Integrating count effort by seasonally correcting animal population estimates (ICESCAPE): a method for estimating abundance and its uncertainty from count data using Adelie penguins as a case study

This work describes a parametric bootstrap model for standardising animal count data to a common reference point of breeding chronology for species with a complex temporal function of sampling availability. ICESCAPE (Integrating Count Effort by Seasonally Correcting Animal Population Estimates) is a suite of routines that implements a general abundance estimator accounting for availability bias, detection bias and sampling fractions less than unity. Within this resampling framework, all reported measures of uncertainty associated with originally published counts are propagated through to the final adjusted estimates. Adjustment for availability bias is achieved by applying an adjustment factor based on independently measured time series of availability throughout a breeding season. Such time series are typically collected at only a limited number of sites, so surrogate availability information for a site is used when none exists. Importantly, a common standardisation procedure allows site-specific estimates to be aggregated to achieve region-scale population estimates. By way of illustration, the method is applied to several examples of published studies of Adelie penguin abundance at breeding sites in Antarctica. These examples focus on adjusting counts of adults to an effective number of breeding pairs, although the software has been developed to accommodate adjustment and aggregation of other count objects typical for penguin species, such as occupied nest or chick counts. While tailored for Adelie penguins, the method and implementation is sufficiently general to be easily adapted for other colonial land-breeding species showing seasonal variation in availability to sampling methodology.