Software

You need the following software to run the course examples

Downloads/ installs needed (in this order please!):

• • Load the most recent version of R

  • Load and install OpenBUGS*

  • Load and install JAGS

  • Load and install MARK (install below will allow you to run MARK from R)

  • Load and install the following libraries from the R menu

    • unmarked (see guide, below)

    • R2OpenBUGS (OpenBugs must be installed first) 

    • jagsUI (JAGS must be installed first)

    • lme4

    • boot

    • reshape

    • RMark (MARK must be installed first)

    • scatterplot3d

    • secr

    • RODBC (needed if you want to access ODBC database files like Access (install this first to enable 64-bit ODBC from R)

  • R2jags (works better with some of the examples than rjags or jagsUI)

• script to install all the above (except the 64-bit ODBC driver) at once from an R session 

  • Load and install Program DISTANCE

Program documentation

R statistical package

Program MARK - A Gentle Introduction

RMark chapter in MARK book

List of MARK/RMark models

Unmarked-  using R to analyze occupancy and other data from unmarked animals

Tips for installing R and JAGS on Apple Mac OS (site maintained by Mike Meredith, contact him for questions)

Code to simulate common data structures in R and perform MLE from simulated data