Outputs of current speed and sea otter abundance models in Glacier Bay, Alaska

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-..., The archive 'current.zip' contains the current speed raster and was produced by Drew et al. (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. Marine Ecology Progress Series, 487, 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 et al. (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 inferen..., 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.

海獭是顶级捕食者（apex predator），能对其所栖息的近岸群落产生显著调控作用。自20世纪初濒临灭绝以来，海獭在阿拉斯加东南部，尤其是全球最大的保护型潮汐冰川峡湾——冰川湾（Glacier Bay）迎来了显著的种群恢复。海獭在冰川湾内的种群扩张，既为监测与管理工作带来了挑战，也为研究新型顶级捕食者在多样且高生产力生态系统中的下行调控效应提供了前所未有的契机。

本研究旨在整合不同营养级、空间与时间维度的监测数据，以量化并绘制出海獭与黄油蛤（Saxidomus gigantea）之间的捕食者-猎物相互作用；黄油蛤是冰川湾优势大型双壳类之一，同时也是海獭偏爱的猎物。为此，我们构建了一套建模框架，用以同时考量影响黄油蛤种群丰度与动态的上行（bottom-up）与下行（top-down）调控因子。针对上行调控因子，我们采用了均方根（root-mean-...）相关分析方法。压缩包"current.zip"包含流速栅格数据，该数据由Drew等人（2013）基于其文中提出的潮汐环流模型生成。

引用文献：Drew, G. S., Piatt, J. F., & Hill, D. F. (2013). 阿拉斯加东南部海洋热点区域内海流与潮汐对海鸟栖息地精细利用的影响. 海洋生态学进展系列, 487, 275–286. https://doi.org/10.3354/meps10304

压缩包"otters.zip"包含本研究基于Lu等人（2019）开发并拟合的海獭生态扩散模型输出结果。该论文及其补充材料详细说明了模型结构，以及用于将模型拟合至海獭航空调查数据、并生成模型参数后验样本的马尔可夫链蒙特卡洛（Markov Chain Monte Carlo, MCMC）算法；这些后验参数可用于生成不同时间下海獭种群丰度后验均值的栅格数据。

引用文献：Lu, X., Williams, P. J., Hooten, M. B., Powell, J. A., Womble, J. N., & Bower, M. R. (2019). 非线性反应-扩散过程模型提升推断（inferen...）

用于读取和处理流速栅格与海獭栅格的R脚本可在https://github.com/clint-leach/otter-clam以及关联的Zenodo存档中获取。脚本"align_data.r"提供了加载流速栅格并从一组经纬度坐标中提取其数值的代码。解压压缩包后，可通过R语言的"raster"包加载流速栅格数据。

压缩包"otters.zip"内含R对象文件（格式为.rds）：其中包含定义冰川湾研究区域的栅格文件"Boundaries.rds"、海獭生态扩散模型的协变量输入文件"lambda_covars.rds"，以及包含生态扩散模型参数的马尔可夫链蒙特卡洛链列表"lambda_mcmc.rds"。R脚本`compute_lambda.r`可利用上述输入文件生成包含不同时间序列下海獭种群丰度后验估计值的栅格砖（raster brick）。