Armidale Animal Breeding Summer Course 2018

Venue:            University of New England, Armidale, NSW Australia

Course Audience:      Postgraduate students and other professionals




Mathematical modeling of infection dynamics in genetically diverse livestock populations


Teachers:     Andrea Doeschl-Wilson and Osvaldo Anacleto     

The Roslin Institute

Edinburgh, Scotland


Dates:              Monday 5 February 2018 (9am) – Thursday 8 February 2018 (4pm)




 To register, please click on the link below



Materials previous Armidale summer courses




2018 Course

Course Materials 2018


Day 1 (Monday):  General introduction to mathematical modelling & to key concepts for infectious diseases in livestock

Lecture 1: Introduction to mathematical modelling (A. Wilson)

Lecture 2: Infectious disease fundamentals (A. Wilson)

Lecture 3: Examples of infectious disease models for livestock (A. Wilson)

Tutorial 1: Designing a mathematical model for bovine Tuberculosis

Tutorial 2: Introduction to probability distributions & R


Intro to R                     Intro to R

                                    Math Modeling in R

                                    Required R Packages



Day 2 (Tuesday): Modelling epidemics (A. Wilson)

Lecture 4: Mathematical essentials

Lecture 5: Deterministic models for homogeneous populations

Tutorial L5: Deterministic models for homogeneous populations

Lecture 6: Deterministic models in heterogeneous populations

Tutorial L6: Deterministic models for heterogeneous populations

Lecture 7: Stochastic & individual based epidemiological models

Tutorial L7: Stochastic models

R-code Epidemics Tutorials


Day 3 (Wednesday): Mathematical models of within host infection dynamics (AW)

Lecture 8: Empirical vs mechanistic models of within-host infection dynamics

Tutorial L8: Exploring empirical & mechanistic models of within-host infection dynamics

R-Code Tutorial Within Host Models


Statistical interference: estimating model parameters (O. Anacleto)

            Intro to Probability

Lecture 9: Introduction to Statistical Inference: the frequentist approach and its application to stochastic epidemic models 

 Tutorial L9: Frequentist inference for proportions & stochastic epidemic models


R-Code Tutorial9a


R-Code Tutorial9b



Day 4 (Thursday): Bayesian interference (O. Anacleto)


 Lecture 10:  Introduction to Bayesian inference & conjugate models

Tutorial L10: Bayesian inference for the beta-binomial model

R-Code Tutorial 10

Lecture 11: Introduction to Bayesian inference using MCMC: Gibbs Sampling and Metropolis Hastings algorithms

Tutorial L11: Markov chains

Lecture 12:  Applications of Bayesian inference using MCMC

Tutorial L12: Analysis of a hierarchical non-linear model for PRRS data

R-code Tutorial 12


Material of previous years:


Armidale Genetics Summer Course 2017    Materials

·         Genotype by environment interaction in breeding programs: Piter Bijma and Han Mulder          


Armidale Genetics Summer Course 2016    Materials


Investigating the Genetic Architecture of Complex Traits  & Prediction of Phenotype

from Genome-wide SNPs - Doug Speed and David Balding


Armidale Animal Breeding Summer Course 2015   Materials

                    Primer to genomic analysis using R:    Cedric Gondro

                    From Sequence Data to Genomic Prediction:   Ben Hayes and Hans Daetwyler


Armidale Animal Breeding Summer Course 2014    Materials

Breeding Program Design with Genomic Selection: Jack Dekkers, Julius van der Werf


Armidale Animal Breeding Summer Course 2012    Materials

Statistical Methods for Genome-Enabled Selection: Daniel Gianola, Gustavo de los Campos 


Armidale Animal Breeding Summer Course 2011    Materials

·         Statistical methods and design in plant breeding and genomics: Ian Mackay

·        IBD inference in genome association studies: Elizabeth Thompson


Armidale Animal Breeding Summer Course 2010    Materials

·         Application of evolutionary algorithms to solve complex problems in quantitative genetics

and bioinformatics:   Brian Kinghorn, Cedric Gondro

·         Bayesian methods in genome association studies:  Dorian Garrick,  Rohan Fernando


Armidale Animal Breeding Summer Course 2009    Materials

·        Quantitative Genetic Theory and Analysis- Selection Theory:    Bruce Walsh

·         Quantitative Genetic Models for social interaction and inherited variability: Piter Bijma


Armidale Animal Breeding Summer Course 2008      Materials 

·         Genomic Selection:       Ben Hayes


Armidale Animal Breeding Summer Course 2007      Materials

·         Generalized Linear Mixed Models:        Steve Kachman


Armidale Animal Breeding Summer Course 2006    Materials

·         Gene Expression:          Toni Reverter

·         Breeding Program Design:         Graser, James, Van der Werf

Armidale Animal Breeding Summer Course 2005    Materials
·         Breeding Objectives: Gibson, Van der Werf, Kinghorn
·         Scientific Writing:          David Lindsay
·         ASReml:           Arthur Gilmour
Armidale Animal Breeding Summer Course 2004    Materials
·         Bayesian for Beginners               Kerrie Mengersen
·         Bayesian Models for QTL analysis        Michel Perez-Enciso
·         Bioinformatics   John McEwan

Armidale Animal Breeding Summer Course 2003    Materials

·         Scientific Writing:  David Lindsay
·         Linear Models for animal breeding:   Julius van der Werf, Mike Goddard
·         QTL mapping for practitioners, from linkage to gene: Ben Hayes, Julius van der Werf
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