aspe: An R Package to Analyse and Visualise River Fish Data in France
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R-CMD-check License: GPL v3 Lifecycle:Maturing DOI

{aspe}: an R package to analyse and visualise river fish data in France

{aspe} fournit des outils autorisant simplement la plupart des traitements de base partir dune sauvegarde (dump SQL) de la base de donnes ASPE de lOFB. Ces traitements comprennent les calculs dabondances, densits, distribution en tailles et la dtection de tendances lchelle de la station. Ces calculs sont accompagns de fonctionnalits graphiques.

The goal of {aspe} is to is to provide a suite of tools for most of the common processing of the ASPE database including importation from a SQL format dump, calculation of abundances, densities, size distributions, temporal trends for populations at the station level, along with graphical output.

La base de donnes ASPE de lOFB contient toutes les donnes dinventaire par pche llectricit par le CSP, lONEMA, lAFB, lOFB ainsi que par certains partenaires sur les rivires de France. Elle est dcrite dans Irz et al. (2022), article produit en visant le respect des principes de la recherche reproductible (Wilkinson et al. 2016). Ses fichiers sources - donnes comprises - sont diffuss sur le dpt DOI

The 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

  • Irz P, Vigneron T, Poulet N, Cosson E, Point T, Baglinire 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.
  • 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.


Si besoin, commencer par installer le package R {devtools} ainsi que la suite Rtools, puis installer {aspe} au moyen de la commande :

If necessary, first install the {devtools} R package and the Rtools suite, then you can install the released version of {aspe} from Github with:


Rpertoires Github associs / Associated Github repositories

Plusieurs dpts Github sont associs au package :

The package comes with a number of associated repos :

  • aspe_data: building of the datasets included in the {aspe} package
  • aspe_test: R Markdown files to test the {aspe} package and to build the tutorials
  • aspe_demo: R Markdown files to pre-process the fish data for a dashboard app
  • aspeQual : R package dedicated to the quality control on the Aspe database

Tutoriels / Vignettes

La documentation gnrale du package est diffuse sur Github pages :

Une srie de tutoriels est en ligne :

Several vignettes (in French) are available online:

Nommage des fonctions / Functions' naming rules

Les familles de fonctions se distinguent par des prfixes :

  • mef_ : mise en forme des dataframes
  • expl_ : exploration de la base
  • export: export des dataframes (.csv ou .RData)
  • geo_ : oprations spatiales
  • gg_ : production de graphiques avec ggplot2
  • imp_ : importation depuis un dump SQL
  • ipr_ : indice poisson rivire
  • misc_ : divers

Functions' names start by group-specific prefixes:

  • mef_: tidying dataframes
  • expl_: exploring the database
  • export: exporting dataframes (.csv or .RData)
  • geo_: spatial processing
  • gg_: plots with ggplot2
  • imp_: importing data from a SQL dump
  • ipr_: fish-based river health index
  • misc_: miscellaneous

Nommage des variables / Variables' naming rules

Dans la quasi-totalit des cas, les variables contenues dans une table sont prfixes en fonction de cette table. Par exemple :

  • sta_ : station
  • pop_ : point_prelevement
  • mei_ : mesure_individuelle

Pour une liste des noms et signification des variables, taper dans la console :


Almost systematically, variables' names start by table-specific prefixes:

  • sta_ : station
  • pop_ : point_prelevement (sampling point)
  • mei_ : mesure_individuelle (individual measurment)

To display a comprehensive list of variables with their meaning (all in French so far, sorry), call:

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