Note: readings are listed in the table below and it is recommended to stay current on the readings in the course.   WNC refers to the Williams et al. (2002) textbook.  CW refers to the on-line MARK manual.

 

Week of: Mon. Lab Tues. Lecture Thurs. Lecture
Aug 28

Course Introduction

(Ch 1, 2, & 3 - WNC)

Estimation & Hypothesis Testing

(Ch. 4 - WNC)

Maximum Likelihood Estimation

(Ch. 1. - CW)
Sep 04 Labor Day - no class

Modeling Known-Fate Survival Data

(Ch 15 - WNC - esp 15.3)

 Modeling known-fate data
Model selection basics

(Ch 4 - CW: pages 4-33 to 4-57)
Sep 11

Lab 1 - Known-fate Survival Modeling

Modeling known-fate data (continued)

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

 Modeling known-fate data with individual covariates
Sep 18 Lab 2 - Incorporating Individual Covariates in Survival models

CJS: Motivating Example
CJS Models

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

CJS Models

 (Ch 17.1-17.2 - WNC)
  (Ch 3 & 4 - CW)
Sep 25 Lab 3 - CJS models
  • 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
 GOF & Overdispersion
   mijarray 
   Overview		  GOF & Overdispersion
   GOF & Overdispersion details
  (Ch 5 - CW)
Oct 02 Lab 4 - CJS models II

(Ch 5 - CW)
Modeling live recapture data using Individual Covariates
    (Ch 17.1-17.2 - WNC)
    (Ch 6 - CW)

Cohort & Age Models

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
Oct 09 Lab 5 - Age + Individual Covariates for models of live recapture models
 Multi-state modeling
  (Ch 17.3 - WNC)
  (Ch 10 - CW)		 Multi-state modeling
  (Ch 17.3 - WNC)
  (Ch 10 - CW)
Oct 16
Lab 6 - Multi-state models
  • 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
Estimating abundance of closed populations
  (Chapter 14.1-14.2 WNC)
  (Ch 14 - CW)

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

Mid-term take-home exam handed out
Oct 23 Lab 7 - Closed models (in-class work only - no written assignment this week so you can work on exam)
  • 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

 

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

 

Jolly-Seber models
   (Chapter 18 - WNC)
   (Ch 12 - CW)
Oct 30
Lab 8 - POPAN models (due Nov 13)
 Review cmr modeling done to date

Review cmr modeling done to date
Nov 06

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

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

 

 Robust Design
    (Ch19 - WNC)
    (Ch 15 - CW)
Nov 13

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.

Occupancy Models
(link to useful reading & exercises)

    (Ch 21 - CW)


Single Species

Occupancy Models
(link to useful reading & exercises)

    (Ch 21 - CW)

Single Species
Nov 20 Lab 10 - Occupancy models

Occupancy Models
Single Species - Multi-season

  (Ch 21 - CW)

Thanksgiving - no class
Nov 27 Lab 11- Occupancy models - multi-season
  • 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
 Occupancy Models
  • 1 species - Multi-state
  • Two Species Models
  • False positives
  • Other

  (Ch 21 - CW)

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

  (Ch 21 - CW)
Dec 04


Topic chosen by class

Topic chosen by class


Final Exam handed out

 Where to from here ...
Dec 11 FINALS WEEK1
Updated: 12/05/2017