Stock assessment with generalized depletion models combined with population dynamics models | - CCMAR -

Stock assessment with generalized depletion models combined with population dynamics models

Segunda, 9 Março, 2020 a Quinta, 12 Março, 2020
Course Description 

Roa-Ureta (R-U) will discuss the state of fisheries management and stocks worldwide and the prospect of achieving sustainable fisheries exploitation in the vast realm of small-scale, coastal fisheries. R-U will present examples of applications of a modelling framework that he and colleagues demonstrated in a paper published in 2015, including cases of sea urchin, cephalopods, eels, and bony fish, from Chile, Mauritania, Madagascar, Taiwan, Spain, Portugal and Saudi Arabia, with particular emphasis on coastal fisheries connected to artificial reefs in the Algarve. Roa-Ureta will conclude with the potential connection of these models to ecosystem-based management of fisheries.


Maximum number of participants: 15 




This course is oriented to marine biologists, fishery managers, statisticians and modellers of the dynamics of marine populations. It shows how to use the R package CatDyn to achieve statistically solid estimations of stock abundance, natural mortality, fishing mortality, exploitation rate, maximum sustainable yield, among other quantities, using elementary fisheries monitoring data. The modelling framework is useful to data-poor and data-limited fisheries, small-scale and coastal fisheries. It is versatile, accommodating different life histories, multi-fleet cases, seasonality, and other common specificities of diverse fisheries. 


List of articles:

Roa-Ureta, R.H, Santos, M.N., Leitao, F. 2019. Modelling long-term fisheries data to resolve the attraction versus production dilemma of artificial reefs. Ecological Modelling 407, 108727.

Lin, Y-J, Tzeng, W-N, Han, Y-S, Roa-Ureta, R.H. 2017. A stock assessment model for transit stock fisheries with explicit immigration and emigration dynamics: application to upstream waves of glass eels. Fisheries Research 195, 134-140.

Roa-Ureta, R., Molinet, C., Bahamonde, N. 2015. Hierarchical statistical framework to combine generalized depletion models and biomass dynamic models in the stock assessment of the Chilean sea urchin (Loxechinus albus) fishery. Fisheries Research 171:59-67.

Roa-Ureta, R. 2015. Stock assessment of the Spanish mackerel (Scomberomorus commerson) in Saudi waters of the Arabian Gulf with extensions of generalized depletion models under severe data-limited conditions. Fisheries Research 171:68-77.

Roa-Ureta, R. 2012. Modeling in-season pulses of recruitment and hyperstability-hyperdepletion in the Loligo gahi fishery of the Falkland Islands with generalized depletion models. ICES Journal of Marine Science 69:1403-1415.



  • A basic understanding of fishery science and population dynamics.
  • A basic understanding of statistical modelling for non-linear processes.
  • OS Windows 7 or higher, 64 bits.
  • The latest version of the R language for statistical programming.
  • Install the latest version of the R package CatDyn and its dependencies (in R, use the dropdown menu, click on Install Package(s), select a CRAN mirror, and select CatDyn from the list; dependencies will be installed automatically).
  • Recommended: separately install ADMB-IDE to be used after CatDyn. I can provide ADMBIDE 11.4 for installation during the course.



Day 1 - March 9th

9:00 to 12:00 - Presentation and discussion. The logic of the models and example applications from fisheries in the Falkland Islands, Chile, Saudi Arabia, Taiwan, Catalonia, Asturias, Iceland and the Algarve

12:00 to 14:00 - Lunch break

14:00 to 17:00 - Work on the computer. Use of R package CatDyn to organize the data and to obtain initial values for parameters in the model


Day 2 - March, 10th

9:00 to 12:00 - Work on the computer. Multi-annual models – The ‘sargo’ (Diplodus vulgaris) fishery from the Algarve, see article 5

12:00 to 14:00 - Lunch break

14:00 to 17:00 - Work on the computer. Combination of the output from CatDyn with a surplus production model of the Pella-Tomlinson type. Here we use ADMB


Day 3 - March 11th

9:00 to 12:00 - Work on the computer.Intra-annual models – The octopus (Enteroctopus megalocyathus) fishery from southern Chile

12:00 to 14:00 - Lunch break

14:00 to 17:00 - Work on the computer.Combination of the output from CatDyn with a surplus production model of the Pella-Tomlinson type. Here we use ADMB


Day 4 - March, 12th

9:00 to 12:00 - Presentation and discussion. The octopus (Octopus vulgaris) fishery from Asturias, northern Spain. Estimation of the spawners-recruitment relationship

12:00 to 14:00 - Lunch break

14:00 to 17:00 - General discussion. This session is open to further work on the computer and to discuss topics raised by the audience

Intended Audience 
Researchers in the area of biological sciences
Scientific Organisation 

Rubén Hernán Roa-Ureta

University of Otago, New Zealand
Rubén Hernán Roa-Ureta , holds a PhD in Statistics and an MSc In Oceanography. Currently, he works for a Saudi Arabia University, the Chilean and Mauritania’s government, a U.K. charity, Spanish regional administrations and is collaborating in fisheries science in Algarve and Iceland. In 2012, he created a class of fishery stock assessment models that delivers advanced results for management with elementary fisheries monitoring data. His aim is to demonstrate that the tools that have permitted successful fisheries management of large-scale fisheries can also be implemented for small-scale.

CCMAR – Centre of Marine Sciences | University of Algarve | Campus de Gambelas | Faro | Portugal

Building 7 | Room 2.31ª

ATT type 
Formação Avançada
Presentation Language 
Fee Covers 

Student: 100€

Non-Students: 150€