Data and code from: River barriers as a driver of elevated mortality rates in an iteroparous anadromous fish
Data files
Feb 26, 2026 version files 102.74 KB
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Other_Tests.zip
9.34 KB
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README.md
9.62 KB
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Receivers.csv
3.38 KB
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Survival_Analysis.zip
65.30 KB
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Weir_Effects.zip
15.09 KB
Abstract
This dataset contains acoustic telemetry–derived survival and spatial mortality data for twaite shad (Alosa fallax) tracked over seven spawning migrations in the River Severn basin, UK. The data constitute the base for analyses described in "River barriers as a driver of elevated mortality rates in an iteroparous anadromous fish". The repository includes .csv data files and annotated R scripts required to reproduce all analyses. Files are organized into three analysis folders (“Survival_Analysis”, “Weir_Effects”, and “Other_Tests”), plus a receiver metadata file. The data include individual-level survival records (start/end times, censoring, and mortality events), biological variables (fork length, sex, spawning history, tagging status, return year), and spatial summaries of observed mortalities and time spent at acoustic receiver stations. Receiver stations are classified by position relative to weirs (downstream, upstream, unimpeded), and detection efficiencies (2018–2024) are provided. The dataset can be reused for survival analyses, spatial mortality assessments, and studies of migratory fish in fragmented river systems. The data contain no personal information and raise no privacy concerns.
Dataset DOI: 10.5061/dryad.stqjq2cgf
The analyses for the accompanying paper can be run in three R scripts. These are in a zip folder each, and the folders are named after the respective analysis they address. The zip folders each include the respective R script as well as the data files required to run the analysis in that R script. The .csv data files required for the analysis can be loaded into the R environment from the same folder. The R scripts will automatically load the data from the .csv files included in the same directory:
Other_Tests.zip
Survival_Analysis.zip
Weir_Effects.zip
This supplementary data repository further includes information of the receivers and their efficiencies:
Receivers.csv
Other Tests
This folder includes code and data to recreate analyses for:
- Assessing effects of Length, Sex, and Spawning History on where shade die (receiver station type)
- Assessing effects of the spatial predictors "catchment penetration" and "river characteristic" on where shad die
Included files are:
Other Tests.R - R code to recreate analyses
dead_shad_info.csv - Data on shad that died with one row per shad. NAs in any columns are data that was not collected or could not be determined with certainty.
- InYear - Year after tagging (Y0 = tagging year, Y1 = first return year, Y2 = second return year)
- Year - Calendar year for data included in the row
- Length_mm - Measured length at tagging (Fork Length, mm)
- Type - Type of receiver station where the shad was last recorded (US Weir, DS Weir, Unimpeded)
- s_mark - Presence (1) or absence (0) of marks of previous spawning on scales
- Sex - Sex (f/m) for individuals where gonads became visible during tagging
newly_tagged_spatial_info.csv - Data on the number of observed mortalities and the time spent at individual receiver stations in individual years for the newly tagged shad.
- Station.name - Name of receiver station
- Observed - Number of mortalities associated with the receiver station
- hours - Hours spent associated with the receiver station by the population of newly tagged shad
- hours_scale - hours, scaled
- Stonebench - Distance to the Stonebench receiver that marks the transition to the estuary
- Stonebench_scale - Stonebench, scaled
- year - Calendar year for data included in the row
returners_spatial_info.csv - Data on the number of observed mortalities and the time spent at individual receiver stations in individual years for the returning shad. Column descriptions are identical to newly_tagged_spatial_info.csv.
Survival Analysis
This folder includes code and data to recreate analyses for:
- Assessing effects of biotic variables length, spawning history (previous vs. virgin), and sex on survival
- Assessing differences in survival between newly tagged vs. returning shad
- Assessing variations of survival within and between years
Included files are:
Survival.R - R code to recreate analyses
ReturnYears.csv - Data on the survival of returning shad (Y1 and Y2).
- Year - Calendar year for data included in the row
- InYear - Year after tagging (Y0 = tagging year, Y1 = first return year, Y2 = second return year)
- ID - Unique ID of the shad
- Start - Timestamp of start of a freshwater presence period
- End - Timestamp of end of a freshwater presence period
- Event - Event at the end of a freshwater presence period (0 = censoring, 1 = death)
- Start_time - Relative (at individual level) time (days) of start of a freshwater presence period
- End_time - Relative (at individual level) time (days) of end of a freshwater presence period
- Start_day1 - Integer ceiling (full days) of Start_time
- End_day1 - Integer ceiling (full days) of End_time
TaggingYear.csv - Data on the survival of newly tagged shad (Y0).
- Year - Calendar year for data included in the row
- InYear - Year after tagging (Y0 = tagging year, Y1 = first return year, Y2 = second return year)
- ID - Unique ID of the shad
- Start - Timestamp of start of a freshwater presence period
- End - Timestamp of end of a freshwater presence period
- Event - Event at the end of a freshwater presence period (0 = censoring, 1 = death)
- Start_time - Relative (at individual level) time (days) of start of a freshwater presence period
- End_time - Relative (at individual level) time (days) of end of a freshwater presence period
- Start_day1 - Integer ceiling (full days) of Start_time
- End_day1 - Integer ceiling (full days) of End_time
Sex.csv - Data on the survival of newly tagged shad (Y0) included in analysis assessing for effects of length and sex.
- Year - Calendar year for data included in the row
- InYear - Year after tagging (Y0 = tagging year, Y1 = first return year, Y2 = second return year)
- ID - Unique ID of the shad
- Start - Timestamp of start of a freshwater presence period
- End - Timestamp of end of a freshwater presence period
- Event - Event at the end of a freshwater presence period (0 = censoring, 1 = death)
- Start_time - Relative (at individual level) time (days) of start of a freshwater presence period
- End_time - Relative (at individual level) time (days) of end of a freshwater presence period
- Start_day1 - Integer ceiling (full days) of Start_time
- End_day1 - Integer ceiling (full days) of End_time
- sex - Sex (f/m) for individuals where gonads became visible during tagging
- length_mm - Measured length at tagging (Fork Length, mm)
SpawningHistory.csv - Data on the survival of newly tagged shad (Y0) included in analysis assessing for effects of length and spawning history.
- Year - Calendar year for data included in the row
- InYear - Year after tagging (Y0 = tagging year, Y1 = first return year, Y2 = second return year)
- ID - Unique ID of the shad
- Start - Timestamp of start of a freshwater presence period
- End - Timestamp of end of a freshwater presence period
- Event - Event at the end of a freshwater presence period (0 = censoring, 1 = death)
- Start_time - Relative (at individual level) time (days) of start of a freshwater presence period
- End_time - Relative (at individual level) time (days) of end of a freshwater presence period
- Start_day1 - Integer ceiling (full days) of Start_time
- End_day1 - Integer ceiling (full days) of End_time
- s_mark - Presence (1) or absence (0) of marks of previous spawning on scales
- length_mm - Measured length at tagging (Fork Length, mm)
- Spawn - Factorization of s_mark
TaggingStatus.csv - Data on the survival of newly tagged shad (Y0) vs. returning shad.
- Year - Calendar year for data included in the row
- InYear - Year after tagging (Y0 = tagging year, Y1 = first return year, Y2 = second return year)
- ID - Unique ID of the shad
- Start - Timestamp of start of a freshwater presence period
- End - Timestamp of end of a freshwater presence period
- Event - Event at the end of a freshwater presence period (0 = censoring, 1 = death)
- Start_time - Relative (at individual level) time (days) of start of a freshwater presence period
- End_time - Relative (at individual level) time (days) of end of a freshwater presence period
- Start_day1 - Integer ceiling (full days) of Start_time
- End_day1 - Integer ceiling (full days) of End_time
- Status - Factorization of InYear as Newly Tagged (Y0) and Returning (Y1 and Y2)
Weir Effects
This folder includes code and data to recreate analyses for:
- Assessing effects of location in relation to weirs (DS Weir, US Weir, Unimpeded) on mortality rates
- Creating a plot of excess mortality to identify mortality rate hotspots
Included files are:
Weir Effects.R - R code to recreate analyses
newly_tagged.csv - Data on observed mortalities and time spent at different receiver stations for newly tagged shad.
- Station.name - Name of receiver Station
- Observed - Number of observed shad mortalities
- hours - hours spent at the receiver station by the shad population
- hours_scale - hours scaled
- Type - Classification of receiver station: DS Weir, US Weir, Unimpeded
- year - Calendar year of data point
returners.csv - Data on observed mortalities and time spent at different receiver stations for returning shad.
- Station.name - Name of receiver Station
- Observed - Number of observed shad mortalities
- hours - hours spent at the receiver station by the shad population
- hours_scale - hours scaled
- Type - Classification of receiver station: DS Weir, US Weir, Unimpeded
- year - Calendar year of data point
newly_tagged_mapping.csv - Data required to recreate figure of excess mortality for newly tagged shad. NAs in any columns are data that was not collected or could not be determined with certainty.
newly_tagged_mapping.csv - Data required to recreate figure of excess mortality for returning shad. NAs in any columns are data that was not collected or could not be determined with certainty.
Receivers.csv
Metadata on Receiver Stations.
- Station - Name of receiver station
- Category - Category of position in relation to weirs
- River - River on which the receiver station was located
- Estuary Distance - Distance to the estuary [km]
- 2018 - Detection efficiency for 2018
- 2019 - Detection efficiency for 2019
- 2020 - Detection efficiency for 2020
- 2021 - Detection efficiency for 2021
- 2022 - Detection efficiency for 2022
- 2023 - Detection efficiency for 2023
- 2024 - Detection efficiency for 2024