, contact us if you did not receive it)
- We will take a one-hour break daily 11:30 AM to 12:30 PM, with additional short breaks between lectures
- Lecture slides will be here:
- Monday 2nd November: 9am-3pm
  - Lecture 1. Welcome & introduction to the course. https://youtu.be/Yc5yh0haC00
  - Lecture 2. Introduction to community ecology (theory, data and methods): how does HMSC relate to ecological theory? https://youtu.be/4QgP9lyULxI
  - Lecture 3. Overview of the structure of HMSC. https://youtu.be/8XD2c-13zek
  - Lecture 4. HMSC in practice: the syntax and typical workflow of the R-package Hmsc. https://youtu.be/WdmH8tVO3mo
- Tuesday 3rd November: 9am-3pm
  - Lecture 5. Building HMSC step by step: single-species modelling. https://youtu.be/IdPO4iIT7xo
  - R-demonstration 1. Linear model with HMSC and Corvus monedula case study. https://youtu.be/4Lv6n1fSYq8
  - Lecture 6. Building HMSC step by step: variation in species niches. https://youtu.be/uBlB2-lojKM Part 2: https://youtu.be/DJ0FJkrbXco
  - R-demonstration 2. Plant case study. skipped
- Wednesday 4th November: 9am-3pm (+4pm-6pm)
  - R-demonstration 3. Bird case study. skipped
  - R-demonstration 4. Selected case studies from the data provided by the participants. https://youtu.be/pTwJrUbdlEM
  - Break-out groups 1 - Europe (1pm-3pm) Possibility to discuss with teachers in small groups in any topics of your interest. In particular, demonstrations of what was done/can be done with your own data, especially for those who submitted pilot data. Links to break-out groups are in the emailed word document.
  - Break-out groups 1 – America (4pm-6pm)
    - Links to break-out groups are in the emailed word document.
- Thursday 5th November: 9am-3pm (+6am-8am and 4pm-6pm)
  - Break-out groups 1 – Australasia (6am-8am)
    - Links to break-out groups are in the emailed word document
  - R-demonstration 5. Selected case studies from the data provided by the participants. https://youtu.be/uBerY_6blRU
  - Lecture 8. How to describe the HMSC analyses in the “Material and Methods” section of your manuscript (based on R-demonstrations 4 and 5). https://youtu.be/Y5QjPd9WIKg
  - Lecture 9. How to describe the HMSC analyses in the “Results” section of your manuscript (based on R-demonstrations 4 and 5). https://youtu.be/qqPGfTrUWgk
  - Break-out groups 2. - Europe (1pm-3pm) Possibility to discuss with teachers in smaller groups in any topics of your interest. In particular, demonstrations of what was done/can be done with your own data, especially for those who submitted pilot data.
  - Break-out groups 2 – America (4pm-6pm)
- Friday 6th November: 9am-3pm (+6am-8am)
  - Break-out groups 2 – Australasia (6am-8am)
  - Lecture 7. Building HMSC step by step: biotic interactions. moved to Friday https://youtu.be/jmW5iLLdaU0
  - Lecture 10. Model selection https://youtu.be/zmLbCSliUCs
  - Lecture 11. Types of data that can be incorporated into Hmsc and types of questions that can be addressed by Hmsc https://youtu.be/vYx0SiKbArs
  - General discussion. Based e.g. on questions that came up in break-out groups that could not be addressed there. https://youtu.be/Brdo61waIAU
  - Lecture 12. Closing words https://youtu.be/YchjbfVPo6M
Registration is now closed. Participants will be prioritized according to registration order and relevance.
You can receive a signed certificate stating that you have successfully completed this 2 ECTS course - hopefully your university will then agree to register the credits.
- To achieve the study credits, you should turn in a learning diary at the end of the course (2 5 pages in total, pdf file), where you summarize in your own words what you learned during each of the course days. Send the pdf file to hmsc-course@helsinki.fi, with email subject learning_diary_surname_firstname , e.g. learning_diary_ovaskainen_otso
- If you are a student at Helsinki, we can register your credits directly.

The main challenge will be that we wish to provide one-on-one guidance on how to analyze your own data, for those participants who plan to come with their own data. As the main tool to achieve this, we will check already before the course that your data are technically ready for HMSC-analyses, including fitting a pilot HMSC-model to your data. This will ensure that during the course we can focus on the actual science, rather than wondering e.g. why a specific error message appears.
Thus, if you wish for support with analyzing your own data with HMSC, send your data after registering! As the first step, read carefully through INSTRUCTIONS.txt (found from the zip-file below) which explains in which format and where you should send your data. The other files in the zip-folder are templates that you should follow when preparing your own data. We will start setting up the pilot HMSC-models in the order that we receive the data, so even if there is no deadline of when you should send your data, we recommend you to send it as soon as possible to ensure that we will have the time to process it before the course.
If you have any questions, email to hmsc-course (at) helsinki.fi with email subject "question_surname_firstname", as explained in more detail in INSTRUCTIONS.txt.