Work Description

Title: Spatially-explicit model code and outputs of Bighead and Silver carp growth rate potential in Lake Michigan Open Access Deposited

http://creativecommons.org/licenses/by/4.0/
Attribute Value
Methodology
  • We developed a spatially-explicit model that quantifies the growth rate potential (GRP) of non-reproducing adult Bighead Carp and adult Silver Carp (collectively bigheaded carp) throughout Lake Michigan. The GRP model provides a quantitative metric for evaluating habitat quality and suitability by translating prey concentrations at a given water temperature into terms of fish biomass production as indexed by individual growth. Suitable habitat is defined as areas in the lake capable of supporting non-negative growth (indicative that the fish is at least maintaining weight). We applied foraging and bioenergetic equations to outputs of prey (phytoplankton, zooplankton, and detritus) and water temperature simulated by a three-dimensional biophysical model of Lake Michigan. Simulated input data (prey and temperature) are representative of lake conditions in 2010. We ran the GRP model on a monthly time step to characterize the spatiotemporal dynamics of bigheaded carp habitat throughout the year. We also ran the model on a daily time step to determine the total weight change each fish would experience over different periods of the year. The GRP model was coded and ran in R.
Description
  • Percent Weight Change Data: The model was run continuously on a daily time step for seasonal intervals (Spring: March thru May; Summer: June thru August; Fall: September thru November) as well as contiguously from Spring to Fall to assess total growth over the likely growing season (March thru November). CSV files represent the simulated weight change (%) of Bighead and Silver Carp for the respective time periods associated with the file name. Initial fish mass for each seasonal interval and growing season was 4350 g for Silver Carp and 5480 g for Bighead Carp. Maximum and mean total weight change (%) was determined for three depth ranges (near surface depths [NS]: 0 – 10 m; deep chlorophyll layer depths [DCL]: 10 - 50 m; and whole water column [WC]). Coordinates are in decimal degrees. File naming convention: speciesSeasonWtChange (e.g. bigheadFallWtChange = % weight change of Bighead Carp from September through November)

  • Monthly Habitat Quality Data: Rdata files contain matrices of Bighead or Silver carp growth rate potential as represented as a mass-proportional growth rate (gram of carp/gram of carp/day [g/g/d]) for the 15th day of each month. Habitats with growth rate potential >= 0 g/g/d were deemed suitable. Matrix attributes: Rows: Row numbers refer to the spatial node with 20 equally-spaced vertical layers. Columns: Columns 1-20 refer to the growth rate potential value for each vertical layer of each node. Vertical layers are evenly spaced based on the total depth of the water column for each node. Depth for each node can be found in the grid attributes data file. Columns 21 ("meanG") and 22 ("Gmax") represent the average and maximum growth rate potential, respectively, of the fish across the whole water column for the corresponding node. File naming convention: species_MonthNumber (e.g. silver_06 = Silver carp growth rate potential in June) Spatial coordinates for each node can be found in the grid attributes data files.

  • Grid attributes data: This Rdata file provides the spatial reference data and other grid attributes. Coordinates are provided in UTM (x & y) and latitude and longitude (decimal degrees). Depth (meters) for each node is listed in this file.

  • GRP Model code: Details bioenergetics equations, foraging equation, functions for running the model on a monthly time-step and daily time step, and functions for basic analyses. Model is coded in R.

  • The simulated input data (prey and temperature) used to run our model is not included in this data set. Instead we provide the model code, grid attributes, and outputs of the model. The readRDS() function (R Base Package v.3.5.1) is required to read in .Rdata files in R.
Creator
Depositor
  • peterals@umich.edu
Contact information
Discipline
Funding agency
  • Other Funding Agency
ORSP grant number
  • PAF ID 16-PAF07794 NOAA Award # NA14OAR4170070
Keyword
Citations to related material
Resource type
Last modified
  • 02/10/2020
Published
  • 09/05/2018
Language
DOI
  • https://doi.org/10.7302/Z2T151WJ
License
To Cite this Work:
Alsip, P. (2018). Spatially-explicit model code and outputs of Bighead and Silver carp growth rate potential in Lake Michigan [Data set]. University of Michigan - Deep Blue. https://doi.org/10.7302/Z2T151WJ

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Files (Count: 35; Size: 28.2 MB)

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Title: Spatially-explicit model outputs of Bighead and Silver carp habitat suitability in Lake Michigan
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Research Overview:
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This research evaluated the suitability of Lake Michigan to support the growth of invasive Bighead and Silver carp (collectively bigheaded carp). We developed a growth rate potential (GRP) model that provides a quantitative metric for evaluating habitat quality and suitability by translating prey concentrations at a given water temperature into terms of fish biomass production as indexed by individual growth. For our model, we simulated the GRP of non-reproducing adult bigheaded carps. This research was conducted by Peter J. Alsip for his master's thesis at the University of Michigan School for Environment and Sustainability. Co-authors and advisors are listed below. This research contributes to ongoing efforts to evaluate the risk of a bigheaded carp invasion in the Great Lakes.

Institutions:
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University of Michigan School for Environment and Sustainability (SEAS)
Cooperative Institute for Great Lakes Research (CIGLR)
National Oceanic and Atmospheric Administration, Great Lakes Environmental Research Laboratory (NOAA-GLERL)
Michigan Department of Natural Resources - Institute for Fisheries Research (IFR)

Contributors:
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Creator: Peter Alsip (SEAS)
Co-authors/advisors: Drs. Hongyan Zhang (CIGLR), Mark Rowe (CIGLR),Edward Rutherford (NOAA-GLERL), Doran Mason (NOAA-GLERL), Catherine Riseng (SEAS), & Zhenming Su (IFR)
Date: 9/7/2018
Primary Contact: Peter Alsip (peterals@umich.edu or PeterAlsip811@gmail.com)

Funding source(s):
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This research was primarily funded through the Michigan Sea Grant Graduate Research Fellowship with matching funds provided by IFR. Additional funding was provided through CIGLR and the Great Lakes Aquatic Nonindigenous Species Information System (GLANSIS).

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Model Design and Methodology:
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The GRP model integrates three main components: 1) a bioenergetics model to estimate individual growth rate potential; 2) a foraging model to estimate consumption inputs for the bioenergetics model; and 3) a spatially explicit 3-D environment. The foraging and bioenergetics sub-models are applied to the three dimensional outputs of prey (phytoplankton, zooplankton, and detritus) and temperature simulated by the Lake Michigan Finite Volume Community Ocean Model - General Ecosystem Module (FVCOM-GEM) developed by Rowe et al. (2015, 2017). Simulated input data (prey and temperature) are representative of lake conditions in 2010.

We ran the GRP model on a monthly time step to characterize the spatiotemporal dynamics of bigheaded carp habitat throughout the year. We also ran the model on a daily time step to determine the total weight change each fish would experience over different periods of the year. The GRP model was coded and ran in R (see BHC_GRPmodelFunctions.R for code).

For more information on bioenergetics and foraging equations please follow the link at the bottom of this document to the thesis document (Alsip 2018).

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File inventory and Data Descriptions:
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Data sets are organized into three distinct categories:
1) Percent Weight Change Data
2) Monthly Habitat Quality Data
3) Spatial Grid Attributes

Model functions are provided in the BHC_GRPmodelFunctions.R. The simulated input data (prey and temperature) used to run our model is not included in this data set. Instead we provide the model code, grid attributes, and outputs of the model. The readRDS() function (R Base Package v.3.5.1) is required to read in .Rdata files in R.

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Percent Weight Change Data:
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The model was run continuously on a daily time step for seasonal intervals (Spring: March thru May; Summer: June thru August; Fall: September thru November) as well as contiguously from Spring to Fall to assess total growth over the likely growing season (March thru November). CSV files represent the simulated weight change (%) of Bighead and Silver Carp for the respective time periods associated with the file name. Initial fish mass for each seasonal interval and growing season was 4350 g for Silver Carp and 5480 g for Bighead Carp. Maximum and mean total weight change (%) was determined for three depth ranges (near surface depths [NS]: 0 – 10 m; deep chlorophyll layer depths [DCL]: 10 - 50 m; and whole water column [WC]). Coordinates are in decimal degrees. Cell values that are NA in the DCL columns are indicative of nodes where the maximum depth is not within the DCL depth range.

File naming convention: speciesSeasonWtChange (e.g. bigheadFallWtChange = % weight change of Bighead Carp from September through November).

Column header Definitions:

column 1 (no header listed): Node ID number
lon: longitude coordinate (decimal degrees) for each node
lat: latitude coordinate (decimal degrees) for each node
NS_mean%: Mean Weight Change (%) across depths of 0 - 10 m at each node for the respective time period
NS_max%: Maximum Weight Change (%) across depths of 0 - 10 m at each node for the respective time period
DCL_mean%: Mean Weight Change (%) across depths of 10 - 50 m at each node for the respective time period
DCL_max%: Maximum Weight Change (%) across depths of 1 - 50 m at each node for the respective time period
WC_mean%: Mean Weight Change (%) of the whole water column at each node for the respective time period
WC_max%: Maximum Weight Change (%) across the whole water column at each node for the respective time period

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Monthly Habitat Quality Data:
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Rdata files contain matrices of Bighead or Silver carp growth rate potential as represented by the gram of carp/gram of carp/day (g/g/d; growth rate proportional to the mass of the fish) for the 15th day of each month. Habitats with growth rate potential >= 0 g/g/d were deemed suitable.

Matrix attributes:

Rows: Row numbers refer to the spatial node with 20 equally-spaced vertical layers. Columns: Columns 1-20 refer to the growth rate potential value for each vertical layer of each node. Vertical layers are evenly spaced based on the total depth of the water column for each node. Depth for each node can be found in the grid attributes data file.

Columns 21 ("meanG") and 22 ("Gmax") represent the average and maximum growth rate potential, respectively, of the fish across the whole water column for the corresponding node.

File naming convention: species_MonthNumber (e.g. silver_06 = Silver carp growth rate potential in June)

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Grid Attributes Data (grid_attr.Rdata):
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This Rdata file provides the spatial reference data and other grid attributes. Coordinates are provided in UTM (x & y) and latitude and longitude (decimal degrees). Depth (meters) for each node is listed in this file.
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Data Citation:
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Alsip, P.J., H. Zhang, M.D. Rowe, D.M. Mason, E.S. Rutherford, C.M. Riseng, and Z. Su. 2018. Spatially-explicit model outputs of Bighead and Silver carp growth rate potential in Lake Michigan [Data set]. University of Michigan Deep Blue Data Repository. https://doi.org/10.7302/Z2T151WJ
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Literature Cited:
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Rowe, M.D., Anderson, E.J., Wang, J., Vanderploeg, H.A., 2015. Modeling the effect of invasive quagga mussels on the spring phytoplankton bloom in Lake Michigan. J. Great Lakes Res. 41, 49–65. doi:10.1016/j.jglr.2014.12.018

Rowe, M.D., Anderson, E.J., Vanderploeg, H.A., Pothoven, S.A., Elgin, A.K., Wang, J., Yousef, F., 2017. Influence of invasive quagga mussels, phosphorus loads, and climate on spatial and temporal patterns of productivity in Lake Michigan: A biophysical modeling study. Limnol. Oceanogr. doi:10.1002/lno.10595

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Link to thesis article in Deep Blue:
https://deepblue.lib.umich.edu/handle/2027.42/145424

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