Eel data (Anguilla anguilla) and associated environment variables for eel in the SUDOE area (SUDOANG project)

1. DESCRIPTION

1.1. THE SUDOANG PROJECT

The SUDOANG project aims at providing common tools to managers to support eel conservation in the SUDOE area (Spain, France and Portugal). 

Three main datasets have been used to implement EDA.

• A database of rivers and their attributes along with tools for chaining
• A database of dams.
• A database of electrofishing (current dataset)

Electrofishing data include site locations, fishing operations which can be done several times at one site, and fish data collected during each operation. The operations are attached to stretches of river or river segments whose characteristics describe the conditions for presence, density, size structure, or silvering rate of the eels. 

The electrofishing operation are classified by type:

• com full two pass fishing
• coa full two pass electrofishing for eel
• iaa eel abundance point sampling
• ber bank sampling
• gm point fishing for large streams
• oth other, or unspecified.

1.2. TEMPORAL SCOPE 

From 1985 to 2018, beware incomplete dataset after 2015 in France.

1.3. GEOGRAPHICAL RANGE

The SUDOE area including Iberian Peninsula and France.

2. DATASETS DESCRIPTION

2.1. DENSITIES AND PRESENCE ABSENCE

Dataset: frsppt_12_2020.Rdata

Most variables are built here. 

The script to create cumulated values for dams can be found here.

For a technical description see the report.

This file contains the following datasets:

• ddd => dataset used to calibrate the presence absence model, 46147 lines
• ddg => dataset used to calibrate the gamma model (only positive values retained), 19993 lines.
• tdd => dataset corresponding to places where transport operation have been identified, presence absence model, 6582 lines.
• tdg => dataset corresponding to places where transport operation have been identified, gamma model (only positive values) 984 lines.

And the following columns (in alphabetical order):

• altitudem: Altitude in meter truncated to 800 m
• area_sudo: Area for recruitment (Drouineau et al., 2021)
• codesea: Code of the Sea, factor A = Atlantic, M = Mediterranean
• country: A factor (FR, SP, PT) for France, Spain and Portugal
• country2: Country with grouping for the Iberian Peninsula (SPPT). Other level is France (FR)
• cs_height_08_n: Cumulated height from the sea, dam height transformed with power 0.8, no prediction for missing values
• cs_height_08_n: Same variable but truncated to 300
• cs_height_08_p: Cumulated height from the sea, dam height transformed with power 0.8, with prediction for missing values
• cs_height_08_p: Same variable but truncated to 300
• cs_height_08_pp: Cumulated height from the sea,  dam height transformed with power 0.8, with prediction for missing values, the height of dam is set to zero if equiped with an efficient fishway for eel
• cs_height_08_pps: Cumulated height from the sea,  dam height transformed with power 0.8, with prediction for missing values, the height of dam is set to zero if a score of efficient passage was attributed for eel on this structure
• cs_height_10_FR: Cumulated height from the sea, no transformation, no prediction for missing values, only the dams from France are considered when building on a transnational water course
• cs_height_10_n: Cumulated height from the sea, no transformation, no prediction for missing values
• cs_height_10_n: Same variable but truncated to 200
• cs_height_10_p: Cumulated height from the sea, no transformation, missing height are extrapolated from two different models in France and the Iberian Peninsula
• cs_height_10_p: Same variable but truncated to 200
• cs_height_10_pass0: Cumulated height from the sea, no transformation, no prediction for missing values, only the dams without pass are used to build the cumulated value
• cs_height_10_pass1: Cumulated height from the sea, no transformation, no prediction for missing values, only the dams with pass are used to build the cumulated value
• cs_height_10_pp: Cumulated height from the sea, no transformation, with prediction for missing values, the height of dam is set to zero if equiped with an efficient fishway for eel
• cs_height_10_ppass0: Cumulated height from the sea, no transformation, including prediction for missing values, only the dams without pass are used to build the cumulated value
• cs_height_10_ppass1: Cumulated height from the sea, no transformation, including prediction for missing values, only the dams with pass are used to build the cumulated value
• cs_height_10_pps: Cumulated height from the sea, no transformation, with prediction for missing values, the height of dam is set to zero if a score of efficient passage was attributed for eel on this structure
• cs_height_10_pscore0: Cumulated height from the sea, no transformation, including prediction for missing values, only the dams without score are used to build the cumulated value
• cs_height_10_pscore1: Cumulated height from the sea, no transformation, including prediction for missing values, only the dams with score (that have been expertised as no or small barrier for eel)  are used to build the cumulated value
• cs_height_10_PT: Cumulated height from the sea, no transformation, no prediction for missing values, only the dams from Portugal are considered when building on a transnational water course
• cs_height_10_score0: Cumulated height from the sea, no transformation, no prediction for missing values, only the dams without score are used to build the cumulated value
• cs_height_10_score1: Cumulated height from the sea, no transformation, no prediction for missing values, only the dams with score (that have been expertised as no or small barrier for eel)  are used to build the cumulated value
• cs_height_10_SP: Cumulated height from the sea, no transformation, no prediction for missing values, only the dams from Spain are considered when building on a transnational water course.
• cs_height_12_n: Cumulated height from the sea,  dam height transformed with power 1.2, no prediction for missing values.
• cs_height_12_n.: Same variable but truncated to 500
• cs_height_12_p: Cumulated height from the sea,  dam height transformed with power 1.2, with prediction for missing values.
• cs_height_12_p.: Same variable but truncated to 500
• cs_height_12_pp: Cumulated height from the sea,  dam height transformed with power 1.2, with prediction for missing values, the height of dam is set to zero if equiped with an efficient fishway for eel
• cs_height_12_pps: Cumulated height from the sea,  dam height transformed with power 1.2, with prediction for missing values, the height of dam is set to zero if a score of efficient passage was attributed for eel on this structure
• cs_height_15_n: Cumulated height from the sea,  dam height transformed with power 1.5, no prediction for missing values
• cs_height_15_n.: Same variable but truncated to 800
• cs_height_15_p: Cumulated height from the sea,  dam height transformed with power 1.5, with prediction for missing values
• cs_height_15_p.: Same variable but truncated to 800
• cs_height_15_pp: Cumulated height from the sea, dam height transformed with power 1.5, with prediction for missing values, the height of dam is set to zero if equiped with an efficient fishway for eel
• cs_height_15_pps: Cumulated height from the sea,  dam height transformed with power 1.5, with prediction for missing values, the height of dam is set to zero if a score of efficient passage was attributed for eel on this structure
• cumnbdamp: Cumulated number of dam from the sea
• cumnbdamso: duplicate of cumnbdamp
• cumwettedsurfacebothkm2.: Surface of water downstream from the segment in the river. Corresponds to both riversegment and waterbodies
• cumwettedsurfacekm2.: Surface of water downstream from the segment in the river. Corresponds only to rivers
• cumwettedsurfaceotherkm2.: Surface of water downstream from the segment in the river. Corresponds only waterbodies (water surfaces, associated with the segment).
• densCS: Density from Carle and Strub, number in second pass extrapolated from efficiency if only one pass
• dist_from_gibraltar_km: Distance to Gibraltar calculated using an enveloppe along the coastline (e.g. the estuaries ingress inland are not counted for this distance).
• distanceseakm: Distance to the sea
• distanceseakm.: Distance to the sea, truncated at 500
• distancesourcem: distance to the source in meters
• downstdrainagewettedsurfaceboth.: Percentage of wetted surface downstream for both rivers and associated waterbodies (cumwettedsurfacebothkm2) divided by land surface for all segments within the basin located at a same or lesser distance to the sea.
• downstreamwettedsurface: Percentage of wetted surface downstream (cumwettedsurfacekm2) divided by land surface for all segments within the basin located at a same or lesser distance to the sea
• drainage_density_perm.: River length / surface of basin in the basin downstream (m-1)  Numeric, multiplied by $10^4$, truncated to 20
• ef_fishingmethod: Fishing method. See details in text and Briand et al., (2022)
• ef_wetted_area: Surface of the electrofishing station
• emu: Eel management unit. See Git WGEEL
• hydraulicdensityperm2.: Number of riversegments per surface of basin (m-2). Numeric Multiplied by 10^6, truncated to 1.5
• idsegment: Unique identifier of the segment TEXT
• laltitudem.: Log transformed value of altitude (truncated)
• lcs_height_10_n.: Log transformed value of cumulated height
• lddws: Log transformed value of downstdrainagewettedsurfaceboth
• ldownstreamwettedsurface: Log of previous column
• lriverwidthm.: Log transformed value of river width
• month: Month
• NCS: Number of eels estimated by Carle and Strub
• ob_id: Operation (observation) identifier
• op_id: Station (observation place) identifier
• riverwidthm: Width of the river in m (comes from various sources: see Atlas and Briand et al., 2022).
• seaidsegment: Identifier of the sea idsegment
• temperature: Average temperature from 1960-2000 from the CCM (Vogt, 2007)
• temperature.1: duplicate of temperature
• transport: code of transport operation
• year: year of electrofishing

2.2. SIZE STRUCTURE OF EELS 

Dataset table_ind.Rdata 

A dataset of 494163 lines. In this dataset, one line correspond to one eel.

• altitudem: Altitude in meter
• altitudem.: Altitude in meter truncated to 800 m
• area_sudo: Area for recruitment (Drouineau et al., 2021)
• basin: Name (or code from bd_carthage France) of the basin
• codesea: Code of the Sea, factor A = Atlantic, M = Mediterranean
• country: A factor (FR, SP, PT) for France, Spain, and Portugal
• cs_height_08_n: Cumulated height from the sea, dam height transformed with power 0.8, no prediction for missing values.
• cs_height_08_n.: Same variable but truncated to 300
• cs_height_08_p: Cumulated height from the sea, dam height transformed with power 0.8, with prediction for missing values.
• cs_height_08_p.: Same variable but truncated to 300
• cs_height_08_pp: Cumulated height from the sea, dam height transformed with power 0.8, with prediction for missing values, the height of dam is set to zero if equiped with an efficient fishway for eel
• cs_height_08_pps: Cumulated height from the sea, dam height transformed with power 0.8, with prediction for missing values, the height of dam is set to zero if a score of efficient passage was attributed for eel on this structure
• cs_height_10_FR: Cumulated height from the sea, no transformation, no prediction for missing values, only the dams from France are considered when building on a transnational water course.
• cs_height_10_n: Cumulated height from the sea, no transformation, no prediction for missing values.
• cs_height_10_n.: Same variable but truncated to 200
• cs_height_10_p: Cumulated height from the sea, no transformation, missing height are extrapolated from two different models in France and the Iberian Peninsula
• cs_height_10_p.: Same variable but truncated to 200
• cs_height_10_pass0: Cumulated height from the sea, no transformation, including prediction for missing values, only the dams with pass are used to build the cumulated value
• cs_height_10_pass1: Cumulated height from the sea, no transformation, including prediction for missing values, only the dams without pass are used to build the cumulated value
• cs_height_10_pp: Cumulated height from the sea, no transformation, with prediction for missing values, the height of dam is set to zero if equiped with an efficient fishway for eel
• cs_height_10_ppass0: Cumulated height from the sea, no transformation, no prediction for missing values, only the dams with pass are used to build the cumulated value
• cs_height_10_ppass1: Cumulated height from the sea, no transformation, no prediction for missing values, only the dams without pass are used to build the cumulated value
• cs_height_10_pps: Cumulated height from the sea, no transformation, with prediction for missing values, the height of dam is set to zero if a score of efficient passage was attributed for eel on this structure
• cs_height_10_pscore0: Cumulated height from the sea, no transformation, no prediction for missing values, only the dams with score (that have been expertised as no or small barrier for eel) are used to build the cumulated value
• cs_height_10_pscore1: Cumulated height from the sea, no transformation, no prediction for missing values, only the dams without score are used to build the cumulated value
• cs_height_10_PT: Cumulated height from the sea, no transformation, no prediction for missing values, only the dams from Portugal are considered when building on a transnational water course
• cs_height_10_score0: Cumulated height from the sea, no transformation, including prediction for missing values, only the dams with score (that have been expertised as no or small barrier for eel) are used to build the cumulated value
• cs_height_10_score1: Cumulated height from the sea, no transformation, including prediction for missing values, only the dams without score are used to build the cumulated value
• cs_height_10_SP: Cumulated height from the sea, no transformation, no prediction for missing values, only the dams from Spain are considered when building on a transnational water course
• cs_height_12_n: Cumulated height from the sea, dam height transformed with power 1.2, no prediction for missing values
• cs_height_12_n.: Same variable but truncated to 500
• cs_height_12_p: Cumulated height from the sea, dam height transformed with power 1.2, with prediction for missing values
• cs_height_12_p.: Same variable but truncated to 500
• cs_height_12_pp: Cumulated height from the sea, dam height transformed with power 1.2, with prediction for missing values, the height of dam is set to zero if equiped with an efficient fishway for eel
• cs_height_12_pps: Cumulated height from the sea, dam height transformed with power 1.2, with prediction for missing values, the height of dam is set to zero if a score of efficient passage was attributed for eel on this structure
• cs_height_15_n: Cumulated height from the sea, dam height transformed with power 1.5, no prediction for missing values
• cs_height_15_n.: Same variable but truncated to 800
• cs_height_15_p: Cumulated height from the sea, dam height transformed with power 1.5, with prediction for missing values
• cs_height_15_p.: Same variable but truncated to 800
• cs_height_15_pp: Cumulated height from the sea, dam height transformed with power 1.5, with prediction for missing values, the height of dam is set to zero if equiped with an efficient fishway for eel
• cs_height_15_pps: Cumulated height from the sea, dam height transformed with power 1.5, with prediction for missing values, the height of dam is set to zero if a score of efficient passage was attributed for eel on this structure
• cumheightdam: Cumulated height of dam (ignore)
• cumnbdamp: Cumulated number of dam from the sea
• cumnbdamso: Cumulated number of dam from the sea only for dams whose height is larger than zero
• densCS: Density from Carle and Strub, number in second pass extrapolated from efficiency if only one pass.
• dist_from_gibraltar_km: Distance to Gibraltar calculated using an enveloppe along the coastline (e.g. the estuaries ingress inland are not counted for this distance).
• distanceseakm: Distance to the sea in kilometers
• distanceseakm.: Distance to the sea, truncated at 500
• distanceseam: Distance to the sea in meters
• distancesourcem: Distance to the source in meters
• ef_electrofishing_mean: Percentage of wetted surface downstream (cumwettedsurfacekm2) divided by land surface for all segments within the basin located at a same or lesser distance to the sea
• ef_fished_length: Length of the fishing operation
• ef_fished_width: Width of the fishing operation
• ef_fishingmethod: Method of electrofishing
• ef_nbpas: Number of pass in the electrofishing operation
• ef_wetted_area: Surface of the electrofishing station
• emu: Eel Management Unit
• id: Comes from uncout R function, which transforms counts into lines
• idsegment: Unique identifier of the segment [data type: UUID]. Use the Atlas to link with spatial table in PostgreSQL
• isendoreic: Is the riversegment coming from an endoreic river?
• issea: Is the riversegment a sea outlet?
• laltitudem.: Log transformed value of altitude (truncated)
• lcs_height_10_n.: Log transformed value of cumulated height
• lengthm: Length of the electroshing station in meters
• lengthriverm: length of the riversegment in meters
• lriverwidthm.: Log transformed value of river width
• medianflowm3ps: Median flow of the river in cubic meter per second
• month: Month
• name: Name of the river (Spain and Portugal)
• nb_size_measured: Number of size measured in the electrofishing operation
• nbp1: Number of eel collected in the first pass
• nbp2: Number of eel collected in the second pass
• nbp3: Number of eel collected in the third pass
• NCS: Number estimated during the electrofishing operation by Carle and Strubb and interpolation of first pass efficiency if only one pass
• nextdownidsegment: Code of the next downstream idsegment
• Npred: Number of eel predicted on the riversegment pdeltagamma * watersurface
• ob_dp_name: Data provider for the operation
• ob_id: Operation (observation) identifier
• ob_starting_date: Date of the operation
• op_id: Station (observation place) identifier
• pdelta: prediction of the delta (presence absence model)
• pdeltagamma: pdelta*pgamma
• pgamma: prediction of the gamma (positive densities model)
• rdelta: residuals of the delta (presence absence model)
• rdeltagamma: rdelta*rgamma
• rgamma: residuals of the gamma (positive densities model)
• riverwidthm: River width in meters
• riverwidthm.: same variable as riverwidthm (no truncation for riverwidth)
• rN: residuals in number (difference in number of eels between observed and predicted there are some NA where we had to get the data from "density" as there was no water surface available
• seaidsegment: Identifier of the sea idsegment
• sector: please ignore
• shreeve: Shreve rank of the segment
• size: Size class, "1 - <150", "2 - [150-300[", "3 - [300-450[", "4 - [450-600[", "5 - [600-750[", "6 - >=750"
• strahler: Strahler rank of the segment
• surfacebvkm2: surface of the watershed in m2
• surfacebvm2: surface of the watershed in km3
• surfaceunitbvm2: surface of the unit basin surrounding the segment in m2
• temperature: Average temperature from 1960-2000 from the CCM (Vogt 2007)
• temperaturejan: January temperature (France)
• temperaturejul: July temperature (France)
• totalnumber: Total number of eel caught during the operation
• transport: transport area
• wettedsurfacem2: Surface of water downstream from the segment in the river. Corresponds only to rivers
• wettedsurfaceotherm2: Surface of water downstream from the segment in the river. Corresponds only waterbodies (water surfaces, associated with the segment).
• year: Year of electrofishing operation

2.3. SILVER EEL DATA

Dataset silver_eel_2020.Rdata

A dataset of  20101 lines corresponding to yellow and silver eel along with their measurements for silvering for eel > 150 mm.

This dataset has been built here, and validated here and here, For more information look at the report especially the annexes.

The columns are:

• BL: Body length
• Dv: Vertical eye diameter
• FL: Pectoral fin length
• MD: Mean eye diameter
• W: Eel weight
• contrast: Body contrast for the eel
• Dh: Horizontal eye diameter
• diam_max: Max of horizontal and vertical eye  diameter
• diam_min: Min of horizontal and vertical eye  diameter
• distance_foyer_c: sqrt(diam_max^2 - diam_min^2)
• excentricite: Eye excentricity = distance_foyer_c / diam_max
• IO: Occular index Pankhurst  = 100*((Dh+Dv/2)^2*pi/BL
• K_ful: Fulton coefficient= 100*W/(BL/10)^3
• maturite_durif: Durif (2009) maturity class
• oc_surface: Occular surface
• sexe_durif: Sex according to Durif (2009)
• silver: Is it a silver eel, corresponds to one of "MII", "FIV", "FV" in Durif stage [data type: Boolean]
• stade_pankhurst: Stage according to Pankhurst
• stage_Durif: I, MII, FII, FIII, FIV, FV see Durif (2009)
• pdeltagamma: Density predicted from the delta gamma model in EDA (Briand et al., 2022)
• dist_from_gibraltar_km: Distance from Gibraltar along the coastline, negative in the Mediterranean
• surfacebvm2: Surface of the watershed in m2
• altitudem.: Altitude in m truncated at 400
• temperature: Average temperature from 1960-2000 from the CCM (Vogt, 2007)
• distanceseakm.: Distance to the sea in km truncated at 500
• strahler: Strahler order of the stream
• month2: Month of electrofishing with values grouped for <=7 or >=10
• month: Month of electrofishing
• year: Year of electrofishing

3. VERSIONS

• 10.5281/zenodo.6023561 1.0.0 - 2022-02-09 - Initial upload (open access)
• 10.5281/zenodo.6397009 1.0.1 - 2023-08-02 - Fixed description (open access)

4. READ MORE

• Atlas of European Eel Distribution (Anguilla anguilla) in Portugal, Spain and France (10.5281/zenodo.7546419)
• Electrofishing data for eel in the Iberian Peninsula (SUDOANG project) (10.5281/zenodo.8348353)
• Cumulated dam impact in France and the Iberian Peninsula (SUDOANG project) (10.5281/zenodo.8348374)

5. FUNDING

Project co-financed by the INTERREG SUDOE Programme through the European Regional Development Fund (ERDF).