M 445 - STATISTICAL, DYNAMICAL, & COMPUTATIONAL MODELING


Instructors

Syllabus

For ,
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Homework Assignments & Code/Data/Papers


Assignment Solutions Due Date (Montana) Code/Data/Papers
Homework #1 Solutions - HW#1 Friday, September 9 Schmid & Robinson (1972) - Parasitology paper
Homework Script - Problems 3,4
Homework #2 Solutions - HW#2 Tuesday, September 27 Arneberg et al. (1998) - Problem 1
Arneberg Data - Problem 1
Calcium Data - Problem 3
Evolution Data - Problem 4
Homework #3 Solutions - HW#3 Monday, October 3 Gagneux et al. (2006) - Science paper
Tuberculosis Data - Problem 1
Test #1 Solutions - Test #1 Friday, October 7 Pressure/Temperature Data - Problem 2  Text version
Knee Rehabilitation Data - Problem 3  Text version
Homework #4 Solutions - HW#4 Monday, October 17
Homework #5 Solutions - HW#5 Friday, October 28
Homework #6 Solutions - HW#6 Monday, November 14
Test #2 Solutions - Test #2 Monday, November 21
Homework #7 Posted at a later date Monday, December 5 Growth Data - Problem 1
Bootstrap Script - Problem 1
Blood Data - Problem 2
bootdriver.m: Driver for bootstrapping Generalized Logistic ODE with sheep data
bootoptimize.m: Function for calling an ODE solver
bootNLM.m: Function for performing bootstrap method 2 on an ODE
bootoutput.m: Code for generating bootstrap output
fungenlogistic.m: Function defining the generalized logistic growth model as an ODE

Daily Log

Date (Montana) Title Papers/MatLab Code
8/29-8/31
Statistics Notes
Exploratory Data Analysis
Schmid & Robinson (1972): The pattern of a host-parasite distribution
Shaw et. al. (1998): Patterns of macroparasite aggregation in wildlife populations
Cox et. al. (2000): Efficacy estimates from parasite count data that include zero counts
9/2
Introduction to MatLab
Handout
SIMPLEprogram1.m: Sample program to graph a function
FORprogram1.m: Sample program with a FOR loop
IFprogram1.m: Sample program with an IF statement
nestedIFprogram1.m: Sample program with a nested IF statement
9/6
Lab 2: Normal Simulation
normalsimdemo.m: Sample program to perform a normal simulation
9/9, 9/12
Statistics Notes
Some Model Fitting Basics
aidsplot.m: Code for plotting and fitting AIDS data
aids.mat: AIDS Data
expgrowth.m: Function defining exponential growth model
9/12-9/19
Statistics Notes
Uncertainty in Statistical Models
zimbabwe.m: Code for plotting and fitting Zimbabwe data
confregplot.m: Function to plot confidence and prediction bands
9/13
Lab 3: Logistic Model Fit
Lab #3 Solutions: Solutions/Code to the Questions in Lab 3
aidslab.m: Code for plotting and fitting logistic growth model to AIDS data
logistic.m: Function defining logistic growth model
genlogistic.m: Function defining generalized logistic growth model
9/20-9/26
Statistics Notes
The General Linear Model
hospital.m: Code for plotting and fitting hospital data
hosp.mat: Hospital data from class notes
meadowfoam.m: Code for fitting linear model to meadowfoam data
9/26-9/30
Statistics Notes
Analysis of Variance
sleep.m: Code for plotting and fitting classroom sleep data
sleep.mat: Sleep data from class notes
10/3-10/11
Dynamics Notes
One Species Models
10/10
Lab 4: Solving ODEs with ODE Solvers
logistic1.m: Function defining logistic differential equation
myfun1.m: Function generating model predictions
FITlogistic1.m: Function to plot and fit logistic growth model
RUNlogistic1.m: Template which solves a logistic model using an ODE Solver
data1.mat: Data1 Dataset
10/12-10/25
Dynamics Notes
Two Species Models
10/21
Lab 5: Solving ODEs with ODE Solvers, and More
ODEtemplate.m: Template for solving a system of ordinary differential equations
LotkaVolterra.m: Function to solve nondimensional Lotka-Volterra equations
10/26-11/4
Dynamics Notes
Phase Plane Analysis of Several Models
11/4
Lab 6: Solving Systems with Three Species
threespecies1.m: Template for solving ODE systems with three species
threespecies2.m: Template for solving ODE systems with three species for two sets of initial conditions
11/7-11/8
Statistics Notes
Nonlinear Statistical Models
sheep.m: Code for fitting generalized logistic model to sheep data
logistic.m: Function defining the logistic growth model
genlogistic.m: Function defining the generalized logistic growth model
sheep.mat: Sheep data from class notes
11/14-11/17
Statistics Notes
Bootstrapping
bootstrap.m: Code for bootstrapping gen. logistic model with sheep data
bootoutput.m: Code for generating bootstrap output with sheep data model
genlogistic.m: Function defining the generalized logistic growth model
sheep.mat: Sheep data from class notes
11/18
Statistics Notes
Bootstrapping ODEs
bootdriver.m: Driver for bootstrapping Generalized Logistic ODE with sheep data
bootoptimize.m: Function for calling an ODE solver
bootNLM.m: Function for performing bootstrap method 2 on an ODE
bootoutput.m: Code for generating bootstrap output
fungenlogistic.m: Function defining the generalized logistic growth model as an ODE
sheep.mat: Sheep data from class notes
blood.mat: Blood chemical concentration data from class notes
11/21-11/22
Lab 7: Fitting ODEs with Data
11/28-11/30
Markov Chain Monte Carlo Methods
12/2
Lab 8: Running MCMC in MatLab
NonlinExampleMCMC.m: Driver for running MCMC with no scaling (Sheep data used as an example)
NonlinExampleMCMCscaling.m: Driver for running MCMC with scaling (Sheep data used as an example)
mcmcoptimize.m: Function for calling an ODE solver to fit an ODE
mcmcchainoutput.m: Function for reading in and plotting the MCMC parameter chain
mcmcoutput.m: Function for generating MCMC chain output
scatterplots.m: Function for plotting the MCMC chain projection on parameter planes
fungenlogistic.m: Function defining the generalized logistic growth model as an ODE
sheep.mat: Sheep data from class notes
12/5-12/9
Dynamics Notes
Continuous Time Population Dynamics

For additional MatLab resources on MCMC, there is an MCMC Toolbox preapred for MatLab by Heikki Haario and Marko Laine. The toolbox contains explanations of the code and several examples illustrating its use.

If you are looking for more information on or help with using MatLab, a great web resource is the MatLab Tutorial Homepage.

Last modified: 8-December-2011
Mail comments to: jgraham@mso.umt.edu