DOI: 10.5061/dryad.vt4b8gtx6
title: Outputs of current speed and sea otter abundance models in Glacier Bay, Alaska

description: Sea otters are apex predators that can exert considerable influence over
 the nearshore communities they occupy. Since facing near extinction in the
 early 1900s, sea otters are making a remarkable recovery in Southeast
 Alaska, particularly in Glacier Bay, the largest protected tidewater
 glacier fjord in the world. The expansion of sea otters across Glacier Bay
 offers both a challenge to monitoring and stewardship and an unprecedented
 opportunity to study the top-down effect of a novel apex predator across a
 diverse and productive ecosystem. Our goal was to integrate monitoring
 data across trophic levels, space, and time to quantify and map the
 predator-prey interaction between sea otters and butter clams (Saxidomus
 gigantea), one of the dominant large bivalves in Glacier Bay and a favored
 prey of sea otters. To do so, we developed a modeling framework to account
 for both bottom-up and top-down drivers of butter clam abundance and
 dynamics. For the bottom-up driver, we used the root-mean-square current
 speed (m/s) predicted by a tidal circulation model of Glacier Bay
 developed by Drew et al. (2013). For top-down sea otter dynamics, we used
 the posterior mean sea otter abundance estimates from Lu et al. (2019).
 This repository contains the current speed raster (100m x 100m resolution)
 produced by Drew et al. (2013) and the files and model output from Lu et
 al. (2019) necessary to generate a time series of rasters (400m x 400m
 resolution raster brick with 26 layers for the years 1993-2018) of
 estimated posterior mean sea otter abundance. These data layers are used
 in Leach et al. (2023) to model butter clam dynamics at sampling sites
 across Glacier Bay.
description: The archive 'current.zip' contains the current speed
 raster and was produced by Drew <em>et al.</em> (2013) from
 the tidal circulation model developed therein. Drew, G. S.,
 Piatt, J. F., & Hill, D. F. (2013). Effects of currents and tides
 on fine-scale use of marine bird habitats in a Southeast Alaska hotspot.
 <em>Marine Ecology Progress Series</em>,
 <em>487</em>, 275–286. https://doi.org/10.3354/meps10304 The archive 'otters.zip' contains the output from the sea otter ecological diffusion model developed and fit in Lu <em>et al. </em>(2019). The manuscript and its supplement contain detailed information on the model structure and the Markov chain Monte Carlo algorithm used to fit the model to sea otter aerial survey data and generate posterior samples of model parameters that can be used to generate a raster of the posterior mean sea otter abundance through time. Lu, X., Williams, P. J., Hooten, M. B., Powell, J. A., Womble, J. N., & Bower, M. R. (2019). Nonlinear reaction–diffusion process models improve inference for population dynamics. <em>Environmetrics</em>, <em>e2604</em>, 1–17. https://doi.org/10.1002/env.2604
description: R scripts to read and process both the current speed and sea
 otter rasters are available at https://github.com/clint-leach/otter-clam and in the linked Zenodo archive. Code to load the current speed raster and extract its values at a set of lat-long coordinates is provided in the script 'align_data.r' provided in that repository. After extracting the zip, the current speed raster can be loaded into R using the 'raster' package. The zipped archive 'otters.zip' contains R object files ('rds' format) that contain a raster defining the Glacier Bay domain ('Boundaries.rds'), covariate inputs to the sea otter ecological diffusion model ('lambda_covars.rds'), and a list containing MCMC chains for the parameters of the ecological diffusion model ('lambda_mcmc.rds'). The R script `compute_lambda.r` uses these inputs to generate a raster brick containing posterior estimates of sea otter abundance across Glacier Bay through time.