1. Dynamic Modeling with Difference Equations
1.3. Analyzing Nonlinear Models
1.4. Variations on the Logistic Model
1.5. Comments on Discrete and Continuous Models
2. Linear Models of Structured Populations
2.1. Linear Models and Matrix Algebra
2.2. Projection Matrices for Structured Models
2.3. Eigenvectors and Eigenvalues
2.4. Computing Eigenvectors and Eigenvalues
3. Nonlinear Models of Interactions
3.1. Simple Predator-Prey Model
3.2. Equilibria of Multipopulation Models
3.3. Linearization and Stability
3.4. Positive and Negative Interactions
4. Modeling Molecular Evolution
4.2. Introduction to Probability
4.3. Conditional Probabilities
4.4. Matrix Models of Base Substitution
4.5. Phylogenetic Distances
5. Constructing Phylogenetic Trees
5.2. Tree Construction: Distance Methods - Basics
5.3. Tree Construction: Distance Methods - Neighbor Joining
5.4. Tree Construction: Maximum Parsimony
5.6. Applications and Further Reading
6.2. Probability Distributions in Genetics
6.4. Gene Frequency in Populations
7. Infectious Disease Modeling
7.1. Elementary Epidemic Models
7.2. Threshold Values and Critical Parameters
7.3. Variations on a Theme
7.4. Multiple Populations and Differentiated Infectivity
8. Curve Fitting and Biological Modeling
8.1. Fitting Curves to Data
8.2. Method of Least Squares
8.3. Polynomial Curve Fitting
A. Basic Analysis of Numerical Data.
