CSUMB 550

e-mail: lisa.schwarz@ucsc.edu

phone: (406) 570-2257

office hours: by appointment

office (if you want to visit me in Santa Cruz):

Long Marine Lab, Center for Ocean Health, Room 148B

Multivariate Statistics

Papers to review:

Principle Components Analysis: PCA_spider webs,  PCA_fish
Cluster Analysis: CA_leopard sharksCA_species commonness
Discriminant Analysis: DA_coot sexDA_fish scales
Canonical Correlation Analysis:  CCorrelA_buffalo

Tentative Schedule:

Oct. 15 (half lecture): Introduction to Multivariate Statistics
Class Notes: Lecture1_Intro to Multivariate Statistics
Oct. 20: Principal Components Analysis
Class Notes: Lecture2_Principal Components Analysis
Homework and Code: CSUMB 550 Homework 6a , HW6_PCA.R
Data: CalSeaLionDivesLtd , BND_Morphs_example
Oct. 22: Dr Eric Crandall (guest lecture)
Oct. 27: Dr Nate Jue (guest lecture)
Oct. 29: Cluster Analysis
Class notes: Lecture3_Cluster Analysis,  ClusterValidationMetrics
Homework: CSUMB 550 Homework 6b  
Newest code: ClusterAnalysis2.R
clValid documentation: click here
Article where the data were analyzed: Villegas-Amtmann et al. 2011
NOTE: You have been provided with a small subset of her data, so do not expect similar answers.
Nov. 3: Discriminant Analysis
Class notes: Lecture4_Discriminant Analysis
Newest code: DiscriminantExample2.R 
Example data: DiscSample
Homework and homework data: CSUMB 550 Homework 6c,  RemoteData 
Nov. 5: Canonical Correlation Analysis
Class notes: Lecture 5_Canonical Correlation
Example data: mmreg
Newest code and interpretation example: CanCorrelExample2.R , CanCorrInterpretation 
Homework and homework data:  CSUMB 550 Homework 6d HappyDolphins 

 

Nov. 10 and 12: Work on the Multivariate Analysis homework. Tentative due date Nov. 17.

Bayesian Analysis

Nov. 17 and 19: Introduction to Bayesian Analysis
Normal analysis:
OpenBugs example files:  BayesNorm_tst.R, NormalmodelNormalmodel2, Norm_tstinits, Norm_tst300data
JAGS example files: Rjags_Normtst.R, Norm_tst300, Normalmodel.bug, Normalmodel2.bug
Dec. 1 – 8: Bayesian Linear Regression
OpenBugs example file: LinRegBRugs.RLinRegmodelLinRegBRugswithDIC.R
Homework 7: CSUMB 550 Homework 7perinatalPupWeanMassSchwarz_MMS_2008
Another OpenBugs example: LinReg2BRugs.R
Posterior work with OpenBugs results: PosteriorLinRegExample.R
Logistic regression models: LogisticBugsModelsHW7bRCode.R
Homework rubric (sort of): Bayesian Homework Points
Dec 8 and 10: Hierarchical Bayesian Models
Great info about hierarchical models: hierarchical slides
Homework 8: HW8data, CSUMB 550 Homework 8HW8RCode.R

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