{"id":13724724,"url":"https://github.com/PascalIrz/aspe","last_synced_at":"2025-05-07T19:30:33.015Z","repository":{"id":37078052,"uuid":"323145117","full_name":"PascalIrz/aspe","owner":"PascalIrz","description":"aspe: An R Package to Analyse and Visualise River Fish Data in France","archived":false,"fork":false,"pushed_at":"2025-02-20T14:52:33.000Z","size":6423,"stargazers_count":14,"open_issues_count":3,"forks_count":11,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-05-02T17:03:31.227Z","etag":null,"topics":["aspe","dataset","electrofishing","fish","france","freshwater","index","map","plot","river","sampling","wfd"],"latest_commit_sha":null,"homepage":"https://pascalirz.github.io/aspe/","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/PascalIrz.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.md","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2020-12-20T19:05:40.000Z","updated_at":"2025-02-20T14:43:45.000Z","dependencies_parsed_at":"2023-02-05T20:46:31.306Z","dependency_job_id":"cc794b0e-7e24-4dd9-b2c0-e1565e5216cf","html_url":"https://github.com/PascalIrz/aspe","commit_stats":{"total_commits":323,"total_committers":8,"mean_commits":40.375,"dds":"0.16718266253869973","last_synced_commit":"c951c038585ec9c893493a87315390d4911deeaa"},"previous_names":[],"tags_count":7,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/PascalIrz%2Faspe","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/PascalIrz%2Faspe/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/PascalIrz%2Faspe/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/PascalIrz%2Faspe/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/PascalIrz","download_url":"https://codeload.github.com/PascalIrz/aspe/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":252943586,"owners_count":21829272,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["aspe","dataset","electrofishing","fish","france","freshwater","index","map","plot","river","sampling","wfd"],"created_at":"2024-08-03T01:02:02.445Z","updated_at":"2025-05-07T19:30:32.958Z","avatar_url":"https://github.com/PascalIrz.png","language":"R","readme":"\u003c!-- badges: start --\u003e\r\n[![R-CMD-check](https://github.com/PascalIrz/aspe/workflows/R-CMD-check/badge.svg)](https://github.com/PascalIrz/aspe/actions)\r\n[![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)\r\n[![Lifecycle:Maturing](https://img.shields.io/badge/Lifecycle-Maturing-007EC6)](https://discourse.jupyter.org/t/should-we-adopt-the-tidyverse-package-lifecycle-badges/1310)\r\n[![DOI](https://zenodo.org/badge/323145117.svg)](https://zenodo.org/record/7458005)\r\n\u003c!-- badges: end --\u003e\r\n\r\n{aspe}: an R package to analyse and visualise river fish data in France \r\n====\r\n\r\n{aspe} fournit des outils autorisant simplement la plupart des\r\ntraitements de base à partir d’une sauvegarde (dump SQL) de la base de\r\ndonnées ASPE de l’OFB. Ces traitements comprennent les calculs\r\nd’abondances, densités, distribution en tailles et la détection de\r\ntendances à l’échelle de la station. Ces calculs sont accompagnés de\r\nfonctionnalités graphiques.\r\n\r\nThe goal of {aspe} is to is to provide a suite of tools for most of the\r\ncommon processing of the ASPE database including importation from a SQL\r\nformat dump, calculation of abundances, densities, size distributions,\r\ntemporal trends for populations at the station level, along with\r\ngraphical output.\r\n\r\nLa base de données ASPE de l’OFB contient toutes les données\r\nd’inventaire par pêche à l’électricité par le CSP, l’ONEMA, l’AFB, l’OFB\r\nainsi que par certains partenaires sur les rivières de France. Elle est décrite\r\ndans Irz *et al.* (2022), article produit en visant le respect des principes de la recherche reproductible (Wilkinson *et al.* 2016). Ses fichiers sources - données comprises - sont diffusés sur le dépôt [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7099129.svg)](https://doi.org/10.5281/zenodo.7099129)\r\n\r\n\r\nThe ASPE database is administrated by the French Office for Biodiversity. It gathers, among others, all the river electrofishing samplings carried out by the former Fisheries Council, National Office for Water and Aquatic Systems and French Agency for Biodiversity. The database is described in Irz *et al.* (2022). This paper was produced to respect the FAIR principles (Wilkinson *et al.* 2016), hence its source files - including the database - are available at [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7099129.svg)](https://doi.org/10.5281/zenodo.7099129)\r\n\r\n- Irz P, Vigneron T, Poulet N, Cosson E, Point T, Baglinière E, Porcher JP. 2022. A long-term monitoring database on fish and crayfish species in French rivers. *Knowl. Manag. Aquat. Ecosyst.* 423, 25, [DOI:10.1051/kmae/2022021](https://doi.org/10.1051/kmae/2022021).\r\n- Wilkinson MD, et al. 2016. The FAIR Guiding Principles for scientific data management and stewardship. *Sci. Data* 3: 160018, [DOI:10.1038/sdata.2016.18](https://doi.org/10.1038/sdata.2016.18).\r\n\r\n\r\nInstallation\r\n------------\r\n\r\nSi besoin, commencer par installer le package R {devtools} ainsi que la suite Rtools, puis installer {aspe} au moyen de la commande :\r\n\r\nIf necessary, first install the {devtools} R package and the Rtools suite, then you can\r\ninstall the released version of {aspe} from\r\n[Github](https://github.com/PascalIrz/aspe) with:\r\n\r\n    devtools::install_github(\"PascalIrz/aspe\")\r\n\r\n\r\nRépertoires Github associés / Associated Github repositories\r\n------------\r\n\r\nPlusieurs dépôts Github sont associés au package :\r\n\r\n- [aspe_data](https://github.com/PascalIrz/aspe_data) : construction des jeux de données inclus dans le package {aspe}\r\n- [aspe_test](https://github.com/PascalIrz/aspe_test) : Fichiers R Markdown pour tester le package {aspe} et produire les tutos\r\n- [aspe_demo](https://github.com/PascalIrz/aspe_demo) : Fichiers R Markdown pour prétraiter les données pour [un tableau de bord interactif](https://gitlab.ofb.fr/cedric.mondy1/aspedashboard)\r\n- [aspeQual](https://github.com/PascalIrz/aspeQual) : package R destiné à la mise en qualité de la base Aspe\r\n\r\nThe package comes with a number of associated repos :\r\n\r\n- [aspe_data](https://github.com/PascalIrz/aspe_data): building of the datasets included in the {aspe} package\r\n- [aspe_test](https://github.com/PascalIrz/aspe_test): R Markdown files to test the {aspe} package and to build the tutorials\r\n- [aspe_demo](https://github.com/PascalIrz/aspe_demo): R Markdown files to pre-process the fish data for [a dashboard app](https://gitlab.ofb.fr/cedric.mondy1/aspedashboard)\r\n- [aspeQual](https://github.com/PascalIrz/aspeQual) : R package dedicated to the quality control on the Aspe database\r\n\r\n\r\nTutoriels / Vignettes\r\n------------\r\n\r\nLa documentation générale du package est diffusée sur Github pages : https://pascalirz.github.io/aspe/\r\n\r\nUne série de tutoriels est en ligne :\r\n\r\n- [Traiter des données Indice Poisson Rivière (IPR)](https://rpubs.com/kamoke/713491)\r\n- [Faire des traitements de base à partir des lots](https://rpubs.com/kamoke/715102)\r\n- [Traiter des mesures individuelles](https://rpubs.com/kamoke/715858)\r\n- [Faire des traitements géographiques](https://rpubs.com/kamoke/716322)\r\n- [Construire des relations taille-poids](https://rpubs.com/kamoke/729779)\r\n\r\nSeveral vignettes (in French) are available online:\r\n\r\n- [Processing the fish-based river health index](https://rpubs.com/kamoke/713491)\r\n- [Base processing on the fish batches data](https://rpubs.com/kamoke/715102)\r\n- [Processing the individual measurements](https://rpubs.com/kamoke/715858)\r\n- [Geographical analysis](https://rpubs.com/kamoke/716322)\r\n- [Fitting length-weight relationships](https://rpubs.com/kamoke/729779)\r\n\r\n\r\nNommage des fonctions / Functions' naming rules\r\n---------------\r\n\r\nLes familles de fonctions se distinguent par des préfixes :\r\n\r\n- `mef_` : mise en forme des dataframes\r\n- `expl_` : exploration de la base\r\n- `export`: export des dataframes (.csv ou .RData)\r\n- `geo_` : opérations spatiales\r\n- `gg_` : production de graphiques avec `ggplot2`\r\n- `imp_` : importation depuis un dump SQL\r\n- `ipr_` : [indice poisson rivière](https://www.kmae-journal.org/articles/kmae/abs/2002/02/kmae2002365p405/kmae2002365p405.html)\r\n- `misc_` : divers\r\n\r\nFunctions' names start by group-specific prefixes:\r\n\r\n- `mef_`: tidying dataframes\r\n- `expl_`: exploring the database\r\n- `export`: exporting dataframes (.csv or .RData)\r\n- `geo_`: spatial processing\r\n- `gg_`: plots with `ggplot2`\r\n- `imp_`: importing data from a SQL dump\r\n- `ipr_`: [fish-based river health index](https://www.researchgate.net/publication/227818978_Development_and_validation_of_a_fish-based_index_FBI_for_the_assessment_of_river_health_in_France)\r\n- `misc_`: miscellaneous\r\n\r\nNommage des variables / Variables' naming rules\r\n---------------\r\n\r\nDans la quasi-totalité des cas, les variables contenues dans une table sont préfixées en fonction de cette table. 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