========================================== # Title of Dataset: Magnitude-duration relationships of physiological sensitivity and environmental exposure improve climate change vulnerability assessments. ========================================== # Author of Dataset: Matthew J. Troia, Department of Integrative Biology, University of Texas at San Antonio troiamj@gmail.com ========================================== # Description of the data and file structure ------------------------------------------ Data tables (.csv, .dbf, or .txt) and R scripts (.R) are provided. Data tables are stored within the following subdirectories: - nwis_site_summary (.csv file): Input for computation of stream temperatures. - nwis_warming_v01 (.csv file): Input for computation of stream temperatures. - rezende_TDT_parameters_v01 (.csv file): Input for computation of warming tolerance. - data_nwis_v01 (subdirectory): Input for computation of warming tolerance. - data_WTcycle_v01 (subdirectory): Output warming tolerance. - data_WTexceed_v01 (subdirectory): Output warming tolerance. - data_warmTol_v01 (subdirectory): Output warming tolerance. - data_warmTol_summary_v01 (subdirectory): Input for maxent models. - data_maxent_ichthymaps_v01 (subdirectory): Input for maxent models. - data_maxent_predictors_natureserve_v01 (subdirectory): Input for maxent models. - data_maxent_predictors_nhd_v01 (subdirectory): Input for maxent models. - data_maxent_predictors_streamcat_v01 (subdirectory): Input for maxent models. - data_maxent_preditors_nsi_v01 (subdirectory): Input for maxent models. - data_maxent_formulas_v01 (subdirectory): Output from maxent models. - data_maxent_projections_v01 (subdirectory): Output from maxent models. ========================================== Variable names and descriptions ------------------------------------------ # nwis_site_summary.csv - site_id: Site ID from National Water Information System (NWIS). - year_min: First year of record. - year_max: Last year of record. - year_n: Number of years of record. ------------------------------------------- nwis_warming_v01.csv - site_id: Site ID from National Water Information System (NWIS). - dec_lat_va: Latitude of site in decimal degrees. - dec_long_v: Longitude of site in decimal degrees. - tmax_hist: Maximum water temperature at site during historical time period in degrees Celsius. - tmax_rcp45: Maximum water temperature at site during future time period (representative concentration pathway 4.5) in degrees Celsius - tmaxChg_hist: Difference in maximum water temperature between historical time period and historical time period. - tmaxChg_rcp45: Difference in maximum water temperature between future time period and historical time period. ------------------------------------------- rezende_TDT_parameters_v01.csv - genus_species: Latin name of species. - Class: Taxonomic class of species. - Stage: Life stage of species - Habitat: aquatic or terrestrial - FB_marine: Occupies marine habitat based on classification by FishBase.org - FB_fresh: Occupies freshwater habitat based on classification by FishBase.org - FB_climate: Occupies polar, nonpolar, temperate, or subtropical realm based on classification by FishBase.org - LT: Percentile of lethal time until death; 50% or 100% - CTmax: Upper critical thermal limit in degrees Celsius; from equation 1 in Rezende et al. 2014. - z: A constant that characterizes the sensitivity to temperature change; from equation 1 in Rezende et al. 2014. - r2: Coefficient of determination for relationship between exposure magnitude (in degrees Celsius) and exposure duration (in minutes) - Reference: Source of data; after Rezende et al. 2014. ------------------------------------------ data_nwis_v01 (subdirectory): - 107 .txt files representing raw downloads from National Water Information System (NWIS). - file names are Site ID from National Water Information System (NWIS). - Variable names and descriptions: -- Column1: Source of data (USGS) -- Column2: Site ID from National Water Information System (NWIS). -- Column3: Date time. -- Column4: Time zone. -- Column5: Temperature in degrees Celsius. -- Column6: Measurement status (approved). ------------------------------------------ data_WTcycle_v01 (subdirectory): - 938 .csv files representing cleaned National Water Information System (NWIS) water temperature time series of hottest day of year. - Variable names and descriptions: -- site_id: Site ID from National Water Information System (NWIS). -- year: Year of record. -- month: Month of record -- day: Day of record -- hours: Hour of record -- tempC: Temperature in degrees Celsius. ------------------------------------------ data_WTexceed_v01 (subdirectory): - 938 .csv files representing duration-magnitude exposure (water temperature) relationship. - Variable names and descriptions: -- WTexceed: Temperature exceeded in degrees Celsius for duration-magnitude exposure (water temperature) relationship. -- site_id.year: Site ID from National Water Information System (NWIS) and year. -- exceed_prop: Proportion of temperature measurements exceeding WTexceed out of 96 daily measurements. -- exceed_hours: Number of hours exceeding WTexceed out of 24 hours. ------------------------------------------ data_warmTol_v01 (subdirectory): - 3752 .csv files representing duration-magnitude exposure (water temperature)relationship, sensitivity (of species) relationship, and warming tolerances. - Variable names and descriptions: -- genus_species: Latin name of species. -- period: Historical or future time period. -- site_id.year: Site ID from National Water Information System (NWIS) and year. -- exceed_hours: Number of hours exceeding WTexceed out of 24 hours. -- WTexceed.sen: Temperature exceeded in degrees Celsius for duration-magnitude sensitivity (of species) relationship. -- WTexceed.exp: Temperature exceeded in degrees Celsius for duration-magnitude exposure (water temperature) relationship. -- warmTol: Difference between WTexceed.sen and WTexceed.exp. ------------------------------------------ data_warmTol_summary_v01 (subdirectory): - Eight .csv files representing warming tolerances for each species-by-period combination. - Variable names and descriptions: -- genus_species: Latin name of species. -- period: Historical or future time period. -- site_id.year: Site ID from National Water Information System (NWIS) and year. -- hours.min -- warmTol.min: Minimum difference between WTexceed.sen and WTexceed.exp; this is the 'prolonged' warming tolerance -- warmTol.acute: Difference between WTexceed.sen and WTexceed.exp at exceed_hours = 0.01; this is the 'acute' warming tolerance ------------------------------------------ data_maxent_ichthymaps_v01 (subdirectory): - One .csv file representing the original IchthyMaps Dataset (Frimpong et al. 2016). - Variable names and descriptions: -- ID: Identifier of each presence record -- Source: This attribute identifies the source of each record -- State: U.S. states (U.S. Postal Service state abbreviations) -- Name_Taxa: Scientific name of fish species or subspecies -- Genus: Taxon classification, genus level -- Species: Taxon classification, species level -- Level_Taxa: Taxon classification level -- ITIS_TSN: Taxonomic Serial Number from the Integrated Taxonomic Information System -- COMID_NHDv2: Unique flowline ID from National Hydrography Dataset (NHD). -- HUC12: 12-digit Hydrologic Unit Code (subwatershed) -- HUC8: 8-digit Hydrologic Unit Code (cataloging unit) -- HUC4: 4-digit Hydrologic Unit Code (subregion) -- Time_frame: Time period from which record was sourced. ------------------------------------------ data_maxent_predictors_natureserve_v01 (subdirectory): - 15 .csv file representing National Hydrography Dataset (NHD) flowlines from 15 2-digit Hydrologic Unit Code (HUC) regions. - Variable names and descriptions: -- COMID: Unique flowline ID from National Hydrography Dataset (NHD). -- ns_ameneb: Ameiurus nebulosus native based on NatureServe Digital Distribution of Native U.S. Fishes by Watershed -- ns_rhiatr: Rhinichthys atratulus native based on NatureServe Digital Distribution of Native U.S. Fishes by Watershed -- ns_salfon: Salvelinus fontinalis native based on NatureServe Digital Distribution of Native U.S. Fishes by Watershed -- ns_sematr: Semotilus atromaculatus native based on NatureServe Digital Distribution of Native U.S. Fishes by Watershed ------------------------------------------ data_maxent_predictors_nhd_v01 (subdirectory): - 15 .csv file representing National Hydrography Dataset (NHD) flowlines from 15 2-digit Hydrologic Unit Code (HUC) regions. - Variable names and descriptions: -- COMID: Unique flowline ID from National Hydrography Dataset (NHD). -- SLOPE: Slope of NHD flowline in meters per kilometer. ------------------------------------------ data_maxent_predictors_streamcat_v01 (subdirectory): - 15 .csv file representing National Hydrography Dataset (NHD) flowlines from 15 2-digit Hydrologic Unit Code (HUC) regions. - BFI_Region##.csv - Variable names and descriptions: -- COMID: Unique flowline ID from National Hydrography Dataset (NHD). -- BFIWs: The Baseflow Index (BFI) is the ratio of baseflow to total flow, expressed as a percentage, within watershed. - Elevation_Region##.csv - Variable names and descriptions: -- COMID: Unique flowline ID from National Hydrography Dataset (NHD). -- ElevCat: Mean catchment elevation (m) - PRISM_1981_2010_Region##.csv - Variable names and descriptions: -- COMID: Unique flowline ID from National Hydrography Dataset (NHD). -- PrecipCat: Mean precipitation (mm) within the catchment. -- TmaxCat: 30-year normal maximum temperature (°C) -- TmeanCat: 30-year normal mean temperature (°C) -- TminCat: 30-year normal minimum temperature (°C) - RefStreamTempPred_Region##.csv - Variable names and descriptions: -- COMID: Unique flowline ID from National Hydrography Dataset (NHD). -- MSST_2008: Predicted (modeled) mean summer stream temperature (July-Aug) for year 2008 -- MSST_2009: Predicted (modeled) mean summer stream temperature (July-Aug) for year 2009 -- MSST_2013: Predicted (modeled) mean summer stream temperature (July-Aug) for year 2013 -- MSST_2014: Predicted (modeled) mean summer stream temperature (July-Aug) for year 2014 ------------------------------------------ data_maxent_preditors_nsi_v01 (subdirectory): - 15 .csv files representing National Hydrography Dataset (NHD) flowlines from 15 2-digit Hydrologic Unit Code (HUC) regions for each of four species. - Variable names and descriptions: -- COMID: Unique flowline ID from National Hydrography Dataset (NHD). -- lat_mdpt: Latitude of flowline in decimal degrees. -- lon_mdpt: Longitude of flowline in decimal degrees. ------------------------------------------ data_maxent_formulas_v01 (subdirectory): - Four .csv files representing selected environmental covariates from MaxEnt models for each species. ------------------------------------------ data_maxent_projections_v01 (subdirectory): - 60 .csv files - Variable names and descriptions: -- COMID: Unique flowline ID from National Hydrography Dataset (NHD). -- lat_mdpt: Latitude of flowline in decimal degrees. -- lon_mdpt: Longitude of flowline in decimal degrees. -- PRO: Habitat suitability score as probability ratio output. ========================================== # Description of the R scripts ------------------------------------------ Twenty two R scripts are provided. These scripts use aforementioned data tables as inputs and/or build the aforementioned data tables as outputs. To run these scripts, (1) change file the file paths to your local working directory and (2) run scripts in order of script name (i.e., code01_XXX.R, code02_XXX.R, code03_XXX.R). - nwis_site_summary (.csv file): Input for computation of stream temperatures. - nwis_warming_v01 (.csv file): Input for computation of stream temperatures. - rezende_TDT_parameters_v01 (.csv file): Input for computation of warming tolerance. - data_nwis_v01 (subdirectory): Input for computation of warming tolerance. - data_WTcycle_v01 (subdirectory): Output warming tolerance. - data_WTexceed_v01 (subdirectory): Output warming tolerance. - data_warmTol_v01 (subdirectory): Output warming tolerance. - data_warmTol_summary_v01 (subdirectory): Input for maxent models. - data_maxent_ichthymaps_v01 (subdirectory): Input for maxent models. - data_maxent_predictors_natureserve_v01 (subdirectory): Input for maxent models. - data_maxent_predictors_nhd_v01 (subdirectory): Input for maxent models. - data_maxent_predictors_streamcat_v01 (subdirectory): Input for maxent models. - data_maxent_preditors_nsi_v01 (subdirectory): Input for maxent models. - data_maxent_formulas_v01 (subdirectory): Output from maxent models. - data_maxent_projections_v01 (subdirectory): Output from maxent models. ========================================== # Sharing/access Information ------------------------------------------ Aforementioned input data were acquired from the following open sources: - USGS National Water Information System: 15-minute water temperature data from 66 study sites. - Rezende et al. 2014. Functional Ecology 28, 799-809: Thermal sensitivity parameters for 4 study species. - IchthyMaps: occurrence records for maxent species distribution models - National Hydrography Dataset: environmental predictors for maxent species distribution models. - National Stream Internet: environmental predictors for maxent species distribution models. - StreamCat: environmental predictors for maxent species distribution models. - Natureserve Digital Distribution of Native U.S. Fishes by Watershed: environmental predictors for maxent species distribution models.