Many criteria for statistical parameter estimation, such as maximum likelihood, are formulated as a nonlinear optimization problem. Automatic Differentiation Model Builder (ADMB) is a programming framework based on automatic differentiation, aimed at highly nonlinear models with a large number of parameters. The benefits of using AD are computational efficiency and high numerical accuracy, both crucial in many practical problems. We describe the basic components and the underlying philosophy of ADMB, with an emphasis on functionality found in no other statistical software. One example of such a feature is the generic implementation of Laplace approximation of high-dimensional integrals for use in latent variable models. We also review the literature in which ADMB has been used, and discuss future development of ADMB as an open source project. Overall, the main advantages of ADMB are flexibility, speed, precision, stability and built-in methods to quantify uncertainty.

Aim Spatial analysis of the distribution and density of species is of continuing interest within theoretical and applied ecology. Species distribution models (SDMs) are being increasingly used to analyse count, presence–absence and presence‐only data sets. There is a growing literature on dynamic SDMs (which incorporate temporal variation in species distribution), joint SDMs (which simultaneously analyse the correlated distribution of multiple species) and geostatistical models (which account for similarity between nearby sites caused by unobserved covariates). However, no previous study has combined all three attributes within a single framework. Innovation We develop spatial dynamic factor analysis for use as a ‘joint, dynamic SDM’ (JDSDM), which uses geostatistical methods to account for spatial similarity when estimating one or more ‘factors’. Each factor evolves over time following a density‐dependent (Gompertz) process, and the log‐density of each species is approximated as a linear combination of different factors. We demonstrate a JDSDM using two multispecies case studies (an annual survey of bottom‐associated species in the Bering Sea and a seasonal survey of butterfly density in the continental USA), and also provide our code publicly as an R package. Main conclusions Case study applications show that that JDSDMs can be used for species ordination, i.e. showing that dynamics for butterfly species within the same genus are significantly more correlated than for species from different genera. We also demonstrate how JDSDMs can rapidly identify dominant patterns in community dynamics, including the decline and recovery of several Bering Sea fishes since 2008, and the ‘flight curves’ typical of early or late‐emerging butterflies. We conclude by suggesting future research that could incorporate phylogenetic relatedness or functional similarity, and propose that our approach could be used to monitor community dynamics at large spatial and temporal scales.

. 2000. Including predation mortality in stock assessments: a case study for Gulf of Alaska walleye pollock. -ICES Journal of Marine Science, 57: 279-293.A separable catch-age stock assessment model that accommodates predation mortality is applied to the Gulf of Alaska walleye pollock (Theragra chalcogramma) assessment. Three predators are incorporated in the model: arrowtooth flounder (Atheresthes stomias), Pacific halibut (Hippoglossus stenolepis), and Steller sea lion (Eumetopias jubatus). The effect of these predators is examined by defining the predation mortality as a type of fishery. The model is used to quantify changes in the relative fit to the survey, fishery, and predator data when the assumption of constant natural mortality is relaxed. Specifically, we examine the effect of assumptions regarding the functional feeding response, residual naturaly mortality, and uncertainty in predator biomass on stock assessment. Total natural mortality rates (including predation) tended to be higher than estimated from life history characteristics of the stock. Models that did not account for uncertainty in natural mortality underestimated uncertainty in current stock biomass by as much as 20%. Our results indicate that independent estimates of survey selectivity, additional food habits data, and estimates of the feeding responses of predators to different prey densities are all needed to improve our ability to develop stock assessment models that address ecosystem concerns. 2000 International Council for the Exploration of the Sea

Mueter, F. J., Bond, N. A., Ianelli, J. N., and Hollowed, A. B. 2011. Expected declines in recruitment of walleye pollock (Theragra chalcogramma) in the eastern Bering Sea under future climate change. – ICES Journal of Marine Science, 68: 1284–1296. A statistical model is developed to link recruitment of eastern Bering Sea walleye pollock (Theragra chalcogramma) to variability in late summer sea surface temperatures and to the biomass of major predators. The model is based on recent advances in the understanding of pollock recruitment, which suggest that warm spring conditions enhance the survival of early larvae, but high temperatures in late summer and autumn are associated with poor feeding conditions for young-of-year pollock and reduced recruitment in the following year. A statistical downscaling approach is used to generate an ensemble of late summer temperature forecasts through 2050, based on a range of IPCC climate projections. These forecasts are used to simulate future recruitment within an age-structured stock projection model that accounts for density-dependent effects (stock–recruitment relationship), the estimated effects of temperature and predation, and associated uncertainties. On average, recruitment in 2040–2050 should expectedly decline by 32–58% relative to a random recruitment scenario, depending on assumptions about the temperature relationship, the magnitude of density-dependence, and future changes in predator biomass. The approach illustrated here can be used to evaluate the performance of different management strategies and provide long-term strategic advice to managers confronted with a rapidly changing climate.

Climate change is impacting fisheries worldwide with uncertain outcomes for food and nutritional security. Using management strategy evaluations for key US fisheries in the eastern Bering Sea we find that Ecosystem Based Fisheries Management (EBFM) measures forestall future declines under climate change over non-EBFM approaches. Yet, benefits are species-specific and decrease markedly after 2050. Under high-baseline carbon emission scenarios (RCP 8.5), end-of-century (2075–2100) pollock and Pacific cod fisheries collapse in >70% and >35% of all simulations, respectively. Our analysis suggests that 2.1–2.3 °C (modeled summer bottom temperature) is a tipping point of rapid decline in gadid biomass and catch. Multiyear stanzas above 2.1 °C become commonplace in projections from ~2030 onward, with higher agreement under RCP 8.5 than simulations with moderate carbon mitigation (i.e., RCP 4.5). We find that EBFM ameliorates climate change impacts on fisheries in the near-term, but long-term EBFM benefits are limited by the magnitude of anticipated change.

A comparison of fisheries biological reference points estimated from temperature-specific multi-species and single-species climate-enhanced stock assessment models, Deep-Sea Research II, http://dx. ABSTRACTMulti-species statistical catch at age models (MSCAA) can quantify interacting effects of climate and fisheries harvest on species populations, and evaluate management trade-offs for fisheries that target several species in a food web. We modified an existing MSCAA model to include temperature-specific growth and predation rates and applied the modified model to three fish species, walleye pollock (Gadus chalcogrammus), Pacific cod (Gadus macrocephalus) and arrowtooth flounder (Atheresthes stomias), from the eastern Bering Sea (USA). We fit the model to data from 1979 through 2012, with and without trophic interactions and temperature effects, and use projections to derive singleand multi-species biological reference points (BRP and MBRP, respectively) for fisheries management. The multi-species model achieved a higher over-all goodness of fit to the data (i.e. lower negative log-likelihood) for pollock and Pacific cod. Variability from water temperature typically resulted in 5-15% changes in spawning, survey, and total biomasses, but did not strongly impact recruitment estimates or mortality. Despite this, inclusion of temperature in projections did have a strong effect on BRPs, including recommended yield, which were higher in single-species models for Pacific cod and arrowtooth flounder that included temperature compared to the same models without temperature effects. While the temperature-driven multi-species model resulted in higher yield MBPRs for arrowtooth flounder than the same model without temperature, we did not observe the same patterns in multi-species models for pollock and Pacific cod, where variability between harvest scenarios and predation greatly exceeded temperature-driven variability in yield MBRPs. Annual predation on juvenile pollock (primarily cannibalism) in the multi-species model was 2-5 times the annual harvest of adult fish in the system, ͵ thus predators represent a strong control on population dynamics that exceeds temperature-driven changes to growth and is attenuated through harvest-driven reductions in predator populations. Additionally, although we observed differences in spawning biomasses at the accepted biological catch (ABC) proxy between harvest scenarios and single-and multi-species models, discrepancies in spawning stock biomass estimates did not translate to large differences in yield. We found that multi-species models produced higher estimates of combined yield for aggregate maximum sustainable yield (MSY) targets than single species models, but were more conservative than singlespecies models when individual MSY targets were used, with the exception of scenarios where minimum biomass thresholds were imposed. Collectively our results suggest that climate and trophic drivers can interact to affect MBRPs, but for prey species with high predation rates, trophic-and man...

No abstract

Age-0 walleye pollock Theragra chalcogramma were collected from the eastern Bering Sea during years when ocean temperatures were anomalously warm (2004)(2005) and cool (2006)(2007). Variability in spatial distribution, food habits, energetic condition, and recruitment to the age-1 life stage was investigated in relation to thermal regime. Age-0 walleye pollock were large in size and widely distributed during warm years, whereas they were small and largely confined to the middle domain of the eastern Bering Sea during cool years. Energy density was positively correlated with body weight and was greater during years when conditions were anomalously cool. The proportion of smaller age-0 walleye pollock in the diet of larger individuals was high when conditions were warm (21.9% of diet by weight), and euphausiids were the most important prey (36.5% of diet by weight) when conditions were cool. Eastern Bering Sea age-0 walleye pollock were abundant and broadly distributed from Bristol Bay to offshore and northern locations during warm years; during cool years, age-0 fish were less abundant and their distribution was constricted to the southeastern Bering Sea. An inverse relationship between brood year abundance and survival from age 0 to age 1 was found. Our results indicate that when spring (summer) sea temperatures on the eastern Bering Sea shelf are very warm and when the water column is highly stratified during summer, age-0 walleye pollock allocate more energy to growth than to lipid storage, leading to low energy density before winter and thus to higher overwinter mortality.