Computer labs

Lab 1: Introduction to R

Overview: A hands-on, guided tour of the basic functionality and controls of the programming language R.
Mainly draws on: Chapter 0
Associated data file: Sight.xls

 

Lab 2: Simple population models

Overview: Dynamic population models track the size of a population with the passage of time. The simplest population models in ecology make several assumptions: Individuals are assumed to be genetically and behaviourally identical, they are fully mixed, they experience the same conditions from their environment and they are not subject to any form of randomness. Nevertheless, even these simple models can display surprisingly complex dynamics. We examine two such models in discrete time one without and one with density dependence.
Mainly draws on: Chapter 2
Associated data file: None

 

Lab 3: Optimisation

Overview: Optimisation has several applications in ecology. The most important is in finding workable compromises between wildlife conservation and industry management. The viability of wildlife populations and the human communities that exploit them is one of the foremost topics of modern applied ecology. In this lab, we will examine a specialist fishing fleet, targeting a single fish species. We will introduce the concept of maximum sustainable yield and calculate it for different types of fisheries.
Mainly draws on: Chapter 4
Associated data file: None

 

Lab 4: Visualising data

Overview: Discovering patterns in raw data is one of the most necessary and satisfying parts of the job of a scientist. In this lab, we learn how to plot different types of variables informatively, how to improve the presentation of these graphics and how to calculate basic descriptive summaries from data sets.
Mainly draws on: Chapter 7
Associated data file: Boto data.xls

 

Lab 5: Age-structured models

Overview: In this lab we will develop a stochastic model for a stage-structured population and use simulation to investigate the sensitivity of numerical output to assumptions and parameter values.
Mainly draws on: Chapter 8 & 9
Associated data file: None

 

Lab 6: Interactions with prey

Overview: In this lab, we build on the single-species system examined in Lab 5 by adding a size-structured, density dependent prey population. We introduce the concept of multispecies functional responses for generalist predators and use them to investigate the consumption of sandeels by seals. We use the prey population model and the multispecies functional response to predict the diet of seals in years of differing prey availability. We quantify the impact of consumption on the predators’ demographic rates but we stop short of examining its consequences for predator dynamics.
Mainly draws on: Chapter 6
Associated data file: None

 

Lab 7: A three-species community: Interactions with fisheries

Overview: In this Lab we examine interactions with a commercial fishery that exploits the largest of the grey seals’ main prey. We first construct a predator-prey model, in which a deterministic, age-structured sandeel population interacts with a stochastic, age-structured grey seal population. We then consider the implications of different management strategies for the sandeel fishery, specifically focusing on the probability of extinction from different levels of proportional harvesting.
Mainly draws on: Chapter 6 & 9
Associated data file: None

 

Lab 8: Simulation

Overview: The complex interactions between life history traits and the environment may favour or disadvantage single individuals or entire populations. These effects are difficult to intuit and their investigation may require the construction of stochastic, individual-based models. Here, we construct such a simulation, loosely based around the life history of female killer whales. We examine the implications on inclusive fitness of four different scenarios of resource richness and environmental variability.
Mainly draws on: Chapter 9
Associated data file: None

 

allometry