This readme.txt file was generated on 2022.04.20 by Jenna Ruzich and updated 2023.02.07 by Holly Kundel ------------------- GENERAL INFORMATION ------------------- 1. Title of Dataset: Data In Support Of Accounting For Spatio-Temporal Variation In Catachability In Joint Species Distribution Models. 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: Joshua North Institution: University of Missouri Address: 146 Middlebush Hall, Columbia, MO 65211 Email: joshuanorth@mail.missouri.edu, jsnorth@lbl.gov ORCID: https://orcid.org/0000-0001-7631-8021 Associate or Co-investigator Contact Information Name: Erin Schliep Institution: University of Missouri Address: 146 Middlebush Hall, Columbia, MO 65211 Email: schliepe@missouri.edu , emschliep@ncsu.edu ORCID: https://orcid.org/0000-0002-2803-3467 Additonal Authors Name: Holly Kundel Institution: University of Minnesota Name: Christopher Custer Institution: Pennsylvania Cooperative Fish and Wildlife Research Unit, Pennsylvania State University Name: Paul McLaughlin Institution: Pennsylvania Cooperative Fish and Wildlife Research Unit, Pennsylvania State University 3. Date published or finalized for release: 2022.04.21 4. Date of data collection (single date, range, approximate date): 2000 - 2019 5. Geographic location of data collection (where was data collected?): Minnesota, USA 6. Information about funding sources that supported the collection of the data: This work was supported by the U.S. Geological Survey Midwest Climate Adaptation Science Center Grant No.G20AC00096. Data were assembled by collaborators at the University of Minnesota - Twin Cities. Original fish data were collected by the Minnesota Department of Natural Resources (MNDNR) as part of their standard sampling program. 7. Overview of the data (abstract): Fish data on six species (black crappie (Pomoxis nigromaculatus), bluegill (Lepomis macrochirus), largemouth bass (Micropterus salmoides), northern pike (Esox lucius), walleye (Sander vitreus), and yellow perch (perca flavescens)) caught in gill nets and trap nets between 2000 and 2019 during Minnesota Department of Natural Resources (MNDNR) fisheries surveys done in the months of June through September. Fish catch and effort (number of nets set overnight) comes from over 1,000 Minnesota lakes. In addition to fisheries data, we included additional information concerning lake characteristics, predicted water temperature, and watershed land use. Lake area and maximum depth were obtained from MNDNR public databases. Watershed land use was calculated using the 2016 National Land Cover Database. Water clarity, which is described by annual lake-specific median values derived from remotely sensed Secchi depth courtesy of Max Gilnes. Lastly, water temperatures simulated with the general lake model were also included. -------------------------- SHARING/ACCESS INFORMATION -------------------------- 1. Licenses/restrictions placed on the data: CC0 1.0 Public Domain Dedication (https://creativecommons.org/publicdomain/zero/1.0/) 2. Links to publications that cite or use the data: North, J.N., E.M. Schliep, G.J.A. Hansen, H. Kundel, C.A. Custer, P. McLaughlin, and T. Wagner. Accounting for Spatio-Temporal Variation in Catchability in Joint Species Distribution Models. In Review. 3. Recommended citation for the data: North, J.N., E.M. Schliep, G.J.A. Hansen, H. Kundel, C.A. Custer, and P. McLaughlin (2022). Accounting for Spatio-Temporal Variation in Catchability in Joint Species Distribution Models. Retrieved from the Data Repository for the University of Minnesota, https://hdl.handle.net/11299/227105. 4. Terms of Use: Data Repository for the U of Minnesota (DRUM) By using these files, users agree to the Terms of Use. https://conservancy.umn.edu/pages/drum/policies/#terms-of-use --------------------- DATA & FILE OVERVIEW --------------------- 1. File List A. Filename: fish_data_raw.csv Short description: Fish catch and effort data, and environmental data for Minnesota lakes used to analyze spatial and temporal variation in catchability and relative abundance. B. Filename: raw_temp.csv Short description: Daily modeled water temperature data throughout the fishing season (not just the surveyed dates) that is used to constrain the effort scaling to have a mean of 1. 2. Relationship between files: Minnesota lakes are indexed by id number (DOW) in both files. Temp_0 (date and location specific surface water temperature) appears in both files and the value in fish_data_raw is the temperature specific to an individual survey date/location. 3. Are there multiple versions of the dataset? No -------------------------- METHODOLOGICAL INFORMATION -------------------------- 1. Description of methods used for collection/generation of data: Fish catch and effort data were collected by the Minnesota Department of Natural Resources (MDNR) between 2000 and 2019 using gill nets and trap nets as part of their standard sampling program (Minnesota Department of Natural Resources (MNDNR) 2017). These gears are designed to index the abundance of sport fishes in the littoral (nearshore) zone, although gill nets are deployed in deeper waters. To account for changes in survey types throughout the time series and to maximize standardization across surveys, we restricted our analysis to a subset of survey types that minimize among-survey variation in survey methodology (Minnesota Department of Natural Resources (MNDNR) 2017). Both gill nets and trap nets were deployed at multiple index stations within a lake. One unit fixed effort consisted of one net (gill net or trap net) deployed for a 24-hour sampling period. Depending on management goals for each lake, sampling occurred during the ice-free season in Minnesota on an every 1-year to every 10-year rotation, resulting in a different number of observations for each lake. The data used in our analysis consist of lakes sampled between June 1 and September 30 during the 20 year time period. The median number of surveys per lake was 3, with a minimum and maximum of 1 and 19, respectively. For a given lake, monitoring is targeted to occur at approximately the same day of year across surveys, but due to limited gear and personnel, and the large number of lakes, variability in the sampling day existed throughout the region both within lake across surveys and across lakes. Catch and effort data are for six ecologically and socioeconomically important species including black crappie (Pomoxis nigromaculatus), bluegill (Lepomis macrochirus), largemouth bass (Micropterus salmoides), northern pike (Esox lucius), walleye (Sander vitreus), and yellow perch (Perca flavescens). For each species, catch was calculated as the sum of individuals captured in each gear type, and effort was the sum of the number of nets deployed for each gear type from a given survey. We included environmental variables associated with fish abundance as possible covariates in our model. Environmental variables were derived from various sources. Lake area and maximum depth were obtained from MNDNR public databases (https://gisdata.mn.gov/dataset/water-lake-basin-morphology). Watershed land use was calculated based on the 2016 National Land Cover Database (Homer et al. 2020), quantified as the proportion of watershed area falling in wetland or urban land use categories and extracted using the LAGOSNE R package (Sorano et al. 2017; Stachelek et al. 2019). Water clarity was quantified using annual lake-specific median values of remotely sensed Secchi depth (Max Gilnes, Rensselear Polytechnic Institute, Personal Communication). Water temperature was included to account for potential seasonal differences in catchability and to quantify differences in abundances related to average thermal conditions. In both cases, we used surface water temperatures simulated using the general lake model (Hipsey et al. 2019) for lakes throughout the upper Midwest (Read et al. 2021). We used lake- and day-specific degree days (base temperature 5°C, calculated up to the date of survey, as an index of seasonality specific to each lake, year, and survey). We used a five-year rolling mean of annual degree days as a measure of lake specific temperatures experienced by the fish over their lifetime, rather than focusing on conditions in an individual year (Massie et al. 2021). We also include daily surface temperature. Works Cited Hipsey, M.R., Bruce, L.C., Boon, C., Busch, B., Carey, C.C., Hamilton, D.P., Hanson, P.C., Read, J.S., de Sousa, E., Weber, M. & Winslow, L.A. (2019) A General Lake Model (GLM 3.0) for linking with high-frequency sensor data from the Global Lake Ecological Observatory Network (GLEON). Geoscientific Model Development, 12, 473–523. https://dx.doi.org/10.5194/gmd-12-473-2019. Homer, C., Dewitz, J., Jin, S., Xian, G., Costello, C., Danielson, P., Gass, L., Funk, M., Wickham, J., Stehman, S., Auch, R. & Riitters, K. (2020) Conterminous United States land cover change patterns 2001–2016 from the 2016 National Land Cover Database. ISPRS Journal of Photogrammetry and Remote Sensing, 162, 184–199. https://dx.doi.org/10.1016/j.isprsjprs.2020.02.019. Massie, D.L., Hansen, G.J., Li, Y., Sass, G.G. & Wagner, T. (2021) Do lake-specific characteristics mediate the temporal relationship between walleye growth and warming water temperatures? Canadian Journal of Fisheries and Aquatic Sciences, 78, 913–923. https://dx.doi.org/10.1139/cjfas-2020-0169. Minnesota Department of Natural Resources. 2014. Lake Basin Morphology. Distributed by Minnesota Geospatial Commons. https://gisdata.mn.gov/dataset/water-lake-basin-morphology Minnesota Department of Naural Resources (MNDNR) (2017) Manual of instructions for lake survey. Minnesota Department of Natural Resources, Special Publication No 180, St. Paul, Minnesota (version 104, released January 2019). Read, J., Appling, A., Oliver, S., Platt, L., Zwart, J., Vitense, K., Hansen, G., Corson-Dosch, H. & Kundel, H. (2021) Data release: Process-based predictions of lake water temperature in the Midwest US: U.S. Geological Survey data release. https://www.sciencebase.gov/catalog/item/5db761e7e4b0b0c58b5a4978 Soranno, P.A., Bacon, L.C., Beauchene, M., Bednar, K.E., Bissell, E.G., Boudreau, C.K., Boyer, M.G., Bremigan, M.T., Carpenter, S.R., Carr, J.W., Cheruvelil, K.S., Christel, S.T., Claucherty, M., Collins, S.M., Conroy, J.D., Downing, J.A., Dukett, J., Fergus, C.E., Filstrup, C.T., Funk, C., Gonzalez, M.J., Green, L.T., Gries, C., Halfman, J.D., Hamilton, S.K., Hanson, P.C., Henry, E.N., Herron, E.M., Hockings, C., Jackson, J.R., Jacobson-Hedin, K., Janus, L.L., Jones, W.W., Jones, J.R., Keson, C.M., King, K.B.S., Kishbaugh, S.A., Lapierre, J.F., Lathrop, B., Latimore, J.A., Lee, Y., Lottig, N.R., Lynch, J.A., Matthews, L.J., McDowell, W.H., Moore, K.E.B., Neff, B.P., Nelson, S.J., Oliver, S.K., Pace, M.L., Pierson, D.C., Poisson, A.C., Pollard, A.I., Post, D.M., Reyes, P.O., Rosenberry, D.O., Roy, K.M., Rudstam, L.G., Sarnelle, O., Schuldt, N.J., Scott, C.E., Skaff, N.K., Smith, N.J., Spinelli, N.R., Stachelek, J., Stanley, E.H., Stoddard, J.L., Stopyak, S.B., Stow, C.A., Tallant, J.M., Tan, P.N., Thorpe, A.P., Vanni, M.J., Wagner, T., Watkins, G., Weathers, K.C., Webster, K.E., White, J.D., Wilmes, M.K. & Yuan, S. (2017) LAGOS-NE: a multi-scaled geospatial and temporal database of lake ecological context and water quality for thousands of US lakes. GigaScience, 6, 1–22. https://dx.doi.org/10.1093/gigascience/gix101. Stachelek, J., Oliver, S. & Masrour, F. (2019) LAGOSNE: Interface to the lake multi-scaled geospatial and temporal database. R package version 202. 2. Methods for processing the data: Programs were written for Program R and STAN (through R) to analyze the data sets included here. Analyses were performed using R version 4.1.2 (2021-11-01) Bird Hippie, and STAN version 2.21.0. Link to the code required for replicating the analyses can be found on GitHub: https://github.com/jsnowynorth/fish_abundance 3. Instrument- or software-specific information needed to interpret the data: Program R is required to run the analysis. 4. People involved with sample collection, processing, analysis and/or submission: Joshua S. North, Erin M. Schliep, Gretchen J.A. Hansen, Holly Kundel, Christopher A. Custer, Paul McLaughlin, Tyler Wagner, and numerous state agency staff. ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: fish_data_raw ----------------------------------------- 1. Number of variables: 32 2. Number of cases/rows: 39,192 3. Missing data codes: None 4. Variable List A. Name: DOW Description: Unique lake identifier B. Name: COMMON_NAME Description: Common name of species C. Name: SURVEYDATE Description: Date of the survey D. Name: TOTAL_CATCH Description: Total fish caught from the survey E. Name: EFFORT Description: Total effort used in survey (number of nets per 24 hour period) F. Name: CPUE Description: Catch per unit effort (total catch / effort) G. Name: MAX_DEPTH_FEET Description: Maximum depth of lake (in feet) H. Name: mean.gdd Description: Mean lake-specific growing degree days (base temperature 5 ℃) from 1980-2018 I. Name: LAKE_AREA_GIS_ACRES Description: Lake area measured by GIS, in acres J. Name: LAKE_CENTER_UTM_EASTING Description: UTM easting K. Name: LAKE_CENTER_UTM_NORTHING Description: UTM northing L. Name: year Description: Year of the survey M. Name: ag Description: Percentage of land use that is agricultural N. Name: urban Description: Percentage of land use that is urban O. Name: wetlands Description: Percentage of land use that is wetlands P. Name: barren Description: Percentage of land use that is barren Q. Name: forest Description: Percentage of land use that is forest R. Name: shrub Description: Percentage of land use that is shrub S. Name: grass Description: Percentage of land use that is grass T. Name: lake_elevation_m Description: Elevation of the lake (in m) U. Name: TN Description: Binary variable: 1 if survey used trap nets, 0 otherwise V. Name: GN Description: Binary variable: 1 if survey used gill nets, 0 otherwise W. Name: DD5 Description: 5 year rolling mean for lake-specific growing degree days ( ℃ * days) at base temperature 5 ℃. Calculated for the five years preceding the survey, inclusive. X. Name: secchi Description: Water clarity as indexed by Secchi disk depth of lake (in m), calculated from remotely sensed data. Y. Name: temp_0 Description: Water surface temperature on the day of the survey (in ℃) Z. Name: DOY Description: Day of the year AA. Name: DOY_sin_semi Description: sin(DOY/121 * 2*pi) - semiannual fishing season cycle BB. Name: DOY_cos_semi Description: sin(DOY/121 * 2*pi) - semiannual fishing season cycle CC. Name: DOY_sin_semi_temp Description: DOY_sin_semi times temp_0 DD. Name: DOY_cos_semi_temp Description: DOY_sin_semi times temp_0 EE. Name: lat Description: Latitude of the lake FF. Name: lon Description: Longitude of the lake ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: raw_temp ----------------------------------------- 1. Number of variables: 4 2. Number of cases/rows: 9,064,800 3. Missing data codes: None 4. Variable List A. Name: SURVEYDATE Description: Date of the survey B. Name: temp_0 Description: Water surface temperature on the day of the survey (in ℃) C. Name: DOW Description: Unique lake identifier D. Name: year Description: Year of the survey