Atlas of European Eel Distribution (Anguilla anguilla) in Portugal, Spain and France

<strong>DESCRIPTION</strong> The SUDOANG project aims at providing common tools to managers to support eel conservation in the SUDOE area (Spain, France and Portugal). VISUANG is the SUDOANG Interactive Web Application that host all these tools . The application consists of an eel distribution atlas (GT1), assessments of mortalities caused by turbines and an atlas showing obstacles to migration<br> (GT2), estimates of recruitment and exploitation rate (GT3) and escapement (chosen as a target by the EC for the Eel Management Plans) (GT4). In addition, it includes an interactive map showing sampling results from the pilot basin network produced by GT6. The eel abundance for the eel atlas and escapement has been obtained using the Eel Density Analysis model (EDA, GT4's product). EDA extrapolates the abundance of eel in sampled river segments to other segments taking into account how the abundance, sex and size of the eels change depending on different parameters. Thus, EDA requires two main data sources: those related to the river<br> characteristics and those related to eel abundance and characteristics. However, in both cases, data availability was uneven in the SUDOE area. In addition, this information was dispersed among several managers and in different formats due to different sampling sources: Water Framework Directive (WFD), Community Framework for the Collection, Management and Use of Data in the Fisheries Sector (EUMAP), Eel Management Plans, research groups, scientific<br> papers and technical reports. Therefore, the first step towards having eel abundance estimations including the whole SUDOE area, was to have a joint river and eel database. In this report we will describe the database corresponding to the river’s characteristics in the SUDOE area and the eel abundances and their characteristics. In the case of rivers, two types of information has been collected: <strong>River topology</strong> (RN table): a compilation of data on rivers and their topological and hydrographic characteristics in the three countries. <strong>River attributes</strong> (RNA table): contains physical attributes that have fed the SUDOANG models. The estimation of eel abundance and characteristic (size, biomass, sex-ratio and silver) distribution at different scales (river segment, basin, Eel Management Unit (EMU), and country) in the SUDOE area obtained with the implementation of the EDA2.3 model has been compiled in the <strong>RNE table (eel predictions)</strong>. <strong>TECHNICAL DESCRIPTION TO BUILD THE POSTGRES DATABASE</strong> <strong>1. Build the database in postgres.</strong> All tables are in ESPG:3035 (European LAEA). The format is postgreSQL database. You can download other formats (shapefiles, csv), here SUDOANG gt1 database. Initial command <pre><code class="language-bash"># open a shell with command CMD # Move to the place where you have downloaded the file using the following command cd c:/path/to/my/folder # note psql must be accessible, in windows you can add the path to the postgres #bin folder, otherwise you need to add the full path to the postgres bin folder see link to instructions below createdb -U postgres eda2.3 psql -U postgres eda2.3 # this will open a command with # where you can launch the commands in the next box </code></pre> Within the psql command <pre><code class="language-sql"> create extension "postgis"; create extension "dblink"; create extension "ltree"; create extension "tablefunc"; create schema dbeel_rivers; create schema france; create schema spain; create schema portugal; -- type \q to quit the psql shell</code></pre> Now the database is ready to receive the differents dumps. The dump file are large. You might not need the part including unit basins or waterbodies. All the tables except waterbodies and unit basins are described in the Atlas. You might need to understand what is inheritance in a database. https://www.postgresql.org/docs/12/tutorial-inheritance.html <strong>2. RN (riversegments)</strong> These layers contain the topology (see Atlas for detail) dbeel_rivers.rn france.rn spain.rn portugal.rn Columns (see Atlas) gid idsegment source target lengthm nextdownidsegment path isfrontier issource seaidsegment issea geom isendoreic isinternational country <pre><code class="language-bash"># dbeel_rivers.rn ! mandatory =&gt; table at the international level from which # the other table inherit # even if you don't want to use other countries # (In many cases you should ... there are transboundary catchments) download this first. # the rn network must be restored firt ! #table rne and rna refer to it by foreign keys. pg_restore -U postgres -d eda2.3 "dbeel_rivers.rn.backup" #france pg_restore -U postgres -d eda2.3 "france.rn.backup" # spain pg_restore -U postgres -d eda2.3 "spain.rn.backup" # portugal pg_restore -U postgres -d eda2.3 "portugal.rn.backup" # with the schema you will probably want to be able to use the functions psql -U postgres -d eda2.3 -f "function_dbeel_rivers.sql"</code></pre> <strong>3. RNA (Attributes)</strong> This corresponds to tables dbeel_rivers.rna france.rna spain.rna portugal.rna Columns (See Atlas) idsegment altitudem distanceseam distancesourcem cumnbdam medianflowm3ps surfaceunitbvm2 surfacebvm2 strahler shreeve codesea name pfafriver pfafsegment basin riverwidthm temperature temperaturejan temperaturejul wettedsurfacem2 wettedsurfaceotherm2 lengthriverm emu cumheightdam riverwidthmsource slope dis_m3_pyr_riveratlas dis_m3_pmn_riveratlas dis_m3_pmx_riveratlas drought drought_type_calc Code : <pre><code class="language-bash">pg_restore -U postgres -d eda2.3 "dbeel_rivers.rna.backup" pg_restore -U postgres -d eda2.3 "france.rna.backup" pg_restore -U postgres -d eda2.3 "spain.rna.backup" pg_restore -U postgres -d eda2.3 "portugal.rna.backup" </code></pre> <strong>4. RNE (eel predictions)</strong> These layers contain eel data (see Atlas for detail) dbeel_rivers.rne france.rne spain.rne portugal.rne Columns (see Atlas) idsegment surfaceunitbvm2 surfacebvm2 delta gamma density neel beel peel150 peel150300 peel300450 peel450600 peel600750 peel750 nsilver bsilver psilver150300 psilver300450 psilver450600 psilver600750 psilver750 psilver pmale150300 pmale300450 pmale450600 pfemale300450 pfemale450600 pfemale600750 pfemale750 pmale pfemale sex_ratio cnfemale300450 cnfemale450600 cnfemale600750 cnfemale750 cnmale150300 cnmale300450 cnmale450600 cnsilver150300 cnsilver300450 cnsilver450600 cnsilver600750 cnsilver750 cnsilver delta_tr gamma_tr type_fit_delta_tr type_fit_gamma_tr density_tr density_pmax_tr neel_pmax_tr nsilver_pmax_tr density_wd neel_wd beel_wd nsilver_wd bsilver_wd sector_tr year_tr is_current_distribution_area is_pristine_distribution_area_1985 Code for restauration <pre><code class="language-bash">pg_restore -U postgres -d eda2.3 "dbeel_rivers.rne.backup" pg_restore -U postgres -d eda2.3 "france.rne.backup" pg_restore -U postgres -d eda2.3 "spain.rne.backup" pg_restore -U postgres -d eda2.3 "portugal.rne.backup"</code></pre> <strong>5. Unit basins</strong> Units basins are not described in the Altas. They correspond to the following tables : dbeel_rivers.basinunit_bu france.basinunit_bu spain.basinunit_bu portugal.basinunit_bu france.basinunitout_buo spain.basinunitout_buo portugal.basinunitout_buo The unit basins is the simple basin that surrounds a segment. It correspond to the topography unit from which unit segment have been calculated. ESPG 3035. Tables bu_unitbv, and bu_unitbvout inherit from dbeel_rivers.unit_bv. The first table intersects with a segment, the second table does not, it corresponds to basin polygons which do not have a riversegment. Source : Portugal https://sniambgeoviewer.apambiente.pt/Geodocs/gml/inspire/HY_PhysicalWaters_DrainageBasinGeoCod.ziphttps://sniambgeoviewer.apambiente.pt/Geodocs/gml/inspire/HY_PhysicalWaters_DrainageBasinGeoCod.zip France In france unit bv corresponds to the RHT (Pella et al., 2012) Spain http://www.mapama.gob.es/ide/metadatos/index.html?srv=metadata.show&amp;uuid=898f0ff8-f06c-4c14-88f7-43ea90e48233 <pre><code class="language-bash">pg_restore -U postgres -d eda2.3 'dbeel_rivers.basinunit_bu.backup' # france pg_restore -U postgres -d eda2.3 "france.basinunit_bu.backup" pg_restore -U postgres -d eda2.3 "france.basinunitout_buo.backup" # spain pg_restore -U postgres -d eda2.3 "spain.basinunit_bu.backup" pg_restore -U postgres -d eda2.3 "spain.basinunit_bu.backup" # portugal pg_restore -U postgres -d eda2.3 "portugal.basinunit_bu.backup" pg_restore -U postgres -d eda2.3 "portugal.basinunitout_buo.backup" </code></pre> <strong>6- Waterbodies</strong> In these tables we have have kept the structure from the source table in WISE or from the bd_topage. dbeel_rivers.waterbody_unitbv portugal.waterbody_unitbv france.waterbody_unitbv spain.waterbody_unitbv In France, corresponds to the hydrographic surface from bd_topage. <br> <br> https://bdtopage.eaufrance.fr/page/documents-ressources In spain it corresponds to . Cuencas hidrográficas de los principales ríos definidos en el artículo 3 de la Directiva Marco del Agua (DMA), in Portugal to HY_PhysicalWaters_DrainageBasinMAgua. <pre><code class="language-bash">pg_restore -U postgres -d eda2.3 "dbeel_rivers.waterbody_unitbv.backup" pg_restore -U postgres -d eda2.3 "portugal.waterbody_unitbv.backup" pg_restore -U postgres -d eda2.3 "france.waterbody_unitbv.backup" </code></pre> <br> 7- functions The functions can be found in dbeel_rivers_functions.sql you can read the examples there and description of the functions, here is a quick example showing the functionalities. dbeel_rivers.get_path provides the path between two idsegments of the same basin : <pre><code class="language-sql">select dbeel_rivers.get_path (113670,114115,'FR') -- FR113618.FR114065.FR114053.FR114042</code></pre> dbeel_rivers.get_distance calculates the distance between two rivers segments (including the distance of the idsegments themselves) <pre><code class="language-sql">select dbeel_rivers.get_distance (113670,114115,'FR'); --12669</code></pre> dbeel_rivers.upstream_segments_rn(TEXT) takes an upstream segment and returns a vector of idsegments attention this function is slower than national counterparts, check in schema spain portugal and france for quicker functions. It is use for instance to calculate all eels coming from the upstream basin. <pre><code class="language-sql">SELECT dbeel_rivers.upstream_segments_rn('FR114042'); /* FR114042 FR114053 FR113982 FR114034 ... */</code></pre> dbeel_rivers.upstream_segments_rn_sti(TEXT) takes an upstream segment and a TABLE with idsegment, target, source, this in more convenient for later use of routing functions (like get path) which require source and target<br> dbeel_rivers.downstream_segments_rn(TEXT) takes a segment and returns the path to the sea. <pre><code class="language-sql">SELECT dbeel_rivers.downstream_segments_rn('SP227795');</code></pre><strong>数据集描述</strong> SUDOANG项目旨在为管理者提供通用工具，以支持SUDOE区域（西班牙、法国及葡萄牙）的鳗鱼保护工作。VISUANG是承载所有上述工具的SUDOANG交互式Web应用程序。该应用包含：鳗鱼分布图集（GT1）、水轮机致死评估与洄游障碍图集（GT2）、补充量与开发率估算（GT3），以及逃逸量（欧盟委员会（EC）指定为鳗鱼管理计划的核心目标指标）（GT4）。此外，应用还包含交互式地图，展示由GT6生成的试点流域网络的采样结果。 用于鳗鱼图集及逃逸量计算的鳗鱼丰度数据，通过鳗鱼密度分析模型（Eel Density Analysis Model, EDA，GT4的产出成果）获取。EDA可将已采样河流分段的鳗鱼丰度外推至其他分段，同时考虑鳗鱼丰度、性别与体型随不同参数的变化规律。因此，EDA需两类主要数据源：与河流特征相关的数据，以及与鳗鱼丰度及自身特征相关的数据。然而，SUDOE区域内这两类数据的可用性均存在不均现象。此外，由于采样来源多样（包括水框架指令（Water Framework Directive, WFD）、渔业数据收集、管理与使用共同体框架（Community Framework for the Collection, Management and Use of Data in the Fisheries Sector, EUMAP）、鳗鱼管理计划、研究团队、学术论文及技术报告），相关信息分散于多位管理者手中，且格式各不相同。 因此，要实现覆盖整个SUDOE区域的鳗鱼丰度估算，首要步骤是构建一套联合的河流与鳗鱼数据库。本报告将对SUDOE区域内的河流特征数据库，以及鳗鱼丰度与自身特征数据库进行说明。针对河流数据，共收集两类信息： <strong>河流拓扑结构（RN表）</strong>：整合了三国境内河流的拓扑与水文地理特征数据。 <strong>河流属性（RNA表）</strong>：包含用于支撑SUDOANG模型的各类物理属性数据。 通过EDA2.3模型计算得到的SUDOE区域内不同尺度（河流分段、流域、鳗鱼管理单元（EMU）及国家层级）的鳗鱼丰度与特征（体型、生物量、性别比例及银化程度）分布结果，已汇总至<strong>RNE表（鳗鱼预测结果）</strong>。 <strong>PostgreSQL数据库构建技术说明</strong> <strong>1. PostgreSQL数据库搭建</strong> 所有表均采用ESPG:3035（欧洲LAEA投影坐标系），数据库格式为PostgreSQL。你可在此处下载其他格式（Shapefile、CSV）的SUDOANG GT1数据库。 初始命令如下： bash # 打开CMD命令行Shell # 使用以下命令切换至已下载文件所在目录 cd c:/path/to/my/folder # 需确保psql可被调用，Windows系统中可将PostgreSQL的bin目录添加至系统路径，否则需完整指定PostgreSQL bin目录路径，详见下方说明链接 createdb -U postgres eda2.3 psql -U postgres eda2.3 # 此时将进入psql命令行环境，可执行后续命令 在psql命令行中执行： sql create extension "postgis"; create extension "dblink"; create extension "ltree"; create extension "tablefunc"; create schema dbeel_rivers; create schema france; create schema spain; create schema portugal; -- 输入q可退出psql Shell 至此，数据库已就绪，可导入各类备份文件。备份文件体积较大，若无需包含流域单元或水体模块，可跳过对应部分。除水体与流域单元表外，其余表的详细说明见本图集。需了解数据库继承机制，详见：https://www.postgresql.org/docs/12/tutorial-inheritance.html <strong>2. RN（河流分段）</strong> 此类图层包含河流拓扑结构（详见本图集），对应表为dbeel_rivers.rn、france.rn、spain.rn、portugal.rn。 字段说明（详见本图集）：gid, idsegment, source, target, lengthm, nextdownidsegment, path, isfrontier, issource, seaidsegment, issea, geom, isendoreic, isinternational, country bash # dbeel_rivers.rn为国际层级的基础表，其余国家层级的rn表均继承自该表 # 即便无需使用其他国家的数据（多数情况下建议保留，因存在跨界流域），需优先下载并恢复该表 # rne与rna表均通过外键引用该rn网络 pg_restore -U postgres -d eda2.3 "dbeel_rivers.rn.backup" # 法国 pg_restore -U postgres -d eda2.3 "france.rn.backup" # 西班牙 pg_restore -U postgres -d eda2.3 "spain.rn.backup" # 葡萄牙 pg_restore -U postgres -d eda2.3 "portugal.rn.backup" # 如需启用相关函数，可执行以下命令 psql -U postgres -d eda2.3 -f "function_dbeel_rivers.sql" <strong>3. RNA（河流属性）</strong> 对应表为dbeel_rivers.rna、france.rna、spain.rna、portugal.rna。 字段说明（详见本图集）：idsegment, altitudem, distanceseam, distancesourcem, cumnbdam, medianflowm3ps, surfaceunitbvm2, surfacebvm2, strahler, shreeve, codesea, name, pfafriver, pfafsegment, basin, riverwidthm, temperature, temperaturejan, temperaturejul, wettedsurfacem2, wettedsurfaceotherm2, lengthriverm, emu, cumheightdam, riverwidthmsource, slope, dis_m3_pyr_riveratlas, dis_m3_pmn_riveratlas, dis_m3_pmx_riveratlas, drought, drought_type_calc bash pg_restore -U postgres -d eda2.3 "dbeel_rivers.rna.backup" pg_restore -U postgres -d eda2.3 "france.rna.backup" pg_restore -U postgres -d eda2.3 "spain.rna.backup" pg_restore -U postgres -d eda2.3 "portugal.rna.backup" <strong>4. RNE（鳗鱼预测结果）</strong> 此类图层包含鳗鱼相关数据（详见本图集），对应表为dbeel_rivers.rne、france.rne、spain.rne、portugal.rne。 字段说明（详见本图集）：idsegment, surfaceunitbvm2, surfacebvm2, delta, gamma, density, neel, beel, peel150, peel150300, peel300450, peel450600, peel600750, peel750, nsilver, bsilver, psilver150300, psilver300450, psilver450600, psilver600750, psilver750, psilver, pmale150300, pmale300450, pmale450600, pfemale300450, pfemale450600, pfemale600750, pfemale750, pmale, pfemale, sex_ratio, cnfemale300450, cnfemale450600, cnfemale600750, cnfemale750, cnmale150300, cnmale300450, cnmale450600, cnsilver150300, cnsilver300450, cnsilver450600, cnsilver600750, cnsilver750, cnsilver, delta_tr, gamma_tr, type_fit_delta_tr, type_fit_gamma_tr, density_tr, density_pmax_tr, neel_pmax_tr, nsilver_pmax_tr, density_wd, neel_wd, beel_wd, nsilver_wd, bsilver_wd, sector_tr, year_tr, is_current_distribution_area, is_pristine_distribution_area_1985 bash pg_restore -U postgres -d eda2.3 "dbeel_rivers.rne.backup" pg_restore -U postgres -d eda2.3 "france.rne.backup" pg_restore -U postgres -d eda2.3 "spain.rne.backup" pg_restore -U postgres -d eda2.3 "portugal.rne.backup" <strong>5. 流域单元</strong> 流域单元未在本图集内说明，对应表为：dbeel_rivers.basinunit_bu、france.basinunit_bu、spain.basinunit_bu、portugal.basinunit_bu、france.basinunitout_buo、spain.basinunitout_buo、portugal.basinunitout_buo。 流域单元指环绕单个河流分段的简单流域，为计算河流分段所用的地形单元，采用ESPG:3035投影坐标系。表bu_unitbv与bu_unitbvout继承自dbeel_rivers.unit_bv，前者与河流分段相交，后者为无对应河流分段的流域多边形。 数据来源： 葡萄牙：https://sniambgeoviewer.apambiente.pt/Geodocs/gml/inspire/HY_PhysicalWaters_DrainageBasinGeoCod.zip 法国：法国流域单元BV对应RHT数据（Pella等，2012） 西班牙：http://www.mapama.gob.es/ide/metadatos/index.html?srv=metadata.show&uuid=898f0ff8-f06c-4c14-88f7-43ea90e48233 bash pg_restore -U postgres -d eda2.3 'dbeel_rivers.basinunit_bu.backup' # 法国 pg_restore -U postgres -d eda2.3 "france.basinunit_bu.backup" pg_restore -U postgres -d eda2.3 "france.basinunitout_buo.backup" # 西班牙 pg_restore -U postgres -d eda2.3 "spain.basinunit_bu.backup" pg_restore -U postgres -d eda2.3 "spain.basinunit_bu.backup" # 葡萄牙 pg_restore -U postgres -d eda2.3 "portugal.basinunit_bu.backup" pg_restore -U postgres -d eda2.3 "portugal.basinunitout_buo.backup" <strong>6. 水体</strong> 本表保留了WISE或bd_topage源表的结构，对应表为dbeel_rivers.waterbody_unitbv、portugal.waterbody_unitbv、france.waterbody_unitbv、spain.waterbody_unitbv。 法国的水体数据来自bd_topage的水文表面数据：https://bdtopage.eaufrance.fr/page/documents-ressources 西班牙的水体对应《水框架指令》（DMA）第3条定义的主要河流流域 葡萄牙的水体对应HY_PhysicalWaters_DrainageBasinMAgua bash pg_restore -U postgres -d eda2.3 "dbeel_rivers.waterbody_unitbv.backup" pg_restore -U postgres -d eda2.3 "portugal.waterbody_unitbv.backup" pg_restore -U postgres -d eda2.3 "france.waterbody_unitbv.backup" <strong>7. 函数工具</strong> 相关函数存于dbeel_rivers_functions.sql文件中，可查看其中的示例与函数说明，以下为功能示例： - dbeel_rivers.get_path：获取同一流域内两个河流分段之间的路径： sql select dbeel_rivers.get_path (113670,114115,'FR') -- 结果：FR113618.FR114065.FR114053.FR114042 - dbeel_rivers.get_distance：计算两个河流分段之间的距离（含分段自身长度）： sql select dbeel_rivers.get_distance (113670,114115,'FR'); --结果：12669 - dbeel_rivers.upstream_segments_rn(TEXT)：输入单个河流分段ID，返回上游所有分段的ID向量。注意该函数速度慢于对应国家的专用函数，可检查spain、portugal、france模式下的更快函数，该函数常用于计算上游流域的总鳗鱼量： sql SELECT dbeel_rivers.upstream_segments_rn('FR114042'); /* 结果：FR114042 FR114053 FR113982 FR114034 ... */ - dbeel_rivers.upstream_segments_rn_sti(TEXT)：输入单个河流分段ID与包含idsegment、target、source字段的表，更便于后续路由函数（如get_path）调用，此类函数需用到source与target字段。 - dbeel_rivers.downstream_segments_rn(TEXT)：输入单个河流分段ID，返回通往海洋的下游路径： sql SELECT dbeel_rivers.downstream_segments_rn('SP227795');