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**Kuala Lumpur, 3 - 9 March 2018**
During our Boot Camp in wildlife study design and data analysis,
we introduce the concepts underlying Bayesian approaches to data
analysis, and we run standard analyses with the `wiqid`
package in R.
The modelling language used by the JAGS package makes it easy to write code for quite
complex models, as the code closely follows the mathematical
expressions we use to define the model. JAGS does not have a stand-alone GUI, but is
closely integrated with R statistical software.
Basic R skills are needed for this workshop, and we ask
applicants to complete an **R
Skills Review** before confirming places.
### Outline of content
We'll begin with a review of probability and Bayes Rule, applying
this to simple examples with just one or two parameters to estimate.
This will be familiar to you if you have recently attended a Boot
Camp, but we'll use different examples.
Next we'll look at modern computer-intensive methods for analysis
of models with more than one parameter to estimate:
- Running JAGS from R via the
`jagsUI` package.
- Understanding what JAGS does: how MCMC (Markov Chain
Monte Carlo) methods work.
- Initial values, burn-in, and convergence; checking for
convergence.
- Error messages and debugging.
- Using the output from JAGS.
Once everyone is familiar with the mechanics of running analyses
in JAGS, we will tackle examples of wildlife-related problems
with emphasis on model building:
- Simple occupancy models with detection probability less than
1.
- Extensions of occupancy models including covariates; species
distribution maps.
- Data augmentation for population estimation modelling.
- Estimating density from spatially-explicit capture recapture
data (SCR/SECR).
Working through these examples will lead to discussion of
detailed issues:
- Prior specification and appropriate non-informative priors.
- Supplying appropriate initial values.
- Calculating derived variables within JAGS.
- Checking model fit.
- Model selection and multimodel inference.
All participants should come with a laptop computer with recent
versions of R and JAGS installed. They will be asked to complete an
R Skills Review before the workshop.
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