This readme.txt file was generated on 2019_11_21 by Gretchen Hansen, updated 2023_02_07 ------------------- GENERAL INFORMATION ------------------- 1. Title: Data and R code for analysis of walleye and yellow perch age-0 length in Minnesota's Large Lakes. 2. Author Information Principal Investigator Contact Information Name: Gretchen Hansen Institution: University of Minnesota Address: 2003 Upper Buford Circle, St. Paul, MN 55108 Email: ghansen@umn.edu ORCID: https://orcid.org/0000-0003-0241-7048 Associate or Co-investigator Contact Information Name: Tyler Ahrenstorff Institution:Minnesota Department of Natural Resources Address:1601 Minnesota Drive, Brainerd, MN 56425 Email:tyler.ahrenstorff@state.mn.us ORCID: Associate or Co-investigator Contact Information Name: Bethany Bethke Institution: Minnesota Department of Natural Resources Address:5351 North Shore Dr, Duluth, MN 55804 Email: bethany.bethke@state.mn.us ORCID: 3. Date of data collection: 1983_07_19 through 2018_08_06 4. Geographic location of data collection (where was data collected?): Minnesota's large walleye lakes. Indexed by DOW number. Lake (DOW) Cass (04003000) Kabetogama (69084500) Leech (11020300) Lake of the Woods (39000200) Mille Lacs (48000200) Rainy (69069400) Upper Red (04003501) Vermilion (69037800) Winnibigoshish (11014700) Shapefiles of lake boundaries can be found here: https://gisdata.mn.gov/dataset/water-large-lakes-in-minnesota 5. Information about funding sources that supported the collection of the data: Data were collected by the Minnesota Department of Natural Resources as part of the Large Lakes Sampling program. Research funding was provided by the Minnesota Environmental and Natural Resources Trust Fund as recommended by the Minnesota Aquatic Invasive Species Research Center (MAISRC) and the Legislative-Citizen Commission on Minnesota Resources (LCCMR). -------------------------- SHARING/ACCESS INFORMATION -------------------------- 1. Licenses/restrictions placed on the data: NONE 2. Links to publications that cite or use the data: Hansen, GJA, TD Ahrenstorff, BJ Bethke, J Dumke, J Hirsch, KE Kovalenko, JF LeDuc, RP Maki, HM Rantala, T Wagner. 2020. Walleye growth declines following zebra mussel and Bythotrephes invasion. Biological Invasions.https://link.springer.com/article/10.1007%2Fs10530-020-02198-5 3. Recommended citation for the data: Hansen, Gretchen J A; Bethke, Bethany J; Ahrenstorff, Tyler D; Dumke, Josh; Hirsch, Jodie; Kovalenko, Katya E; LeDuc, Jaime F; Maki, Ryan P; Rantala, Heidi M (2019). Data and R code for analysis of walleye and yellow perch age-0 length in Minnesota's Large Lakes. Retrieved from the Data Repository for the University of Minnesota, https://doi.org/10.13020/t9tr-y063. --------------------- DATA & FILE OVERVIEW --------------------- 1. File List A. Filename: wae_length_data.csv Short description: lengths of age-0 walleye collected using beach seines in Minnesota's large lakes B. Filename: yep_length_data.csv Short description: lengths of age-0 yellow perch collected using beach seines in Minnesota's large lakes C. Filename: WalleyeModel.R Short description: Contains code for fitting Bayesian Hierarchical model of age-0 walleye growth. Generates output of predicted lengths and parameter estimates for generating figures. D. Filename: PerchModel.R Short description: Contains code for fitting Bayesian Hierarchical model of age-0 yellow perch growth. Generates output of predicted lengths and parameter estimates for generating figures. E. Filename: Predicted_lengths_figures_WAE.R Short description: Contains code for predicting age-0 walleye length as a function of zebra mussel and Bythotrephes invasion status across a range of degree day values based on model estimated parameters. Generates figures 3 and 4 from Hansen et al. manuscript. Can call model fit code directly from this file, or read in .RDS file generated from WalleyeModel.R F. Filename: Predicted_lengths_figures_YEP.R Short description: Contains code for predicting age-0 yellow perch length as a function of zebra mussel and Bythotrephes invasion status across a range of degree day values based on model estimated parameters. Generates figures 5 and 6 from Hansen et al. manuscript. Can call model fit code directly from this file, or read in .RDS file generated from PerchModel.R G. Filename: Bugsout_new_swf_zm_yep.rds Short description: 30,000 MCMC samples of posterior distributions for parameters of the Bayesian hierarchical model of yellow perch length fit in PerchModel.R. H. Filename: Bugsout_new_swf_zm_wae.rds Short description: 30,000 MCMC samples of posterior distributions for parameters of the Bayesian hierarchical model of walleye perch length fit in WalleyeModel.R. 2. Relationship between files: Length data for both species were collected simultaneously, we have separated walleye and yellow perch data into two files for analysis. Code for model fitting (WalleyeModel.R and PerchModel.R) are identical except for they call and analyze species-specific datasets. Code for generating figures (Predicted_lengths_fitures_WAE.R and Predicted_lengths_fitures_YEP.R) can call model fitting code (WalleyeModel.R and PerchModel.R) and fit models to generate outputs required for figures. These files are identical except for they call and use species-specific datasets and model outputs. Model results (Bugsout_new_swf_zm_wae.rds and Bugsout_new_swf_zm_yep.rds) are MCMC samples of posterior distributions of parameter estimates generated from WalleyeModel.R and PerchModel.R, respectively. 3. Additional related data collected that was not included in the current data package: Numbers and lengths of other fish species were also collected during these surveys and not included here. 4. Are there multiple versions of the dataset? no -------------------------- METHODOLOGICAL INFORMATION -------------------------- 1. Description of methods used for collection/generation of data: For length data: Age-0 walleye and yellow perch were collected from 1983-2018 by shoreline seining as part of the Minnesota Department of Natural Resources standardized large lakes monitoring program (Wingate and Schupp 1984) and supplemented by additional sampling as a part of this research. A 30-m long, 2-m deep, 6.4-mm bar mesh bag seine was used with a fixed pole seining technique, where one braille is fixed on shore while the other begins perpendicular to shore and is pulled toward shore in a sweeping motion while keeping the net taut. Seining began in 1983 for several lakes and was conducted annually with some exceptions. An average of 13 stations (range 6-23 stations) were sampled in each lake during each sampling year. The same stations within each lake were typically sampled weekly, from mid-July to mid-August. All fishes were identified and enumerated. Walleye and yellow perch total length (TL) was measured to the nearest mm. To account for differences in age-0 fish length due to differences in temperature, we calculated cumulative degree days with a 5�C base for each sample date in each lake. Because we lacked water temperature data for the time period of analysis, we used air temperature as a proxy for surface water temperature when calculating degree days. We acquired daily air temperature data for degree day calculation from NCEP North American Regional Reanalysis (NARR) provided by the NOAA/OAR/ESRL PSD, Boulder, Colorado, USA, from their Web site at https://www.esrl.noaa.gov/psd/. Grid resolution for NARR data is approximately 0.3 degrees (32 km) at the lowest latitude. Lake-specific daily air temperatures were extracted using the geoknife package (Read et al. 2015) in R version 3.5.1 (R Core Team 2018) with lake centroids as inputs. Read, J. S., J. I. Walker, A. P. Appling, D. L. Blodgett, E. K. Read, and L. A. Winslow. 2015. geoknife: reproducible web-processing of large gridded datasets. Ecography 39:349-408. Wingate, P., and D. H. Schupp. 1984. Large Lake Sampling Guide. Minnesota DNR Special Publication 140:30pp. 2. Methods for processing the data: To verify that only age-0 individuals were used in subsequent analyses, the data were quality checked by plotting length-frequency histograms for each species by lake, year, and week (nested within year). Data considered out of range of age-0 cohorts (either erroneous data or suspected age-1+ individuals) were removed. Data collected after Julian Date 250 were not included in the analysis. Programs were written for Program R and all code required to replicate analysis is included. 3. Instrument- or software-specific information needed to interpret the data: 4. Standards and calibration information, if appropriate: 5. Environmental/experimental conditions: 6. Describe any quality-assurance procedures performed on the data: To verify that only age-0 individuals were used in subsequent analyses, the data were quality checked by plotting length-frequency histograms for each species by lake, year, and week (nested within year). Data considered out of range of age-0 cohorts (either erroneous data or suspected age-1+ individuals) were removed. Winnibigoshish YEP data were updated so HAUL number was also changed to STATION number. HAUL to STATION numbers for 2007-2016 YEP data: "1"/"2"/"13"/"14" = 1; "3"/"4"/"15"/"16" = 2; "5"/"6"/"17"/"18" = 3; "7"/"8"/"19"/"20" = 4; "9"/"10"/"21"/"22" = 5; "11"/"12"/"23"/"24" = 6. Removed Winnibigoshish YEP from 1994, 1995, and 1996 referenced as stations 7, 8, or 9, as these sample came from Cut Foot Sioux lake rather than Winnibigoshish. Made station abbreviation name changes for Winnibigoshish YEP data to correspond to MNDNR recommendations: "Richards Townsite"/"RIT"/"RCH"/"RT" = 1; "West Winnie"/"WW" = 2; "Mallard Point"/"MAL" = 3; "North Shore"/"NS" = 4; "Bowens"/"BOW" = 5; "Tamarack Point"/"TAM" = 6. Some sample stations in Leech Lake were not well documented and no UTM coordinates could be found: to maintain continuity with our numeric station naming system, the station abbreviated names for Leech Lake were changed: "Agency Bay" = 6, "SE_UK" = 7, "Two Points" = 8, "Walker Bay" = 9. Rainy Lake 2012 and 2013 YEP weights had errors so acquired the original dataset from the MN DNR Large Lakes biologist, and joined new (correct) weights. 7. People involved with sample collection, processing, analysis and/or submission: Gretchen Hansen, Bethany Bethke, Josh Dumke, Tyler Ahrenstorff, numerous MN DNR staff over >30 years. ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: wae_length_data.csv ----------------------------------------- 1. Number of variables: 23 2. Number of cases/rows: 50012 3. Missing data codes: Code/symbol " " Definition: Data not available Code/symbol NA Definition: Not applicable or data not available 4. Variable List A. Name: Station Description: Sampling station name - Lake Specifi. Blank values indicate no station was recorded. B. Name: Lake Description: Lake name from which data were collected C. Name: Date Description: Date of fish collection D. Name: Year Description: Year when sampling took place. Based off sample date E. Name: UID Description: Unique Identification for each data row F. Name: Gear Description: Gear used to collect fish. "Seine" indicates large lake beach seine, 30-m, 2-m deep, 6.4-mm bar mesh. G. Name: Month Description: Month of year when sampling took place. Based off sample date H. Name: Week Description: Week of year when sampling took place. Used WEEKNUM function in Excel based off sample date I. Name: Code Description: Concantenated code for year_week combination J. Name: Species Description: Species abbreviation WAE = Walleye; YEP = Yellow Perch K. Name: Length Description: Fish total length in milimeters (mm) L. Name: DOW Description: Division of Waterbodies number used as lake identifier in the state of Minnesota M. Name: mean.daily.temp Description: Average air temperature (degrees C) for the sampling date and location acquired from NCEP North American Regional Reanalysis (NARR) provided by the NOAA/OAR/ESRL PSD, Boulder, Colorado, USA, from their Web site at https://www.esrl.noaa.gov/psd/. N. Name: TempC5 Description: Difference between mean daily temp and 5, used to calculate degree days. O. Name: DD Description: Cumulative degree days (base temperature 5 degrees C) for the sampling date P. Name: DOY Description: Julian date of sample Q. Name: Treatment Description: Whether invasive spiny water flea or zebra mussels were present at time of sample, lake and year specific SWF=Spiny water flea ZM= Zebra mussel None=neither invasive species present ZM, SWF= both zebra mussel and spiny water flea present R. Name: ZM Description: Year of zebra mussel invasion in lake, where applicable. Lake-specific S. Name: SWF Description: Year of spiny water flea invasion in lake, where applicable. Lake-specific T. Name: ZM.status Description: Whether a lake was invaded by zebra mussels at the time of sample, lake and year specific Uninvaded=adult zebra mussels not present Invaded=adult zebra mussels present U. Name: SWF.status Description: Whether a lake was invaded by spiny water fleas at the time of sample, lake and year specific Uninvaded=Spiny water fleas not present Invaded=Spiny water fleas present V. Name: utm.x Description: (aka "easting"). Sampling station coordinate, where available. Universal Transverse Mercator Datum 83; zone 15 W. Name: utm.y Description: (aka "northing"). Sampling station coordinate, where available. Universal Transverse Mercator Datum 83; zone 15 ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: yep_length_data.csv ----------------------------------------- 1. Number of variables: 23 2. Number of cases/rows: 176983 3. Missing data codes: Code/symbol " " Definition: Data not available Code/symbol NA Definition: Not applicable or data not available 4. Variable List A. Name: Station Description: Sampling station name - Lake Specific B. Name: Lake Description: Lake name from which data were collected C. Name: Date Description: Date of fish collection D. Name: Year Description: Year when sampling took place. Based off sample date E. Name: UID Description: Unique Identification for each data row F. Name: Gear Description: Gear used to collect fish. "Seine" indicates large lake beach seine, 30-m, 2-m deep, 6.4-mm bar mesh. G. Name: Month Description: Month of year when sampling took place. Based off sample date H. Name: Week Description: Week of year when sampling took place. Used WEEKNUM function in Excel based off sample date I. Name: Code Description: Concantenated code for year_week combination J. Name: Species Description: Species abbreviation WAE = Walleye; YEP = Yellow Perch K. Name: Length Description: Fish total length in milimeters (mm) L. Name: DOW Description: Division of Waterbodies number used as lake identifier in the state of Minnesota M. Name: mean.daily.temp Description: Average air temperature (degrees C) for the sampling date and location acquired from NCEP North American Regional Reanalysis (NARR) provided by the NOAA/OAR/ESRL PSD, Boulder, Colorado, USA, from their Web site at https://www.esrl.noaa.gov/psd/. N. Name: TempC5 Description: Difference between mean daily temp and 5, used to calculate degree days. O. Name: DD Description: Cumulative degree days (base temperature 5 degrees C) for the sampling date P. Name: DOY Description: Julian date of sample Q. Name: Treatment Description: Whether invasive spiny water flea or zebra mussels were present at time of sample, lake and year specific SWF=Spiny water flea ZM= Zebra mussel None=neither invasive species present ZM, SWF= both zebra mussel and spiny water flea present R. Name: ZM Description: Year of zebra mussel invasion in lake, where applicable. Lake-specific S. Name: SWF Description: Year of spiny water flea invasion in lake, where applicable. Lake-specific T. Name: ZM.status Description: Whether a lake was invaded by zebra mussels at the time of sample, lake and year specific Uninvaded=adult zebra mussels not present Invaded=adult zebra mussels present U. Name: SWF.status Description: Whether a lake was invaded by spiny water fleas at the time of sample, lake and year specific Uninvaded=Spiny water fleas not present Invaded=Spiny water fleas present V. Name: utm.x Description: (aka "easting"). Sampling station coordinate, where available. Universal Transverse Mercator Datum 83; zone 15 W. Name: utm.y Description: (aka "northing"). Sampling station coordinate, where available. Universal Transverse Mercator Datum 83; zone 15