README: Large females connect Atlantic cod spawning sites

https://doi.org/10.5061/dryad.tb2rbp074

The data sets were collected east of the Smøla archipelago in mid-Norway during 2017 - 2019. Details for each dataset are provided in the README file.
Data sets included:
1) Atlantic cod captures in traps
·      Individual tags used
·      Body size measurements of tagged cod
·      Information about sex, maturity stage, location and year of capture and release
2) Acoustic telemetry receiver array
·      Position and depth of deployed acoustic receivers
3) Individual cod detection files
·      Time stamp and location (receiver) for each detection
·      Sensor values (depth) for each detection
4) Cod movement data
·      Summary of network analyses conducted on individual cod
5) Map data
·      Coastline coordinates needed for mapping fish movements.
Missing values are denoted by empty cells.

Description of the data and file structure

1. File List:
 
A) tel_cod.csv
B) stationinfo.csv
C) Vemco User Environment (VUE) csv-files
D) transmitters.csv
E) cod_network.csv
F) mfishnet.csv
G) Movement network csv-files for fish displayed on map
H) smola_kyst.gpkg
 
2. Relationship between files\, if important:
 
A) The transmitter serial number is provided in both the tel_cod file and the cod_network file, for linking movement data to fish body size data and
B) the transmitters file contain both the unique tag IDs and serial numbers, needed for linking VUE detection file summaries to the tel_cod file
C) The receiver serial number is provided in both the stationinfo file and the VUE detection files, needed for quantifying fish movements (connectivity).
 
These relationships are also explained in the R-scripts, showing how files are combined.
 
3. Additional related data collected that was not included in the current data package: None
 
4. Are there multiple versions of the dataset? No
            A. If yes, name of file(s) that was updated: NA
                        i. Why was the file updated? NA
                        ii. When was the file updated? NA
 
#########################################################################
 
DATA-SPECIFIC INFORMATION FOR: tel_cod.csv
 
1. Number of variables: 7
 
2. Number of cases/rows: 558
 
3. Variable List:
           
·      serial: acoustic tag serial number
·      length: fish total body length (mm)
·      weight: fish total weight (g)
·      sex: fish sex (F= female, M = male)
·      area: area of tagging (1 = Glasøysvaet, 2 = Lauvøysvaet, 3 = Araneset, 4 = Åkvika, 5 = Dromnessundet)
·      year: year of tagging
·      matst: maturity stage (1 = spawning, 0 = juvenile/resting)
 
4. Missing data codes: Empty cells
 
5. Specialized formats or other abbreviations used: None
 
#########################################################################
 
DATA-SPECIFIC INFORMATION FOR: stationinfo.csv
 
1. Number of variables: 7
 
2. Number of cases/rows: 37
 
3. Variable List:
 
·      st_no: station number
·      st_lat: latitude of station (decimal degrees)
·      st_lon: longitude of station (decimal degrees)
·      st_depth_m: depth at station (meters)
·      receiver: acoustic receiver deployed at station (serial number)
·      area_name: tagging area where the station is located
·      area_no: tagging area number
 
4. Missing data codes: None
 
5. Specialized formats or other abbreviations used: None
 
#########################################################################
 
DATA-SPECIFIC INFORMATION FOR: Vemco User Environment (VUE) csv-files
 
1. Number of variables: 10
 
2. Number of cases/rows: Usually several thousand\, but this will vary among individual files
 
3. Variable List:
 
·      DateandTime(UTC): Time stamp for a fish detection, showing UTC date and time
·      Receiver: serial number of receiver where the detection is logged
·      Transmitter: ID of transmitter being detected and stored at the receiver
·      TransmitterName: extended name of transmitter
·      TransmitterSerial: serial number of transmitter
·      Sensor value: Logged level of the depth sensor carried by the transmitter
·      SensorUnit: Unit of logged sensor value (ADC)
·      StationName: Name of site where the receiver was deployed
·      Latitude: Latitude where the receiver was deployed (decimal degrees)
·      Longitude: Longitude where the receiver was deployed (decimal degrees)
 
4. Missing data codes: Empty cells
 
5. Specialized formats or other abbreviations used: None
 
#########################################################################
 
DATA-SPECIFIC INFORMATION FOR: transmitters.csv
 
1. Number of variables: 17
 
2. Number of cases/rows: 2433
 
3. Variable List:
 
·      serial_no: transmitter serial number
·      tag_family: transmitter specifications (diameter, sensor type and battery)
·      VUE_tag_ID: transmitter ID as displayed in the detection data
·      tag_life_d: Expected battery life of transmitter (days)
·      power: tag transmission power (low or high)
·      acc_on_sec: transmission interval (sec) for tags having an accelerometer sensor
·      min_delay_sec: minimum interval between two transmissions (sec)
·      max_delay_sec: maximum interval between two transmissions (sec)
·      sensor: type of sensor carried by the tag
·      sensor_range: maximum value the sensor can register and transmit
·      sensor_unit: unit of tag sensor (depth = meters)
·      slope: slope parameter for calculating sensor value
·      intercept: intercept parameter for calculating sensor value
·      acc_algo: algorithm for accelerometer sensors
·      acc_sampl_sec: sampling interval for accelerometer sensors
·      trans_ratio: ratio between transmissions for tags having multiple sensor types
·      ship_date: date of shipping tags from producer
 
4. Missing data codes: Empty cells
 
5. Specialized formats or other abbreviations used: None
 
#########################################################################
 
DATA-SPECIFIC INFORMATION FOR: cod_network.csv
 
1. Number of variables: 9
 
2. Number of cases/rows: 547
 
3. Variable List:
 
·      serial: transmitter tag serial number
·      ddays: number of days with stored detections of transmitter
·      stations: number of stations with stored detections of transmitter
·      moves: number of registered movements between stations
·      mmovedur: mean duration of moves (sec)
·      areas: number of tagging areas with stored detections of transmitter
·      edges: number of unique routes (movements between stations) registered
·      keep: denoting whether the observations will be kept for statistical analyses or not (y/n)
·      comment: additional information determining whether the fish will be included in analyses
 
4. Missing data codes: Empty cells
 
5. Specialized formats or other abbreviations used: None
 
#########################################################################
 
DATA-SPECIFIC INFORMATION FOR: mfishnet.csv
 
1. Number of variables: 15
 
2. Number of cases/rows: 465
 
3. Variable List:
           
·      serial: transmitter tag serial number
·      ddays: number of days with stored detections of transmitter
·      moves: number of registered movements between stations
·      mmovedur: mean duration of moves (sec)
·      areas: number of tagging areas with stored detections of transmitter
·      edges: number of unique routes (movements between stations) registered
·      length: fish total body length (mm)
·      weight: fish total weight (g)
·      sex: fish sex (F= female, M = male)
·      area: area of tagging (1 = Glasøysvaet, 2 = Lauvøysvaet, 3 = Araneset, 4 = Åkvika, 5 = Dromnessundet)
·      year: year of tagging
·      daterel: date of fish handling
·      matst: maturity stage (1 = spawning, 0 = juvenile/resting)
·      RI: residency index (0-1)
·      lcm: fish total body length (cm)
 
4. Missing data codes: Empty cells
 
5. Specialized formats or other abbreviations used: None
 
#########################################################################
 
DATA-SPECIFIC INFORMATION FOR: Movement network csv-files
 
1. Number of variables: 8
 
2. Number of cases/rows: This will vary (1-18) depending on how each fish has moved.
 
3. Variable List:
·      from: site of departure (receiver station number)
·      to: site of arrival (receiver station number)
·      weight: total number of registered movements between two particular stations
·      from_degree: centrality of departure station
·      from_lat: latitude of departure station (decimal degrees)
·      from_lon: longitude of departure station (decimal degrees)
·      to_lat: latitude of arrival station (decimal degrees)
·      to_lon: longitude of arrival station (decimal degrees)
 
4. Missing data codes: Empty cells
 
5. Specialized formats or other abbreviations used: None
 
#########################################################################
 
DATA-SPECIFIC INFORMATION FOR: smola_kyst.gpkg
 
1. Number of variables: 1
 
2. Number of cases/rows: 1703
 
3. Variable List:
 

1. geom: a multipolygon of geographical coordinates

 
4. Missing data codes: None
 
5. Specialized formats or other abbreviations used: None
 
 

Sharing/Access information

This is a section for linking to other ways to access the data, and for linking to sources the data is derived from, if any.

Links to other publicly accessible locations of the data:
Data was derived from the following sources:

Code/Software

Data processing and analyses / making of figures were conducted using the R software. All R-scripts are provided here. They are numbered from 1-8 reflecting the various stages of processing, filtering and analysing the data. Each script has comment paragraphs that explain in more detail what the code does. The files uploaded in the scripts (also the names) are identical to the ones provided here.