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aspe

aspe: An R Package to Analyse and Visualise River Fish Data in France

https://github.com/pascalirz/aspe

Science Score: 49.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 12 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: researchgate.net, zenodo.org
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (8.4%) to scientific vocabulary

Keywords

aspe dataset electrofishing fish france freshwater index map plot river sampling wfd
Last synced: 6 months ago · JSON representation

Repository

aspe: An R Package to Analyse and Visualise River Fish Data in France

Basic Info
Statistics
  • Stars: 14
  • Watchers: 2
  • Forks: 11
  • Open Issues: 3
  • Releases: 7
Topics
aspe dataset electrofishing fish france freshwater index map plot river sampling wfd
Created about 5 years ago · Last pushed 6 months ago
Metadata Files
Readme License

README.md

R-CMD-check License: GPL v3 Lifecycle:Maturing DOI <!-- badges: end -->

{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 à partir d’une sauvegarde (dump SQL) de la base de données ASPE de l’OFB. Ces traitements comprennent les calculs d’abondances, densités, distribution en tailles et la détection de tendances à l’échelle de la station. Ces calculs sont accompagnés de fonctionnalités 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 données ASPE de l’OFB contient toutes les données d’inventaire par pêche à l’électricité par le CSP, l’ONEMA, l’AFB, l’OFB ainsi que par certains partenaires sur les rivières de France. Elle est décrite dans 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

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, 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.
  • 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.

Installation

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:

devtools::install_github("PascalIrz/aspe")

Répertoires Github associés / Associated Github repositories

Plusieurs dépôts Github sont associés au package :

  • aspe_data : construction des jeux de données inclus dans le package {aspe}
  • aspe_test : Fichiers R Markdown pour tester le package {aspe} et produire les tutos
  • aspe_demo : Fichiers R Markdown pour prétraiter les données pour un tableau de bord interactif
  • aspeQual : package R destiné à la mise en qualité de la base Aspe

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 générale du package est diffusée sur Github pages : https://pascalirz.github.io/aspe/

Une série 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 préfixes :

  • mef_ : mise en forme des dataframes
  • expl_ : exploration de la base
  • export: export des dataframes (.csv ou .RData)
  • geo_ : opérations spatiales
  • gg_ : production de graphiques avec ggplot2
  • imp_ : importation depuis un dump SQL
  • ipr_ : indice poisson rivière
  • 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-totalité des cas, les variables contenues dans une table sont préfixées 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 :

data("data_dictionnaire")
View(data_dictionnaire)

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:

data("data_dictionnaire")
View(data_dictionnaire)

Owner

  • Login: PascalIrz
  • Kind: user
  • Location: Rennes, France
  • Company: Office Français de la Biodiversité

Ecologist and datascientist

GitHub Events

Total
  • Push event: 10
Last Year
  • Push event: 10

Committers

Last synced: 7 months ago

All Time
  • Total Commits: 326
  • Total Committers: 8
  • Avg Commits per committer: 40.75
  • Development Distribution Score (DDS): 0.123
Past Year
  • Commits: 19
  • Committers: 3
  • Avg Commits per committer: 6.333
  • Development Distribution Score (DDS): 0.526
Top Committers
Name Email Commits
PascalIrz p****z@g****m 286
Cedric Mondy c****y@g****m 16
richaben b****b@g****m 12
manue6 1****6 5
IRZ Pascal p****z@a****r 3
LilianBonnaf 1****f 2
cedricbriandgithub c****0@g****m 1
cedric.mondy c****y@G****l 1
Committer Domains (Top 20 + Academic)
afbiodiversite.fr: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 12
  • Total pull requests: 14
  • Average time to close issues: 3 months
  • Average time to close pull requests: 2 days
  • Total issue authors: 3
  • Total pull request authors: 6
  • Average comments per issue: 1.08
  • Average comments per pull request: 0.64
  • Merged pull requests: 14
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 1
  • Average time to close issues: N/A
  • Average time to close pull requests: 1 day
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • PascalIrz (9)
  • nicolaspoulet (2)
  • cedricbriandgithub (1)
Pull Request Authors
  • richaben (5)
  • CedricMondy (5)
  • manue6 (4)
  • LilianBonnaf (2)
  • cedricbriandgithub (1)
  • PascalIrz (1)
Top Labels
Issue Labels
enhancement (5)
Pull Request Labels

Packages

  • Total packages: 2
  • Total downloads: unknown
  • Total dependent packages: 0
    (may contain duplicates)
  • Total dependent repositories: 0
    (may contain duplicates)
  • Total versions: 14
proxy.golang.org: github.com/PascalIrz/aspe
  • Versions: 7
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 5.4%
Average: 5.6%
Dependent repos count: 5.8%
Last synced: 6 months ago
proxy.golang.org: github.com/pascalirz/aspe
  • Versions: 7
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 5.4%
Average: 5.6%
Dependent repos count: 5.8%
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • dplyr * imports
  • forcats * imports
  • ggiraph * imports
  • ggplot2 * imports
  • ggpubr * imports
  • ggtext * imports
  • lubridate * imports
  • patchwork * imports
  • purrr * imports
  • readr * imports
  • readxl * imports
  • rlang * imports
  • scales * imports
  • sf * imports
  • shiny * imports
  • stringi * imports
  • stringr * imports
  • tibble * imports
  • tidyr * imports
  • knitr * suggests
  • rmarkdown * suggests
.github/workflows/R-CMD-check.yaml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • actions/upload-artifact main composite
  • r-lib/actions/setup-pandoc v1 composite
  • r-lib/actions/setup-r v2 composite