This Cosumnes River Floodplain Fish Outmigration Cues readme.txt file was generated on 2022-01-23 by Mollie H. Ogaz GENERAL INFORMATION 1. Title of Dataset: Cosumnes River Floodplain Fish Outmigration Cues 2. Author Information A. Principal Investigator Contact Information Name: Mollie H. Ogaz Institution: UC Davis Address: One Shields Ave., Davis, CA 95616 Email: mhogaz@ucdavis.edu B. Associate or Co-investigator Contact Information Name: Carson A. Jeffres Institution: UC Davis Address: One Shields Ave., Davis, CA 95616 Email: cajeffres@ucdavis.edu 3. Date of data collection (single date, range, approximate date): 2018-01-26 - 2019-07-08 4. Geographic location of data collection: 38°16'16.90"N, 121°23'44.61"W 5. Information about funding sources that supported the collection of the data: California Trout Inc. SHARING/ACCESS INFORMATION 1. Licenses/restrictions placed on the data: NA 2. Links to publications that cite or use the data: NA 3. Links to other publicly accessible locations of the data: flow data from CDEC: https://cdec.water.ca.gov/dynamicapp/req/CSVDataServlet?Stations=MHB&SensorNums=1&dur_code=H&Start=2018-01-01&End=2019-08-01 4. Links/relationships to ancillary data sets: NA 5. Was data derived from another source? Flow data from CDEC 6. Recommended citation for this dataset: Ogaz, M and Jeffres, C (2022) Data from: Should they stay or should they go: Do behavioral cues enable native fishes to exit a California floodplain? Dryad Digital Repository. DATA & FILE OVERVIEW 1. File List: -cosumnes_floodplain_connection_status: for each date in the study, notation of whether the outlet and inlet breaches are connected or disconected to the river -cosumnes_floodplain_DOBO_dissolved_oxygen: from the dissolved oxygen logger installed on the interior of the floodplain, the dissolved oxygen values in milligrams every 15 minutes -cosumnes_floodplain_DOBO_temp:from the dissolved oxygen logger installed on the interior of the floodplain, the water temperature values in celcius every 15 minutes -cosumnes_floodplain_fish_catch: for each fish caught during the study: species (common name), length in millimeters, date of capture, location fo the trap the fish was caught in, whether it was native or non-native (alien), and whether it was a young-of-year (YOY) or not. -cosumnes_river_flow_cfs: from USGS Michigan Bar gage station (USGS #11335000): flow measured in cubic feet per second in hourly intervals cosumnes_floodplain_model_dataframe- compilation of all data variables used in the bayesian models 2. Relationship between files, if important: the temperature and dissolved oxygen values were measured on the same Onset HOBO U26 Dissolved Oxygen Logger 3. Additional related data collected that was not included in the current data package: no 4. Are there multiple versions of the dataset? no METHODOLOGICAL INFORMATION 1. Description of methods used for collection/generation of data: -cosumnes_floodplain_connection_status: known flow (cfs) values that the floodplain connects and disconnects at (from authors' personal experience) -cosumnes_floodplain_DOBO_dissolved_oxygen: Onset HOBO U26 Dissolved Oxygen Logger attached to a t-post on the interior of the floodplain -cosumnes_floodplain_DOBO_temp:Onset HOBO U26 Dissolved Oxygen Logger attached to a t-post on the interior of the floodplain -cosumnes_floodplain_fish_catch: fyke nets deployed at outlets and within the interior of the floodplain. All captured fish were processed (ID'd, lengths measured) and released downstream of nets before they were reset. -cosumnes_river_flow_cfs: from USGS Michigan Bar gage station (USGS #11335000), downloaded from the California Data Exchange Center (CDEC) -cosumnes_floodplain_model_dataframe: compiled through the above 5 files using R 2. Methods for processing the data: The flow data was downloaded directly from the CDEC website. The temperature and dissolved oxygen data were downloaded directly from the instrument. The connection status was designated based on flow, using the USGS gage data. The was done with an "ifelse" statement in R. The fish catch data was entered into an Access database, QAQC'd, and exported as a csv. "Origin" and "YOY" columns were added in R with "ifelse" statements, using knowledge of the fish species and literature (Moyle, PB. 2002. Inland Fishes of California). The model dataset was created by compiling and manipulating pertinent data from the above 5 files using the R package "tidyverse". 3. Instrument- or software-specific information needed to interpret the data: All analysis was done using the software R version 3.6.1 (R Core Team 2019). The "brms" package was used to create the Bayesian models that predicted outmigration timing of native and non-native fishes. The "tidyverse" package was used for all data manipulation and creation of figures. The "cowplot" package was used to combine multiple plots. 4. Standards and calibration information, if appropriate: NA 5. Environmental/experimental conditions: NA 6. Describe any quality-assurance procedures performed on the data: All data entries were checked by a different person than entered it originally. 7. People involved with sample collection, processing, analysis and/or submission: Mollie Ogaz, Carson Jeffres, Eric Holmes, Nicholas Corline, Noah Christe, Marissa Levinson, Kelly Neal, Miranda Tilcock, and Gabe Saron. DATA-SPECIFIC INFORMATION FOR: cosumnes_floodplain_connection_status 1. Number of variables: 3 2. Number of cases/rows: 286 3. Variable List: date: the date in mm/dd/YYYY format outlet_conn: outlet connection status- either "connected" or "disconnected" in_conn: inlet connection status- either "connected" or "disconnected" 4. Missing data codes: NA 5. Specialized formats or other abbreviations used: NA DATA-SPECIFIC INFORMATION FOR: cosumnes_floodplain_DOBO_dissolved_oxygen 1. Number of variables: 2 2. Number of cases/rows: 25,628 3. Variable List: datetime: date and time in mm/dd/YYYY hh:mm format dissolved_oxygen_mg: dissolved oxygen values, measured in milligrams, for each datetime 4. Missing data codes: NA 5. Specialized formats or other abbreviations used: NA DATA-SPECIFIC INFORMATION FOR: cosumnes_floodplain_DOBO_temp 1. Number of variables: 2 2. Number of cases/rows: 27,700 3. Variable List: datetime: date and time in mm/dd/yyyy hh:mm format temperature_deg_celcius: temperature values, measured in celcius, for each datetime 4. Missing data codes: NA = no data available 5. Specialized formats or other abbreviations used: NA DATA-SPECIFIC INFORMATION FOR: cosumnes_floodplain_fish_catch 1. Number of variables: 9 2. Number of cases/rows: 27,943 3. Variable List: Species: common name for the fish species Length_mm: fork length of ifsh, measured in millimeters Date_Pulled: date the trap was removed from the water, in mm/dd/yyyy format Month: 1-2 digit number of the month from date_pulled Day: 1-2 digit number of the day from date_pulled Year: 4 digit number of the year from date_pulled Trap_Location: location of the trap the fish was captured in Origin: whether the fish is native to California or non-native (listed as alien in the file) YOY: Y/N of whether the fish was a young-of-year or not 4. Missing data codes: NA 5. Specialized formats or other abbreviations used: TW = Triangle West (the outlet breach to the west) TE- Triangle East (the outlet breach to the east) TW- POND = the trap set within the interior pond of the floodplain, closest to the western exit breach TE- POND = the trap set within the interior pond of the floodplain, closest to the eastern exit breach DATA-SPECIFIC INFORMATION FOR: cosumnes_river_flow_cfs 1. Number of variables: 2 2. Number of cases/rows: 15,683 3. Variable List: datetime: date and time in mm/dd/yyyy hh:mm format flow_cfs: flow of the river at the gage, measured in cubic feet per second 4. Missing data codes: NA 5. Specialized formats or other abbreviations used: NA DATA-SPECIFIC INFORMATION FOR: cosumnes_floodplain_model_dataframe 1. Number of variables: 40 2. Number of cases/rows: 1,233 3. Variable List: WY: water year DOY: day of year Date_Pulled: date (mm/dd/yyyy) the trap was pulled Region: pond or outlet breach Set: Y/N whether a net was set in that region or not on that day in_conn: whether the inlet was connected to the river or not outlet_conn: whether the outlet was connected to the river or not Species: common name for the fish species Origin: native or non-native (designated as "Alien") YOY: young-of-year Y/N N: number of that fish species caught on that day netsperday: number of nets set at the region on that day (there was a possible toal of 2 per day) CPUE: catch per unit effort of the species per day c.catch: cummulative catch of the species per day avg.temp: average daily temperature (celcius) max.temp: maximum daily temperature (celcius) min.temp: minimum daily temperature (celcius) med.temp: median daily temperature (celcius) temp.diff: difference in average temperature from the previous day (the current day value minus the previous day's) avg.do: average daily dissolved oxygen value (milligrams) max.do: maximum daily dissolved oxygen value (milligrams) min.do: minimum daily dissolved oxygen value (milligrams) med.do: median daily dissolved oxygen value (milligrams) do.diff: difference in average dissolved oxygen from the previous day (the current day value minus the previous day's) avg.q: average daily flow (cubic feet per second) q.diff: difference in average flow from the previous day (the current day value minus the previous day's) norm.avg.temp: normalized average daily temperature (celcius) norm.max.temp: normalized maximum daily temperature (celcius) norm.min.temp: normalized minimum daily temperature (celcius) norm.med.temp: normalized median daily temperature (celcius) temp.rate: change in flow from the previous day (daily rate of temperature change) norm.avg.do: normalized average daily dissolved oxygen value (milligrams) norm.max.do: normalized maximum daily dissolved oxygen value (milligrams) norm.min.do: normalized minimum daily dissolved oxygen value (milligrams) norm.med.do: normalized median daily dissolved oxygen value (milligrams) do.rate: change in dissolved oxygen from the previous day (daily rate of dissolved oxygen change) norm.avg.q: normalized average daily flow (cubic feet per second) q.rate: change in flow from the previous day (daily rate of flow change) q.seven.avg: seven day rolling average of the average daily flow logeffort: the logarithm of the number nets set per day (effort) 4. Missing data codes: NA 5. Specialized formats or other abbreviations used: NA