Hierarchical modelling of the species communities (HMSC)

Time: December 13, 2019
Place: Lecture Room MA337, Linnanmaa Campus, University of Oulu
Extent: 1 cr

The course presents the conceptual, statistical and software framework of Ovaskainen et al. (2017) and Ovaskainen and Abrego (in press). The course participants will learn how to integrate data on species occurrences (or abundances) with data on environmental conditions, and optionally on species traits, phylogenetic relationships, and the spatio-temporal context of the study, to address topical questions on community ecology, such as the roles of biotic and abiotic filtering in shaping community assembly. The course participants will learn how to analyze data with the R-package Hmsc.

The course is designed for doctoral students and postdoctoral researchers in the field of biology, especially community ecology. Doctoral students get 1 ECTS credit for attendance and participation.

Application information
The maximum number of participants is 20 students, and the application is open in Weboodi until December 4th, 2019. If Weboodi is not available to you, please sign-up by e-mailing Tamara Hiltunen (tamara.hiltunen(at)oulu.fi).

How to prepare for the course
If you have the possibility to spend a couple of hours to prepare for the course, you are recommended to have a look at the Ovaskainen et al. (2017) ELE paper and install Hmsc from CRAN to your computer. You may also look at through the vignettes that come with Hmsc. If you have even more time, you are recommended to skim through the book Ovaskainen and Abrego (in press). The book will be published by Cambridge University Press in April 2020, but the participants will receive a draft version. If you have data that you would like to analyze with HMSC, you may prepare a max. 2 min presentation where you describe the data and your study question, so we can use your data to discuss how HMSC can be used in practice. If you have the data ready, bring it in a format that can be read in with R!

Course programme:

The course will mainly consist of practical work with the R-package Hmsc. The teacher will demonstrate how to run example scrips (to be provided by the teacher) line by line, and the participants are recommended to run the example scripts also with their own computers.

 09:15 – 11:45 Learning how to set up different types of Hmsc models, how to fit Hmsc models, and how to evaluate MCMC convergence.

11:45 – 12:45 Lunch break

12:45 – 14:45 Learning how to evaluate model fit in terms of explanatory and predictive powers, how to interpret the parameter estimates (e.g. species niches, their dependency on traits and phylogeny, species association matrices), and how to use the model for prediction.

14:45 – 15:15 Coffee break: Biology Coffee Room B235– Coffee Provided

15:15 – 17:15 Discussion session aimed to clarify any remaining issues, and to discuss how to apply Hmsc to your own data. If you bring your own data and are ready to present in max 2 minutes how the data looks like and what is your study question, we may use your data as an example.


  1. Ovaskainen, O., Tikhonov, G., Norberg, A., Blanchet, F. G., Duan, L., Dunson, D., Roslin, T. and Abrego, N. 2017. How to make more out of community data? A conceptual framework and its implementation as models and software. Ecology Letters 20, 561-576
  2. Ovaskainen, O. and Abrego, N. Joint Species Distribution Modelling – With Applications in R. Cambridge University Press, in press.

More about the course  in Oodi.


Last updated: 29.11.2019