Course Schedule for 2017 (more recent years available through MSU's internal student sites)

Course Introduction

• Course logistics
• Scientific Process
• Intro. to Models & Inference
• Zip file with input files for all labs

(Ch 1, 2, & 3 - WNC)

Estimation & Hypothesis Testing

• lecture 02
• lecture_02_R_code.Rmd
• lecture_02_R_code.pdf

(Ch. 4 - WNC)

Maximum Likelihood Estimation

• BinomialDistribution
• lecture_03_R_code.Rmd
• lecture_03_R_code.pdf

(Ch. 1. - CW)

Modeling Known-Fate Survival Data

• Logistic regression
• lecture_04_R_code.Rmd
• lecture_04_R_code.pdf

(Ch 15 - WNC - esp 15.3)

• PIMs & Design Matrices
• Design Matrices in R

• MLE, likelihood, AIC
• Model averaging introduction

(Ch 4 - CW: pages 4-33 to 4-57)

Lab 1 - Known-fate Survival Modeling

• Input file - after opening the file, copy it into a text editor (e.g., Notepad) and save the file as "ducknoco.inp"
• lab01-R-code.R
• RMark
• code
• web page

Modeling known-fate data (continued)

• Probability odds, and log-odds (Rmd)
• Probability, odds, and log-odds (pdf)
• Working with logistic regression output
• BackTransform.Rmd
• BackTransform.pdf
• Uncertainty - Rmd
• Uncertainty - pdf

(Ch 4 - CW: pages 4-33 to 4-57)

• Summarizing covariates
  • FawnsDataSummary.Rmd
  • FawnsDataSummary.pdf
• likelihood w/ind. cov.
• Uncertainty (delta method)
  • Uncertainty - Rmd
  • Uncertainty - pdf

• Input file - after opening the file, copy it into a text editor (e.g., Notepad) and save the file as "lab02-fawns.inp"
• Data summary
  • FawnsDataSummary.Rmd
  • FawnsDataSummary.pdf
• Understanding Model Structures
  • lab02-extra.Rmd
  • lab02-extra.pdf
  • External site with 3-D plots
• RMark code
  • code
  • web page
• Analyses with glm in R using Markdown
  • code
  • web page
• Equations in R Markdown

CJS: Motivating Example
CJS Models

• Key concepts & likelihood

(Ch 17.1-17.2 - WNC)
  (Ch 3 & 4 - CW)

CJS Models

• Key concepts & likelihood
• Multinomials and CJS
  • multinomCJS.Rmd
  • multinomCJS.pdf

 (Ch 17.1-17.2 - WNC)
  (Ch 3 & 4 - CW)

• Input file - after opening the file, copy it into a text editor (e.g., Notepad) and save the file as "ed-males.inp"
• Recap
• RMark code
• code
• web page

• Input file - after opening the file, copy it into a text editor (e.g., Notepad) and save the file as "AA.inp"
• Variance of Estimated Difference
  • R markdown code
  • pdf output
• RMark code
• code
• web page

(Ch 5 - CW)

Cohort & Age Models

• Ch 7 - CW

Individual Covariates

• Ch 11 - CW- 1st 31 pages
• Example data analysis
  
  • age at capture varies within a group
  • age &time-varying env'tl covariates as individual covariates
  • work with files named "indcovsAgeEnvt" in zip file
    
• CJS example with individual covariates.
  • work with files named "indcov1" in zip file
    

• Input file - after opening the file, copy it into a text editor (e.g., Notepad) and save the file as "SwampSquirrels.inp"
• Summarizing Covariates
  • SquirrellsDataSummary.Rmd
  • SquirrellsDataSummary.pdf
• RMark code
• code
• web page

• lab_06.inp - after opening the file, copy it into a text editor (e.g., Notepad) and save the file as "lab06.inp"
• RMark code
• code
• web page

Estimating abundance of closed populations
  (Chapter 14.1-14.2 WNC)
  (Ch 14 - CW)  

Mid-term take-home exam handed out

• ClosedSim.inp - after opening the file, copy it into a text editor (e.g., Notepad) and save the file as "ClosedSim.inp"
• capture.inp - after opening the file, copy it into a text editor (e.g., Notepad) and save the file as "capture.inp"
• RMark code
• code
• web page

Jolly-Seber models
   (Chapter 18 - WNC)
   (Ch 12 - CW)

Jolly-Seber models
   (Chapter 18 - WNC)
   (Ch 12 - CW)

• chaseAd.inp - after opening the file, copy it into a text editor (e.g., Notepad) and save the file as "chaseAd.inp"
• Ch 12 - CW
• RMark code
• code
• web page

Review cmr modeling done to date

Mid-term take-home exam handed in by 5 pm in Jay's Ecology mailbox

Robust Design
    (Ch19 - WNC)
    (Ch 15 - CW)

Lab 9 - Robust design
  Input files - for each of the input files, open it in your browser, copy and paste all of lines in the file into a text editor (e.g., notepad), and then save as the name indicated below.

• primary #1 - save as "rd_simple_pocc1.inp"
• primary #2 - save as "rd_simple_pocc2.inp"
• primary #3 - save as "rd_simple_pocc3.inp"
• primary #4 - save as "rd_simple_pocc4.inp"
• primary #5 - save as "rd_simple_pocc5.inp"
• cjs - save as "rd_simple_cjs.inp"
• robust design - save as "rd_simple.inp"
• RMark code
  
  • code
  • web page

Occupancy Models
(link to useful reading & exercises)

    (Ch 21 - CW)

Single Species

• 1 season
• (Donovan & Hines 2007 - Exercise 3)

Occupancy Models
(link to useful reading & exercises)

    (Ch 21 - CW)

Single Species

• 1 season
• (Donovan & Hines 2007 - Exercise 3)

• Weta input file - after opening the file, copy it into a text editor (e.g., Notepad) and save the file as "wetaTwoGroups.inp"
• Study background
• RMark code
• code
• web page

Occupancy Models
Single Species - Multi-season

  (Ch 21 - CW)

• Nichols et al. 2007
• MacKenzie et al. 2009
• (Donovan & Hines 2007 - Exercise 16)

Thanksgiving - no class

• nso.inp - after opening the file, copy it into a text editor (e.g., Notepad) and save the file as "nso.inp"
• nso.xls
• RMark code
• code
• web page

• 1 species - Multi-state
• Two Species Models
• False positives
• Other

  (Ch 21 - CW)

• 1 species - Multi-state
• Two Species Models
• False positives
• Other

  (Ch 21 - CW)

Topic chosen by class

• Simulation studies
  • Power analyses in R (intro)
  • Simulations in MARK (Appendix A - CW)

Topic chosen by class

• Nest survival & ragged telemetry
  • download zip file
• Use of multi-state models for nest survival and known-fate analyses
  • Devineau et al. 2014

Final Exam handed out

• CMR Analysis forum
• CMR workshops
• Other websites
• e.g., UVM' occupancy site
• other
• WILD 501