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This is a vignette for the R package eggCounts version 2.0. The packageimplements a suite of Bayesian hierarchical models dealing with faecal eggcount reductions. The models are designed for a variety of practicalsituations, including individual treatment efficacy, zero inflation, smallsample size (less than 10) and potential outliers. The functions are intuitiveto use and their output are easy to interpret, such that users are protectedfrom being exposed to complex Bayesian hierarchical modelling tasks. Inaddition, the package includes plotting functions to display data and resultsin a visually appealing manner. The models are implemented in Stan modellinglanguage, which provides efficient sampling technique to obtain posteriorsamples. This vignette briefly introduces different models, and provides ashort walk-through analysis with example data.

EggCounts: a Bayesian hierarchical toolkit to model faecal egg count reductions