The associated cleaned data files are:
Tags.csv – cleaned tagging metadata, including study year, species, acoustic transmitter identifiers, physical fish identifiers, release location, release date/time and release coordinates. Multiple transmitter IDs may be associated with the same physical fish, with tag_serial_number used to link those transmitter records back to the individual fish.
Detections_Study_Array.csv – cleaned acoustic detections recorded on the Aberdeen Bay study receiver array, including fish/tag identifiers, species, receiver/station information, detection date/time and receiver coordinates.
Physical_Fish_Detection_Status.csv – fish-level summary indicating whether each tagged physical fish was subsequently detected after release.
Study_Array_Detection_Rates_By_Species.csv – year- and species-level summaries of fish deployed, fish subsequently detected and associated detection rates.
Study_Array_Summary_By_Species.csv – additional year- and species-level summary statistics for detections within the study array.
Study_Receiver_Locations.csv – receiver metadata and summarised receiver activity, including receiver IDs, station names, coordinates, first and last detections, detection counts and numbers of physical fish detected.
External_Receiver_Detections_Validated.csv – validated detections of study fish recorded on receivers outside the main Aberdeen Bay study array, including receiver/station information, date/time and geographic coordinates.
External_Receiver_Validated_Summary.csv – summary information derived from the validated external receiver detections.
Sensor_Data_Calibrated.xlsx – cleaned sensor datasets used to explore fish depth, temperature and potential predation events. The workbook includes calibrated temperature/depth observations, fish-level predation information and predation summaries.
The Shiny application derives additional working datasets from these files, including physical-fish metadata, consolidated receiver coordinates, receiver visits, movement segments and individual fish routes. These derived objects are used to visualise movement between receivers while retaining the distinction between individual acoustic transmitters and physical fish.
]]>Cleaned tagging metadata for fish included in the Aberdeen Bay acoustic telemetry study.
Each row represents an acoustic transmitter record. A physical fish may be associated
with more than one transmitter record, particularly for some 2017 sensor tags.
tag_serial_number is used to link transmitter records that belong to the same physical fish.
COLUMNS
year
Study year associated with tagging and release.
full_tag_id
Cleaned transmitter identifier constructed from tag_code_space and tag_id_code where
both are available. The format is "-". If code space is
missing, tag_id_code alone is retained. Therefore, this field is not guaranteed to
contain a code space for every record.
tag_serial_number
Identifier for the physical tag/fish unit. Used to group multiple acoustic transmitter
records that belong to the same physical fish.
tag_code_space
Acoustic transmitter code space, where supplied.
tag_id_code
Numeric/tag ID component of the transmitter identifier.
tag_type
Tag type recorded in the source tagging metadata.
tag_manufacturer
Manufacturer of the transmitter.
tag_model
Transmitter model.
species_common
Standardised common name of the tagged fish species.
species_scientific
Scientific name of the tagged fish species.
life_stage
Life stage recorded for the tagged fish.
wild_or_hatchery
Wild/hatchery status of the fish. "W" indicates a wild fish.
stock
River of origin for the tagged fish, for example the River Dee or River Don.
capture_location
Capture-location description from the source tagging metadata.
capture_latitude
Capture latitude in decimal degrees.
capture_longitude
Capture longitude in decimal degrees.
release_location
Release-location description.
release_latitude
Release latitude in decimal degrees.
release_longitude
Release longitude in decimal degrees.
release_datetime
Release date and time, parsed as UTC by the cleaning workflow.
length_m
Fish length in metres. For 2018, the source length and weight columns were known to be
reversed and were intentionally swapped during cleaning.
weight_kg
Fish weight in kilograms. For 2018, the source length and weight columns were known to
be reversed and were intentionally swapped during cleaning.
NOTES
Missing information is represented by blank/NA values as appropriate.
full_tag_id identifies an acoustic transmitter record, while tag_serial_number is the
physical fish/tag grouping identifier used where multiple transmitter IDs belong to the
same fish.
COLUMNS
year
Study year associated with the tagged fish/detection.
detection_category
Detection category carried from the upstream filtered source (for example,
"Probable"). The build workflow uses the supplied filtered categories rather than
recreating their original classification rules.
input_source
Source input file from which the cleaned detection originated.
full_tag_id
Acoustic transmitter identifier associated with the study tag metadata.
detection_full_tag_id
Full acoustic transmitter identifier recorded in the detection data.
tag_serial_number
Identifier for the physical tag/fish unit.
tag_match_method
Method used to match the detected transmitter to the study tag metadata. "Exact full
tag ID" indicates a match on study year plus the complete transmitter identifier.
"Numeric fallback" indicates that no exact full-ID match was found and the final
numeric component of the detected transmitter ID was matched to a unique study-tag
numeric ID within the same year.
organism_id
Identifier associated with the tagged organism/fish.
species_common
Standardised common name of the tagged fish species.
species_scientific
Scientific name of the tagged fish species.
station
Receiver station name.
receiver_id
Identifier of the acoustic receiver.
receiver_latitude
Receiver latitude in decimal degrees.
receiver_longitude
Receiver longitude in decimal degrees.
bottom_depth_m
Water/bottom depth at the receiver location in metres, where available.
receiver_depth_m
Depth of the deployed receiver in metres, where available.
detection_datetime
Cleaned/corrected date and time of detection.
uncorrected_detection_datetime
Original detection date and time before any applied time correction.
sensor_name
Sensor name associated with the transmitter/detection, where available.
sensor_type
Sensor or transmitter type associated with the detection.
sensor_raw
Raw sensor value recorded with the detection, where available.
sensor_value
Processed sensor value, where available.
sensor_unit
Unit associated with the processed sensor value, where available.
distance_km
Distance in kilometres.
distance_category
Classification describing how likely a detection is to be genuine, based on detection
rate and biological probability.
step_distance_km
Distance travelled between sequential detections, in kilometres.
time_difference
Time difference between sequential detections.
speed_kmh
Calculated movement speed in kilometres per hour, using detection dates and times
between receivers.
impossible_jump
Flag identifying detections between receivers that are not considered biologically
possible based on the calculated speed and time difference.
detection_id
Identifier for the individual detection record.
original_source_file
Original source file from which the detection record was derived.
NOTES
This file contains detections retained for the Aberdeen Bay study array after the relevant
cleaning and filtering steps. Some sensor-related fields are only populated for
sensor-enabled tags.
COLUMNS
year
Study year.
species_common
Standardised common name of the fish species.
tag_serial_number
Identifier for the physical tag/fish unit.
just_released_data_available
TRUE when the study year is represented in the cleaned "Just Released" detection
dataset; FALSE otherwise. No reconstructed "Just Released" dataset is available for
2019.
detected_just_after_release
TRUE when at least one detection exists for the fish in the cleaned "Just Released"
category; FALSE when that category is available for the year but no such detection
exists; NA where "Just Released" data are not available for that year.
subsequently_detected_probable
TRUE when at least one qualifying "Probable" detection record is present for the fish;
FALSE otherwise.
first_probable_detection
Date and time of the first qualifying "Probable" detection, where present.
last_probable_detection
Date and time of the last qualifying "Probable" detection, where present.
probable_detection_records
Number of qualifying "Probable" detection records for the fish.
probable_stations_visited
Number of distinct stations represented by qualifying "Probable" detections.
probable_receivers_visited
Number of distinct receivers represented by qualifying "Probable" detections.
NOTES
The exact upstream time window/rule used to create the original "Just Released" detection
category is not defined in the dashboard build scripts available here. It should be
confirmed from the original filtering methodology before stating a specific post-release
time window in the DOI documentation.
A lack of subsequent "Probable" detections is not interpreted as mortality.
]]>COLUMNS
year
Study year.
species_common
Standardised common name of the fish species.
fish_deployed
Number of physical fish deployed.
fish_subsequently_detected
Number of deployed physical fish with one or more qualifying subsequent detections.
fish_not_subsequently_detected
Number of deployed physical fish without a qualifying subsequent detection.
subsequent_detection_rate
Percentage of deployed fish that were subsequently detected.
NOTES
The detection rate is expressed as a percentage rather than a proportion.
COLUMNS
year
Study year.
species_common
Standardised common name of the fish species.
detection_records
Number of detection records.
transmitter_ids
Number of distinct acoustic transmitter IDs represented in the detections.
physical_fish
Number of distinct physical fish represented in the detections.
receivers
Number of distinct receivers recording detections.
NOTES
The number of transmitter IDs can be greater than the number of physical fish because a
single physical fish may be associated with more than one acoustic transmitter ID.
COLUMNS
receiver_station_key
Composite key identifying a receiver/station combination within a study year.
receiver_year_key
Composite key identifying a receiver within a study year.
year
Study year.
receiver_id
Identifier of the acoustic receiver.
station
Receiver station name.
receiver_latitude
Receiver latitude in decimal degrees.
receiver_longitude
Receiver longitude in decimal degrees.
bottom_depth_m
Water/bottom depth at the receiver location in metres, where available.
receiver_depth_m
Deployment depth of the receiver in metres, where available.
first_detection
Date and time of the first retained study detection recorded for the receiver/year.
last_detection
Date and time of the last retained study detection recorded for the receiver/year.
detection_records
Number of retained detection records associated with the receiver/year.
detected_tags
Number of distinct acoustic transmitter IDs detected by the receiver/year.
physical_fish
Number of distinct physical fish detected by the receiver/year.
NOTES
A receiver may appear in more than one year. Composite key fields are included to
distinguish receiver records across years and stations.
COLUMNS
year
Study year associated with the tagged fish/detection.
detection_category
Detection category carried from the upstream filtered source (for example,
"Probable"). The build workflow uses the supplied filtered categories rather than
recreating their original classification rules.
input_source
Source input file from which the cleaned detection originated.
full_tag_id
Acoustic transmitter identifier associated with the study tag metadata.
detection_full_tag_id
Full acoustic transmitter identifier recorded in the detection data.
tag_serial_number
Identifier for the physical tag/fish unit.
tag_match_method
Method used to match the detected transmitter to study tag metadata.
organism_id
Identifier associated with the tagged organism/fish.
species_common
Standardised common name of the tagged fish species.
species_scientific
Scientific name of the tagged fish species.
station
External receiver station name.
receiver_id
Identifier of the external acoustic receiver.
receiver_latitude
Receiver latitude in decimal degrees.
receiver_longitude
Receiver longitude in decimal degrees.
bottom_depth_m
Water/bottom depth at the receiver location in metres, where available.
receiver_depth_m
Depth of the deployed receiver in metres, where available.
detection_datetime
Cleaned/corrected date and time of detection.
uncorrected_detection_datetime
Original detection date and time before any applied time correction.
sensor_name
Sensor name associated with the transmitter/detection, where available.
sensor_type
Sensor or transmitter type associated with the detection.
sensor_raw
Raw sensor value recorded with the detection, where available.
sensor_value
Processed sensor value, where available.
sensor_unit
Unit associated with the processed sensor value, where available.
distance_km
Distance in kilometres.
distance_category
Classification describing how likely a detection is to be genuine, based on detection
rate and biological probability.
step_distance_km
Distance travelled between sequential detections, in kilometres.
time_difference
Time difference between sequential detections.
speed_kmh
Calculated movement speed in kilometres per hour, using detection dates and times
between receivers.
impossible_jump
Flag identifying detections between receivers that are not considered biologically
possible based on the calculated speed and time difference.
detection_id
Identifier for the individual detection record.
original_source_file
Original source file from which the detection record was derived.
NOTES
These records are detections outside the primary Aberdeen Bay study array that were
retained following validation. External receiver locations may therefore be geographically
distant from Aberdeen Bay.
COLUMNS
year
Study year.
detection_records
Number of validated external detection records.
transmitter_ids
Number of distinct acoustic transmitter IDs represented.
physical_fish
Number of distinct physical fish represented.
receivers
Number of distinct external receivers recording validated detections.
stations
Number of distinct external receiver stations recording validated detections.
NOTES
This is an aggregated summary of External_Receiver_Detections_Validated.csv.
Excel workbook containing cleaned and calibrated sensor data and derived predation
summaries for sensor-tagged fish. The dashboard directly uses three worksheets:
'Temperature Depth Data', 'Predation by Fish', and 'Predation Summary'.
========================================================================
WORKSHEET: Temperature Depth Data
Cleaned temperature and depth sensor observations associated with tagged fish.
year
Study year.
species_common
Standardised common name of the fish species.
serial_number
Identifier for the physical tag/fish unit in the sensor dataset.
datetime
Date and time of the sensor observation/detection.
receiver_project
Receiver project/array associated with the observation.
receiver
Receiver identifier/name.
transmitter
Acoustic transmitter identifier associated with the sensor observation.
sensor_system
Sensor/tag system from which the measurement originated.
measurement
Sensor measurement type. Values used by the dashboard are Depth and Temperature.
sensor_value
Raw numeric sensor value.
calibrated_value
Sensor value after calibration to the relevant physical unit.
calibrated_units
Unit of calibrated_value; observed units are metres (m) for depth and degrees Celsius
(°C) for temperature.
suspected_predation
"Yes"/"No" flag used for the known 2018 suspected temperature-predation example.
Fish serial number 1282372 is flagged "Yes" in 2018 because its temperature record
reached approximately 36.4 °C and had previously been interpreted as consistent with
ingestion by a warm-blooded predator. The event is treated as suspected rather than
confirmed predation.
========================================================================
WORKSHEET: Predation by Fish
Fish-level classification for fish fitted with digestion/predation sensor tags.
year
Study year.
serial_number
Identifier for the physical tag/fish unit.
species_common
Standardised common name of the fish species.
transmitter
Acoustic transmitter identifier.
predation_status
Fish-level predation classification. "Predated" is assigned when at least one
digestion-sensor value is between 4 and 255 inclusive. Fish with no value in this range
are classified as "Not Predated". This rule applies to digestion/predation tags.
========================================================================
WORKSHEET: Predation Summary
Aggregated counts of fish by year, species and predation classification.
year
Study year.
species_common
Standardised common name of the fish species.
predation_status
Predation classification derived using the rule described above.
number_of_fish
Number of fish in the corresponding year/species/predation-status group.
The workbook contains additional worksheets used during sensor-data processing and quality
assurance. These are not directly read by the current Shiny dashboard and are therefore
not described in this README.