Introduction to Bayesian Modeling and Inference for Fisheries Scientists

Doll, Jason C.; Jacquemin, Stephen J.

doi:10.1002/fsh.10038

Cited by 24 publications

(25 citation statements)

References 42 publications

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“…Bayesian inference methodology was used to fit the model (Doll and Jacquemin ) by applying Stan version 2.18.0 and the RStan package version 2.17.3 in R version 3.6.1 (Stan Development Team 2018a, 2018b; R Core Team 2019). Vague prior probability distributions were used for all of the unknown model parameters.…”

Section: Methodsmentioning

confidence: 99%

Population Estimate of the State and Federally Threatened Spotfin Chub Using Underwater Observations

Doll

Etchison

Owensby

2020

N American J Fish Manag

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Determining the population demographics of threatened or endangered species can be difficult if the methods that are used must be minimally invasive. However, knowing the population status of species that are of conservation interest must be understood for successful management. We used underwater observations (i.e., snorkeling) to determine population estimates for Spotfin Chub Erimonax monachus in the Cheoah River in North Carolina, a species that is listed as threatened at both state (North Carolina) and federal levels. Seven sites were randomly selected between the Santeetlah Dam and the confluence with the Little Tennessee River. Each site was surveyed by three snorkelers who completed multipass snorkeling from July 17 to 25, 2019. The population estimates were generated with an N-mixture model and incorporated site-specific habitat. Four hundred and sixty-six observations of Spotfin Chub were recorded across all of the sites and passes. The simple model without covariates of abundance estimated a total population size of 12,139 (95% credible interval [CRI] = 9,821-15,453). Incorporating site-specific percentage of bedrock improved model fit and indicated that the percentage of bedrock was positively related to site-specific abundance. The total population size as estimated with the covariate model was 13,905 (95% CRI = 11,620-22,181). Our results yielded new insight into the status of a threatened species while confirming previous knowledge about its microhabitat use. Locally, the results of this work suggest that Spotfin Chub are well established in the Cheoah River and maintain a substrate affinity to bedrock. Broadly, the field methods that were used here are logistically feasible, cost efficient, and minimally stressful for the fish. We suggest that this methodology be considered when total and site-specific population estimates are needed to manage species of concern. Additionally, more detailed site-specific habitat can improve model estimates by explaining site-specific variability in abundance, resulting in more precise total population estimates.

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Section: Methodsmentioning

confidence: 99%

Population Estimate of the State and Federally Threatened Spotfin Chub Using Underwater Observations

Doll

Etchison

Owensby

2020

N American J Fish Manag

Self Cite

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“…We used R2WinBUGS (Sturtz, Ligges, & Gelman, ), a package in Program R (R Core Team, ), that allowed us to organise data in R and directly call WinBUGS, a software package for performing Bayesian inference using Gibbs sampling (Gilks, Thomas, & Spiegelhalter, ; Lunn, Spiegelhalter, Thomas, & Best, ; Lunn, Thomas, Best, & Spiegelhalter, ). WinBUGS uses Markov Chain Monte Carlo (MCMC) sampling (Doll & Jacquemin, ).…”

Section: Methodsmentioning

confidence: 99%

Brook trout (Salvelinus fontinalis) movement and survival after removal of two dams on the West Branch of the Wolf River, Wisconsin

Easterly

Isermann

Raabe

et al. 2019

Ecology of Freshwater Fish

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Dam removals allow fish to access habitats that may provide ecological benefits and risks, but the extent of fish movements through former dam sites has not been thoroughly evaluated for many species. We installed stationary PIT antennas in 2016 and 2017 to evaluate movements and survival of brook trout Salvelinus fontinalis in the West Branch of the Wolf River (WBWR) in central Wisconsin following removal of two dams and channel modifications designed to promote fish movement. These changes provided access to lacustrine habitats that might provide suitable winter habitat or act as ecological sinks. We used multistate models to estimate transition probabilities between river sections, to determine whether brook trout: (a) moved between multiple river sections and (b) entered lacustrine habitats as seasonal refuges, but eventually returned to lotic habitat. We also used a Cormack‐Jolly‐Seber model to evaluate whether apparent survival of brook trout in the WBWR was comparable to other populations. Few fish moved among river sections or used lacustrine habitat (<5% of tagged fish); most brook trout remained in sections where they were initially tagged, potentially due to quality habitat located throughout the river. Like other studies, brook trout in the WBWR appear to experience high mortality based on low number of detections, few physical recaptures and an estimated eight‐month apparent survival rate of 0.27. In scenarios where fish can already access suitable habitat, removal of dams may not result in substantial increases in fish movement and colonisation of newly accessible habitat may not occur immediately.

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“…Bayesian inference was used to fit the model ( Doll & Jacquemin, 2018 ) in the programing languages R 3.6.1 ( R Core Team, 2019 ), Stan ( Stan Development Team, 2018a ), and rstan 2.17.3 ( Stan Development Team, 2018b ). All parameters were given non-informative priors ( Table 2 ).…”

Section: Methodsmentioning

confidence: 99%

“…where g s;site is a random effect term for species s at sampling site, and e i;s is a random effect for the individual to capture overdispersion. Bayesian inference was used to fit the model (Doll & Jacquemin, 2018) in the programing languages R 3.6.1 (R Core Team, 2019), Stan (Stan Development Team, 2018a), and rstan 2.17.3 (Stan Development Team, 2018b). All parameters were given noninformative priors (Table 2).…”

Section: Observation Process Modelmentioning

confidence: 99%

Incorporation of feeding functional group information informs explanatory patterns of long-term population changes in fish assemblages

Doll

Jacquemin

2021

PeerJ

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The objective of this study was to evaluate long term trends of fish taxa in southern Lake Michigan while incorporating their functional roles to improve our understanding of ecosystem level changes that have occurred in the system over time. The approach used here highlighted the ease of incorporating ecological mechanisms into population models so researchers can take full advantage of available long-term ecosystem information. Long term studies of fish assemblages can be used to inform changes in community structure resulting from perturbations to aquatic systems and understanding these changes in fish assemblages can be better contextualized by grouping species according to functional groups that are grounded in niche theory. We hypothesized that describing the biological process based on partial pooling of information across functional groups would identify shifts in fish assemblages that coincide with major changes in the ecosystem (e.g., for this study, shifts in zooplankton abundance over time). Herein, we analyzed a long-term Lake Michigan fisheries dataset using a multi-species state space modeling approach within a Bayesian framework. Our results suggested the population growth rates of planktivores and benthic invertivores have been more variable than general invertivores over time and that trends in planktivores can be partially explained by ecosystem changes in zooplankton abundance. Additional work incorporating more ecosystem parameters (e.g., primary production, etc.) should be incorporated into future iterations of this novel modeling concept.

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Introduction to Bayesian Modeling and Inference for Fisheries Scientists

Cited by 24 publications

References 42 publications

Population Estimate of the State and Federally Threatened Spotfin Chub Using Underwater Observations

Population Estimate of the State and Federally Threatened Spotfin Chub Using Underwater Observations

Brook trout (Salvelinus fontinalis) movement and survival after removal of two dams on the West Branch of the Wolf River, Wisconsin

Incorporation of feeding functional group information informs explanatory patterns of long-term population changes in fish assemblages

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