Data from: A new acoustic telemetry tag that identifies carrier mortality by monitoring activity level
Data files
Mar 24, 2026 version files 10.83 MB
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01_make_rawMortSensor_dataAndPlots_2026-03-23.R
5.77 KB
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02_ggplot_and_cowplot_mapsWithRawSensor_2026-03-23.R
28.37 KB
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DataForSubmission_01_detsOfFish_2026-03-23.rds
268.37 KB
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DataForSubmission_02_mortSensorData_forMapInsets_2026-03-23.rds
437.93 KB
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DataForSubmission_03_fishTracks_2026-03-23.rds
10.08 MB
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DataForSubmission_04_biologicalTable_2026-03-23.rds
1.12 KB
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README.md
5.29 KB
Abstract
Current acoustic telemetry technology relies on complex data modelling, interpretation of environmental sensor data, or the occurrence of a predation event to determine the death of a studied individual. We present a new acoustic telemetry tag capable of detecting whether its carrier stops moving for long enough to presume the organism has died, and of reporting the time elapsed since movement ceased. This tag was designed to increase the power of acoustic telemetry for investigating population dynamics and ecological threat processes in aquatic ecosystems by making it easier to establish when, where, and how the animals of interest die. We present a field test of these tags conducted in a freshwater lake in New Brunswick, Canada, using a combination of fixed-position tags together with tags implanted into two species of salmonid fish. We demonstrate that the new tag achieves its main objective of indicating mortality events, but that the programming of the inactivity sensor needs careful consideration for species that are routinely inactive for extended periods. The tag will be a valuable addition to the acoustic telemetry toolbox, and we describe example applications for its use in studying the survival of migratory salmonids. --
All RDS files in the dataset were created with R v4.5.2. Some older versions of R may not be able to open them, but, based on R's track record, forward compatibility is likely strong. All RDS files in the dataset include objects of R's 'data table' class, and require the package 'data.table' to be loaded prior to importing. The scripts also require the following R packages: ggplot2, cowplot, stringr
File '01_make_rawMortSensor_dataAndPlots_2026-03-23.R'
R script that processes, formats, and plots 'raw sensor' data from the new mortality-sensing tags. Part of this processing is to prepare the data for the next script, and part of it is to visualise how the two focal species differ in implied activity.
File '02_ggplot_and_cowplot_mapsWithRawSensor_2026-03-23.R'
R script that produces the fish movement figures in the main document and the supplementary material
File 'DataForSubmission_01_detsOfFish_2026-03-23.r ds'
When read into R, the data is an R list object of 20 data tables, one for each fish in the dataset. List entries are named with the tags of their respective fish. This data is necessary for running script '01_make_rawMortSensor_dataAndPlots_2026-03-23.R'.
Each datatable has 5 columns, and each row is one detected tag transmission:
- DT.char = date-time of ping (UTC, rounded to seconds, presented as character variable)
- TagID = full unique tag ID (one value per table, as each table is one tag)
- SensorVal = 'raw [sensor] data' transmitted by the tag. Pasting from the legend of Table S1: "As with all Innovasea/Vemco pulse position modulation ('PPM') tags, sensor 'raw data' (the term used in data offloaded from Innovasea receivers) is transmitted as an 8-bit number, i.e, an integer in the range 0-255."
- TagStatus = sensor value converted into biological information, indicating the tag's assessment of the current status of the fish
- DaysSinceTrig = if the tag has been triggered into 'Cold-Blooded Digestion, 'Warm-Blooded Digestion,' or 'Mortality by Inactivity' mode, this column reports elapsed time in days since triggering.
File 'DataForSubmission_02_mortSensorData_forMapInsets_2026-03-23.rds'
Very similar to 'DataForSubmission_01_detsOfFish_2026-03-23.rds', but modified by
and saved by script '01_make_rawMortSensor_dataAndPlots_2026-03-23.R'.
Relative to 'DataForSubmission_01...', this table has a POSIXct version of date-time, and a column of logical data indicating whether the tag is reporting the carrier as 'alive' (TRUE) or 'dead' (FALSE)
Note that the date suffix in the RDS file was added to the filename by R's Sys.Date() function, and rerunning that script will result in the creation of a file with the current day's date.
File 'DataForSubmission_03_fishTracks_2026-03-23.rds'
This is the bread and butter data - the data needed to plot the fish tracks in both the main document AND the supplementary material. File is used by script '02_ggplot_and_cowplot_mapsWithRawSensor_2026-03-23.R'. When read into R, it is a 2-element R list. The first element ('recs') is a data table of receiver coordinates. The second element ('fishTracks') is another list - 20 data tables of coordinates, with one data table for each fish.
List element 'recs': 7-column datatable, giving the coordinates (lat and long), depths, and deployment/retrieval dates for receivers used in the study.
List element 'fishTracks': 20 6-column datatables, with one table per tagged fish. Each row is one ping of positional data. Each row gives the coordinates, date-time, and tag status (active, mortality, etc.). The column 'ColBlock' is used by the plotting functions in '02_ggplot_and_cowplot_mapsWithRawSensor_2026-03-23.R'.
File 'DataForSubmission_04_biologicalTable_2026-03-23.rds'
Biological information on each fish in the dataset, used by script '02_ggplot_and_cowplot_mapsWithRawSensor_2026-03-02.R'. When read into R, it is a data table straight away, i.e., it is not a list of data tables. Most of the information is presented in Table 1 of the main document and Table S2 of the supplementary material.
Columns:
- TagID = unique tag code of focal fish
- Species = 'AS' for Atlantic salmon, and 'LT' for lake trout
- DateTagged = date on which the focal fish was tagged
- LastDet = date of final detection of the tag
- NDetDays = number of days with at least one detection of the tag on the array
- NRecs = number of receivers on which the tag was detected in the course of the study
- InactvScore.num = leftover from an older version of the manuscript. Higher values mean that a tag entered Inactivity Latching mode more frequently
- InactvScore.char = character version of InactvScore.num, rounded to 2 dp, from when the variable was included in the annotation of older plots
- FinalStatus = sensor report (active, mortality, digested, etc.) from final detection
- TrackInference = track-based inference, from visual inspection, of the tagged fish's fate
- Verdict = manual assessment of whether sensor-reported status and track-based inference reconcile
- DatID = variable used in the plotting functions
- PlotFate = variable used in the plotting functions
- ForkLength = fork length of the focal fish, in mm