The models

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shadia contains life-history based simulation models of American shad and blueback herring population dynamics. Each model uses simulated fish populations to predict responses to user-specified fish passage scenarios at dams. The user can change settings for upstream and downstream passage standards, in addition to commercial, sustenance, and recreational fishing mortality rates. Model outputs include reach-specific and whole-basin abundances, percent repeat spawners, and other metrics as they are added.

A description of the status and versioning for each model is provided below, and detailed descriptions of each can be found at corresponding links. Briefly, these models rely on best available information to parameterize a combination of cohort- and individual-based models to simulate annual population dynamics and spawning migrations. The majority of the functions and parameters included in the models are the same (e.g., behavioral parameters). The balance are derived from river-specific information about habitat, environmental conditions, and biological characteristics. For a detailed explanation of model inputs and outputs, please see Stich et al. (2019), who used the penobscotRiverModel() as a case study for application. Please see the links below for overviews of river-specific data.

The models provided through shadia can be used for a variety of purposes, from management strategy evaluation to quantifying scope of single-project or catchment-wide dam impacts, to exploring life-history uncertainty and sensitivities. Because these models are continually evolving and new models are still being added, it is strongly recommended that users contact the package maintainer, Dan Stich (daniel.stich at oneonta.edu), before using them for research or management. For examples of how the models can be used, please see the this page.

Models that are currently implemented in shadia (with current status) include :

androscogginRiverModel This model is currently undergoing review with fishery and habitat scientists and managers at the Maine Deparment of Marine Resources.

connecticutRiverModel This model has been vetted with cooperators and fishery managers during the course of several years. Version 2.0 is currently in preparation for submission for peer-review as part of a cross-sectional analysis with the Merrimack, Penobscot, and Susquehanna rivers. Version (1.8.0) is described in Gilligan (2020). This model was used previously to inform federal hydropower relicensing (v 1.3.0).

kennebecRiverModel This model has undergone review with fishery and habitat managers at Maine Department of Marine Resources and the National Oceanic and Atmospheric administration Habitat Division. System-specific blueback herring data are used in this model.

merrimackRiverModelThis model has undergone preliminary review with fishery scientists and managers with United States Fish and Wildlife Service and the National Oceanic and Atmospheric administration Habitat Division. Version 1.8.0 is described in Gilligan (2020). Version 2.0 is currently in preparation for submission for peer-review as part of a cross-sectional analysis with the Connecticut, Penobscot, and Susquehanna rivers.

mohawkHudsonRiverModel This model has undergone review with agency collaborators at the New York State Department of Environmental Conservation and the Cornell Cooperative Extension. System-specific blueback herring data are used in this model. Version 2.0 is currently in preparation for submission for peer-review as an applied fishery management article.

penobscotRiverModel This model, which forms the basis for all others, is peer-reviewed Stich et al. (2019). This model has been used previously to inform federal hydropower relisencing (v 1.3.0). Version 2.0 is currently in preparation for submission for peer-review as part of a cross-sectional analysis with the Connecticut, Merrimack, and Susquehanna rivers.

sacoRiverModel This model has undergone preliminary review with fishery and habitat managers at Maine Department of Marine Resources and the National Oceanic and Atmospheric administration Habitat Division.

susquehannaRiverModel This model has undergone preliminary review with fishery scientists and managers with United States Fish and Wildlife Service and US Geological Survey. Version 1.8.0 is detailed in Gilligan (2020). Version 2.0 is currently in preparation for submission for peer-review as part of a cross-sectional analysis with the Connecticut, Merrimack, and Susquehanna rivers.



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