Past HMSC workshops

On this page you will find the materials for past HMSC workshops.
HMSC course 2022

HMSC COURSE AUGUST 15TH – AUGUST 19TH 2022

ORGANIZED AS PART OF JYVÄSKYLÄ SUMMER SCHOOL

Teachers: Otso Ovaskainen, Gleb Tikhonov, Jari Oksanen, Ryan Burner, Jenni Niku, Mirkka Jones and Sara Taskinen.

GENERAL INFORMATION

NB: THE SATURDAY 6 AM SESSION IS CANCELLED. Please send any outstanding questions via email.

The course is organized in the hybrid mode: physically at Jyväskylä University, and remotely through zoom.

The zoom link to all sessions is the same: https://helsinki.zoom.us/j/8066261697?pwd=a0FsZHhpVkorNUN6cjVmbmFENGc2dz09

All plenary sessions will be recorded and made available on YouTube asap after the session: https://www.youtube.com/channel/UCgSflScNO81Nxw39rTLMZXw

All course material (R-scripts and datafiles) are placed in the section “Course materials downloads” below

The recommended version of the R-package Hmsc to be used during the course is the version available at CRAN at the beginning of the course. Thus, you are recommended to update your Hmsc package just before starting the computer exercises.

The daily schedule is the same for all days (all times are given in Finnish time which is EEST = Eastern European Summer Time; currently UTC + 3):

9am – 2pm (including lunch break at 12-13): Plenary sessions (lectures and R-demonstrations). Both physical (Agora building Ag B103 = Auditorium 3) and on Zoom.

2pm – 4pm: Alternative 1 for computer exercises. Both physical (Ag B112.1 for those without laptop and Ag C231.1 for those with laptop) and on Zoom. In the zoom session, there will be multiple teachers. In the main zoom room (which you enter by clicking the zoom link above), you can ask for help with the computer exercise by asking questions either via the chat or by raising your hand and opening your microphone when the teacher indicates that it is your turn to ask a question. Questions that do not relate to the given exercise will be answered in separate break-out rooms to which you can move from the main zoom room. The teacher will let you know in which break-out room your question will be discussed.

7pm – 9pm (11am – 1pm US Central time): Alternative 2 for computer exercises (targeted especially for American time zones). Zoom only, with one teacher available to answer questions.

10pm – 12pm (2pm – 4pm US Central time): Alternative 3 for computer exercises (targeted especially for American time zones). Zoom only, with one teacher available to answer questions.

the next morning 6am – 8am (1pm – 3pm Sydney time): Alternative 4 for computer exercises (targeted especially for Australian time zones). Zoom only, with one teacher available to answer questions. NB: CANCELLED SATURDAY

By default, you are expected join only one of these three break-out groups daily. You don’t need to register beforehand, just join the session that fits you the best. However, you are welcome to visit a second group if you have any further questions after your initial session has ended.

 

DAILY PROGRAMME

Monday 15th August 2022

Plenary sessions

  • Lecture (by Otso Ovaskainen). Welcome & introduction to the course.
  • Lecture (by Otso Ovaskainen). Overview of HMSC.
  • Introduction to case studied used in this course: plants, birds, fungi, and phenology.
  • R demonstration (by Otso Ovaskainen). What is the Hmsc pipeline and how to apply it? Setting up a model, fitting it, and producing standard output.
  • Lecture (by Otso Ovaskainen). Introduction to the case study to be used in the break-out groups.

Break-out groups

Exercise 1. Apply the Hmsc pipeline to the provided case study data. Define a simplified Hmsc model (no traits, no phylogeny, no random effects), and follow the Hmsc pipeline to generate basic output on parameter estimates. Participants are encouraged to work independently, the teacher is there mainly to help if questions arise.

Tuesday 16th August 2022

Plenary sessions

  • R demonstration (by Otso Ovaskainen). Recap of Exercise 1.
  • Lecture (by Otso Ovaskainen). The fixed and random effect components of HMSC and their links to ecological theory.
  • Lecture (by Sara Taskinen): Using variational approximation for fast estimation of joint species distribution models with various response distributions (note: this lecture is not related to HMSC but to joint species distribution modelling more generally).

Break-out groups

Exercise 2. Continue from Exercise 1 by defining a full HMSC model (with traits, phylogeny, and random effects) and apply the Hmsc pipeline to produce some basic model outputs.

Wednesday 17th August 2022

Plenary sessions

  • R demonstration (by Otso Ovaskainen). Recap of Exercise 2.
  • R demonstration (by Otso Ovaskainen). Measuring explanatory and predictive power by different cross-validation strategies.
  • R demonstration (by Otso Ovaskainen). Making predictions over environmental gradients.
  • R demonstration (by Otso Ovaskainen). Checking MCMC convergence and examining model fit.
  • Lecture (by Gleb Tikhonov). How is Hmsc fitted to data? Overview on prior distributions and posterior sampling.
  • R demonstration (by Gleb Tikhonov). How to modify the prior distributions and make choices related to posterior sampling.

Break-out groups

Exercise 3. Continue from Exercise 2 by checking MCMC convergence, examining model fit, and making predictions over environmental gradients.

Thursday 18th August 2022

Plenary sessions

  • R demonstration (by Otso Ovaskainen). Recap of Exercise 3.
  • R demonstration (by Otso Ovaskainen). How to set up different types of random levels in Hmsc: hierarchical, spatial and temporal.
  • R demonstration (by Otso Ovaskainen). Setting up different response distributions.
  • R demonstration (by Otso Ovaskainen). Making predictions over spatial gradients.
  • Lecture and R demonstration (by Otso Ovaskainen). Variable selection, reduced rank regression, and other methods to deal with cases with many potential covariates.

Break-out groups

  • Exercise 4. Continue from Exercise 3 by trying out different models and selecting among them.

Friday 19th August 2022

Plenary sessions

  • R demonstration (by Otso Ovaskainen). Recap of Exercise 4.
  • Discussion session (lead by Otso Ovaskainen, Gleb Tikhonov and Jari Oksanen). Recent and future development needs of HMSC: Overview of recently implemented and ongoing developments, and discussion on what users would like to see implemented.
  • Discussion session. Based, e.g., on questions that came up during lectures and/or break-out groups that could not have been addressed there.

Break-out groups

In the break-out groups, discussions on topics suggested by the participants, including guidance on working with their own data.

NB: 6 AM SATURDAY SESSION CANCELLED

6 pm. Workshop dinner for participants physically present in Jyväskylä

 

Course materials downloads:

Lecture 1: Welcome (pdf)

Lecture 2: Overview of HMSC (pdf)

Lecture 3: Fixed and random effects (pdf, updated Aug 16)

Lecture 4: Fast ML based estimation of JSDMs (pdf)

Lecture 5: How is HMSC fitted to data? (pdf)

Lecture 6: Model selection (pdf)

Lecture 7: Ongoing developments (pdf)

Hmsc development (pdf)

Introduction to case studies (pdf)

How to apply the Hmsc pipeline (pdf)

Hmsc pipeline (zipped folder via Dropbox)

Case study: Plants (zipped folder via Dropbox, updated Aug 16)

Case study: Birds (zipped folder via Dropbox, updated Aug 22)

Case study: Fungi (zipped folder via Dropbox)

Case study: Phenology (zipped folder via Dropbox)

Case study: Exercises (zipped folder via Dropbox, updated Aug 22)
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
    • Tuesday 3rd November: 9am-3pm
    • 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)
  • 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.