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n2kanalysis

https://github.com/inbo/n2kanalysis

Science Score: 54.0%

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

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 5 committers (20.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (14.6%) to scientific vocabulary

Keywords

analysis monitoring natura2000 package r
Last synced: 6 months ago · JSON representation ·

Repository

Basic Info
  • Host: GitHub
  • Owner: inbo
  • License: gpl-3.0
  • Language: R
  • Default Branch: main
  • Size: 2.24 MB
Statistics
  • Stars: 1
  • Watchers: 4
  • Forks: 2
  • Open Issues: 1
  • Releases: 14
Topics
analysis monitoring natura2000 package r
Created about 10 years ago · Last pushed 11 months ago
Metadata Files
Readme Changelog Contributing License Code of conduct Citation Zenodo

README.md

Project Status: Active – The project has reached a stable, usable state and is being actively developed. License Release codecov

The n2kanalysis package

The n2kanalysis package contains the main infrastructure for the analysis of the Natura 2000 Monitoring. The import from the raw data into the analysis object is done by dedicated packages, one for each monitoring scheme.

Rationale

n2kanalysis is part of the collection of R packages created to analyse the data gathered during the Natura 2000 monitoring.

  • n2kanalysis: R package with generic functions for the analysis
  • watervogelanalysis: R package to extract the raw data from the wintering bird survey database and prepare the analyses
  • abvanalysis: R package to extract the raw data from the common breeding birds survey database and prepare the analyses
  • n2khelper: auxiliary functions used in the other packages
  • n2kresult: Liquibase scripts to set-up the database in which the results of the analyses are stored
  • n2kupdate: R package to read and write to the n2kresult database
  • Rn2k: Docker image with all the required dependencies to run the analyses

The main goal of n2kanalysis is to assist traceable analysis of monitoring data. The S4 classes in n2kanalysis allow to defines self-contained analysis objects. Besides the required data and definition on the model, the object also contains relevant meta-data. Each object contains two fingerprints: the file fingerprint and the status fingerprint. Both are SHA-1 hashes based on the current object. The file fingerprint is based on the parts of the object which won't change during the analysis. E.g. most meta-data, the data and the definition of the model. The status fingerprint is based on both the file fingerprint and all relevant part of the object that do change during the fitting process. Publishing both fingerprints along with the results ensures an easy matching between results and the object from which they originated.

Folder structure

The folder structure is that of a typical R package with the mandatory R folder (definition of the functions) and man (help files in Rd format). inst is an optional folder in which some auxiliary scripts are stored. The optional tests folder contains the unit tests using the infrastructure from the testthat package.

n2kanalysis |-- inst |-- man |-- R |-- tests |-- testthat

Owner

  • Name: Research Institute for Nature and Forest (INBO)
  • Login: inbo
  • Kind: organization
  • Location: Belgium

Open source, data and science initiatives of the Research Institute for Nature and Forest (INBO)

Citation (CITATION.cff) 

cff-version: 1.2.0
message: If you use this software, please cite it using these metadata.
title: "n2kanalysis: Generic Functions to Analyse Data from the 'Natura 2000' Monitoring"
authors:
- given-names: Thierry
  family-names: Onkelinx
  affiliation: Research Institute for Nature and Forest (INBO)
  orcid: 0000-0001-8804-4216
keywords:
- analysis, reproducible research, natura 2000, monitoring
contact:
- given-names: Thierry
  family-names: Onkelinx
  affiliation: Research Institute for Nature and Forest (INBO)
  orcid: 0000-0001-8804-4216
doi: 10.5281/zenodo.3576047
license: GPL-3.0
repository-code: https://github.com/inbo/n2kanalysis/
type: software
abstract: "All generic functions and classes for the analysis for the 'Natura 2000'
  monitoring. The classes contain all required data and definitions to fit the model
  without the need to access other sources. Potentially they might need access to
  one or more parent objects. An aggregation object might for example need the result
  of an imputation object. The actual definition of the analysis, using these generic
  function and classes, is defined in dedictated analysis R packages for every monitoring
  scheme. For example 'abvanalysis' and 'watervogelanalysis'."
identifiers:
- type: doi
  value: 10.5281/zenodo.3576047
- type: url
  value: https://inbo.github.io/n2kanalysis/
version: 0.4.0

GitHub Events

Total
  • Release event: 1
  • Delete event: 1
  • Push event: 18
  • Pull request event: 2
  • Create event: 2
Last Year
  • Release event: 1
  • Delete event: 1
  • Push event: 18
  • Pull request event: 2
  • Create event: 2

Committers

Last synced: 6 months ago

All Time
  • Total Commits: 759
  • Total Committers: 5
  • Avg Commits per committer: 151.8
  • Development Distribution Score (DDS): 0.008
Past Year
  • Commits: 50
  • Committers: 1
  • Avg Commits per committer: 50.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Thierry Onkelinx t****x@i****e 753
Floris Vanderhaeghe f****e@i****e 2
ThierryO g****t@m****e 2
Peter Desmet p****k@g****m 1
Dr Tom August t****g@c****k 1
Committer Domains (Top 20 + Academic)
inbo.be: 2 ceh.ac.uk: 1 muscardinus.be: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 1
  • Total pull requests: 30
  • Average time to close issues: about 1 hour
  • Average time to close pull requests: 26 days
  • Total issue authors: 1
  • Total pull request authors: 4
  • Average comments per issue: 1.0
  • Average comments per pull request: 0.7
  • Merged pull requests: 26
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 3
  • Average time to close issues: N/A
  • Average time to close pull requests: 4 months
  • 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
  • peterdesmet (1)
Pull Request Authors
  • ThierryO (25)
  • peterdesmet (3)
  • florisvdh (3)
  • AugustT (1)
Top Labels
Issue Labels
Pull Request Labels

Dependencies

DESCRIPTION cran
  • R >= 3.1.2 depends
  • MASS * imports
  • RODBC * imports
  • assertthat >= 0.2.1 imports
  • aws.s3 * imports
  • digest >= 0.6.23.2 imports
  • dplyr * imports
  • methods * imports
  • multimput >= 0.2.10 imports
  • n2khelper >= 0.5.0 imports
  • purrr * imports
  • rlang * imports
  • tibble * imports
  • tidyr >= 0.4.0 imports
  • yaml * imports
  • INLA >= 19.09.03 suggests
  • Matrix * suggests
  • littler * suggests
  • parallel * suggests
  • sn * suggests
  • testthat >= 2.0.1 suggests
.github/workflows/check_on_branch.yml actions
  • inbo/actions/check_pkg checklist-0.3.6 composite
.github/workflows/check_on_different_r_os.yml actions
  • actions/checkout v3 composite
  • r-lib/actions/check-r-package v2 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/check_on_main.yml actions
  • inbo/actions/check_pkg checklist-0.3.6 composite
.github/workflows/release.yml actions
  • actions/checkout v3 composite
  • ncipollo/release-action v1 composite