agTrend: An R package for estimating trends of aggregated abundance

1. We describe an open source R package agTrend for analyzing regional trends of abundance from sites with uneven sample schedules. 2. The package agTrend uses an abundance summary approach to estimate trends. By considering abundance trends in this fashion, rather than a model parameter, we can easily augment missing observations to calculate aggregated abundance and trends. 3. The package uses two hierarchical models to augment missing abundance measurements , while accounting for survey methodology changes and variability due to survey replication. A zero-inflated log-normal distribution is used to model abundance (normalized for methodology changes) and a log-normal distribution to model the observed abundance conditional on the true normalized abundance. 4. The use of agTrend is demonstrated with an analysis for regional abundance index trends of Steller sea lions (Eumitopias jubatus) in Alaska. 5. The package will be of most use to ecologists and resource managers interested in estimating regional trends of abundance surveys aggregated over several sites when sites have not been surveyed at concurrent times. Hence, regional abundance measurements cannot be directly calculated.