On this page, you will find two things:

        (1) Code used in my research
                     - Simulations
                     - JAGS model code
                     - Bayesian posterior-predictive checks

        (2) Course materials developed by others and myself

Please feel free to use and distribute, but cite the source appropriately

Code used in my research

Data requirements for an occupancy study in the diverse tropics 

Objective: To determine how many sites to survey and how many surveys per site is adequate in a diverse community
Code: Learn to simulate and analyze data for species that range in occupancy and detection probability

Multi-state disease structured N-mixture model

Objective: To estimate survival and population growth for a population of unmarked individuals that differ in infection status
Code: Learn to simulate and analyze data for a stage-structured (i.e., age, size, sex, or any other discrete category) population when marking individuals is not possible

Multi-state Jolly-Seber model

 Objective: To estimate survival and population growth for a population of marked individuals that differ in infection status
Code: Learn to simulate and analyze capture-mark-recapture data for a stage-structured (i.e., age, size, sex, or any other discrete category) population


​Course materials from others and myself

Bayesian hierarchical modeling at SESYNC

Course materials for the SESYNC Bayesian modeling for ecologists and social scientists short course. Material was created by Dr. Tom Hobbs, Dr. Chris Che-Castaldo, and Dr. Mary Collins.

Open science and research reproducibility by Dr. Christie Bahlai

Course materials for an open science and reproducible research course targeted at organismal ecologists. Material was created by Dr. Christie Bahlai.

Introduction to R course by Alex Forde and myself

Under construction....