Modeling, Data Analysis and Numerical Techniques for Geochemistry

This page was last modified 15 November 2008

Shift clicking on the individual lecture numbers will download the specific lecture's m-file. Naming that m-file something like "lect02.m" in your current directory will allow you to run that script and repeat the operations that were demonstrated in class. Those m-files marked with a NAY are not yet available.

Data analysis and statistics
- Lecture 1 : Resources, MATLAB primer and intro to linear algebra
  an m-file repeating commands used in lecture
  - BGI redux an example m-file, from class
  Lecture 2 : Measurement theory, probability distributions, error propagation and analysis
  an m-file repeating commands used in lecture 5 Sep 2008
  Bouncing Balls the demonstration of the central limit theorem and lognormality, from class
  standardiz.m a m-file to standardize your data
  
  Lecture 3: Least Squares and regression techniques, goodness of fit and tests, non-linear least squares techniques
  Lect03 Example 1: First example from lecture 3
  Lect03 Example 2: Second example from lecture 3
  Model Function: m-function file need for example two
  linfit.m fit a straight line
  lsqfitma.m type II regression
  lsqcubic.m the least squares cubic Type-II
  surfit.m polynomial fit a surface in 2-D
  nlleasqr.m non-linear least square, Levenberg-Marquardt
  dfdp.m a helper program for Levenberg-Marquardt
  
  Lecture 4 and 5: Principle Components and Factor Analysis 18 Sep 2008
  lect04.m an m-file repeating commands used in lecture
  ex4p1.dat the data file for the lecture m-file
  BATSNSi.m an m-file going through the simple 2D example in notes
  BATSNSi.txt the data file for the simple 2D example in notes
  do2d.m an m-file displaying rank deficient vectors in 3D
  do3d.m an m-file displaying rank=3 vectors in 3D
  pca2.m an m-file to perform principal component analysis
  varimax.m m-file to perform Varimax rotation
  vfunct.m a helper file for varimax.m
  
  Lecture 6 : Time Series Analysis, Correlation and Autocorrelation
  Lecture 7 : Fourier and Spectral Analysis
  
  lect07.m lecture demo file 6 Oct 2008
  erfinv.m seems to be missing from athena
  lomb.m computes Lomb's normalized periodogram
  Lombtest.m an example of how to use lomb.m
  
  Lecture 8 and 9: Objective mapping and Kriging
  surfit.m Bill's polynomial trend surface fitting program
  cokri.m Marcotte's co-kriging program
  cokri2.m helper file for cokri.m
  trans.m a helper file for cokri2.m
  variof1.m function to compute variogram or covariogram
  variof2.m function to compute variograms, cross-variograms, covariograms, cross-covariograms and pseudo-cross-variograms
  means.m calculates row averages, used by cokri2.m
  excise.m removes any rows in a matrix containing Nan's
Modeling Techniques
- Lecture 10 : ODEs and 0-D Box Models
- Lecture 11 : Tutorial of Numerical Modeling
  - euler_demo.m Euler integration demo program
  - euler_rk.m Euler integration demo program WITH Runge-Kutta 2-3
  - rk_demo.m R-K integration demo program
  - simexp.m a simple "nugget" function to compute (NOT Kriging)
  - phos2.m 2 box global ocean phosphate
  - phos2b.m 2 box global ocean phosphate with biology
  - TwoBox.m two box global ocean phosphate model
  - phos2g.m 2 box global ocean phosphate with GLOBAL
  - FiveBox.m five box global ocean phosphate main program
  - phos5.m 5 box global ocean phosphate model
  - OptTwoBox.m main driver program for optimizing TwoBox Phosphate model
  - CostTwoBox.m hypothetical cost function for TwoBox Phosphate model
- Lecture 12 : Model Analysis and Optimization
  - ecopz.m A function m-file for a simple ecosystem model
  - ecopz_costfxn.m Toy 2-box ecosystem model cost function
  - ecopz_main.m Toy 2-box ecosystem model
  - ecopz_opt_main.m Main driver for optimizer of toy 2-box ecosystem model
  - ecopz_outR14.mat Toy 2-box ecosystem model output (R14, v7)
  - ecopz_outR13.mat Toy 2-box ecosystem model output (R13, v6.5)
  - phos2_sens.m Toy 2-box global model of ocean phosphorus
  - phos2_sens_main.m Toy 2-box global model of ocean phosphorus, main driver
- Lecture 13 and 14 : NAY
  Advection-Diffusion Equations and Turbulence
  Lecture 15 and 16 : Introduction to finite difference techniques
  - dopipe1.m Models the flow of North Atlantic Surface Water down a long pipe
  - InitializePipe.m Sets up parameters and loads in data for dopipe1.m
  - MakeWeights.m Compute the weights (w's) for dopipe1.m
  - PlotData.m Plots the model simulation at annual intervals from DoPipe1.m
  - PlotFinalData.m Makes plots for dopipe1.m
  - PlotTHe.m Plot model T-He curves
  - PlotObs.m Compares observations with model called by PlotTHe.m
  - natrsf.dat The atmospheric source function of tritium
  - Obs1981.mat Observations from the North Atlantic subtropics
  - dostep.m First upwind differencing method calculation of pure advection of a step function
  - InitializeFUDM.m Sets up values for Step Demo for FUDM
  - ComputeFUDMWeights.m Compute FUDM weights
  - PlotStepData.m For FUDM demo program doStep.m
  - vnsa.m Bill's unit circle of stability m-file
  - vnsa2.m Bill's contour stability plot m-file
  Lecture 17 : NAY
  1-D Open Ocean Advection-Diffusion Models
  Lecture 18 : 1-D Models in Sedimentary Systems
  
  ch4_prof.m CH₄ boundary layer problem in anoxic sediments
  tridiag.m function file to solve the tridiagonal matrix problem
  ch4.dat CH₄ data from FOAM site
Modeling Case Studies
- Lecture 19 : 1-D: Upper-Ocean Seasonal Models
  - PWP_Model.zip a ZIP file of the PWP model (physical, gas and bio subdirectories plus forcing and initialization MAT files)
- Lecture 20 : NAY
  2-D: Gyre models
  Lecture 21 : NAY
  3-D: General Circulation Models
  Lecture 22 & 23 : 3-D: Ocean Inversions
  
  doney1.m Demonstration m-file from lectute 22
  
  Lecture 24 : NAY
  Scientific Visualization