DOI: 10.5281/zenodo.6397009
title: Eel data (Anguilla anguilla) and associated environment variables for eel  in the SUDOE area (SUDOANG project)

description: 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).