DOI: 10.5061/dryad.stqjq2cgf
title: Data and code from: River barriers as a driver of elevated mortality rates in an iteroparous anadromous fish

description: 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.
description: # Data and code from: River barriers as a driver of elevated mortality
 rates in an iteroparous anadromous fish 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