dubicube

An R package to explore calculation, interpretation and visualisation of uncertainty related to indicators based on biodiversity data cubes.

https://github.com/b-cubed-eu/dubicube

Science Score: 67.0%

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
Found 3 DOI reference(s) in README
✓
Academic publication links
Links to: zenodo.org
○
Academic email domains
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (16.4%) to scientific vocabulary

Keywords

biodiversity-indicators data-cubes r rpackage uncertainty-quantification uncertainty-visualisation

Last synced: 6 months ago · JSON representation ·

Repository

An R package to explore calculation, interpretation and visualisation of uncertainty related to indicators based on biodiversity data cubes.

Basic Info

Host: GitHub
Owner: b-cubed-eu
License: other
Language: R
Default Branch: main
Homepage: https://b-cubed-eu.github.io/dubicube/
Size: 5.39 MB

Statistics

Stars: 1
Watchers: 2
Forks: 0
Open Issues: 7
Releases: 21

Topics

biodiversity-indicators data-cubes r rpackage uncertainty-quantification uncertainty-visualisation

Created over 1 year ago · Last pushed 6 months ago

Metadata Files

Readme Changelog Contributing License Code of conduct Citation Codemeta Zenodo

dubicube

The dubicube package aims to deliver measures for assessing the applicability of biodiversity data cubes, whether for general use or specific biodiversity indicators. These measures facilitate data exploration by providing insights into data quality and reliability. Additionally, the package includes functions for calculating indicator uncertainty using bootstrapping, as well as tools for interpreting and visualising uncertainty in biodiversity indicators derived from occurrence cubes.

Installation

Install dubicube in R:

r install.packages("dubicube", repos = c("https://b-cubed-eu.r-universe.dev", "https://cloud.r-project.org"))

You can install the development version from GitHub with:

```r

install.packages("remotes")

remotes::install_github("b-cubed-eu/dubicube") ```

Key Features

The dubicube package offers:

🔍 1. Data Exploration & Variability Assessment

Gain insights into the structure and sensitivity of biodiversity data cubes.

cross_validate_cube()
Perform cross-validation (leave-one-out or k-fold) to assess group-level sensitivity of indicators and evaluate how individual categories influence results.
📘 Read the tutorial →

🛠️ Additional data quality diagnostics are on the way!

📈 2. Estimating Indicator Uncertainty

Use bootstrap methods to understand variability, bias, and confidence in your indicators.

bootstrap_cube()
Create bootstrap replicates to estimate indicator variability, bias, and standard error.
📘 Read the tutorial →
calculate_bootstrap_ci()
Compute confidence intervals (percentile, BCa, normal, basic), with optional transformations and bias correction.
📘 Read the tutorial →

🧠 3. Interpretation & Visualisation

Put your results in context with reference values and uncertainty thresholds.

add_effect_classification()
Classify indicator trends (e.g. increase, stable, decrease) by comparing confidence intervals to thresholds.
📘 Read the tutorial →
Spatial and temporal interpretation
Learn how to visualise and assess patterns across space and time using indicator uncertainty.
📘 Best practices for temporal trends →
📘 Best practices for spatial trends →

🔗 Learn more at our website or explore the documentation.

Owner

Name: B-Cubed
Login: b-cubed-eu
Kind: organization

Website: https://b-cubed.eu
Repositories: 1
Profile: https://github.com/b-cubed-eu

Biodiversity Building Blocks for Policy

Citation (CITATION.cff)

cff-version: 1.2.0
message: If you use this software, please cite it using these metadata.
title: "dubicube: Calculation and Interpretation of Data Cube Indicator Uncertainty"
authors:
- given-names: Ward
  family-names: Langeraert
  affiliation: Research Institute for Nature and Forest (INBO)
  orcid: 0000-0002-5900-8109
- given-names: Toon
  family-names: Van Daele
  affiliation: Research Institute for Nature and Forest (INBO)
  orcid: 0000-0002-1362-853X
keywords:
- uncertainty quantification
- uncertainty visualisation
- biodiversity indicators
- data cubes
contact:
- given-names: Ward
  family-names: Langeraert
  affiliation: Research Institute for Nature and Forest (INBO)
  orcid: 0000-0002-5900-8109
doi: 10.5281/zenodo.14850237
license: MIT
repository-code: https://github.com/b-cubed-eu/dubicube/
type: software
abstract: "This R package provides functions to explore data cubes using simple measures
  and cross-validation techniques. It can also be used for uncertainty calculation
  using the bootstrap resampling method, and functionality is provided for efficient
  interpretation and visualisation of uncertainty related to indicators based on occurrence
  cubes."
identifiers:
- type: doi
  value: 10.5281/zenodo.14850237
- type: url
  value: https://b-cubed-eu.github.io/dubicube/
version: 0.9.5

CodeMeta (codemeta.json)

{
  "@context": "https://doi.org/10.5063/schema/codemeta-2.0",
  "@type": "SoftwareSourceCode",
  "identifier": "dubicube",
  "description": "This R package provides functions to explore data cubes using simple measures and cross-validation techniques. It can also be used for uncertainty calculation using the bootstrap resampling method, and functionality is provided for efficient interpretation and visualisation of uncertainty related to indicators based on occurrence cubes.",
  "name": "dubicube: Calculation and Interpretation of Data Cube Indicator Uncertainty",
  "relatedLink": [
    "https://b-cubed-eu.github.io/dubicube/",
    "https://doi.org/10.5281/zenodo.14850237"
  ],
  "codeRepository": "https://github.com/b-cubed-eu/dubicube",
  "issueTracker": "https://github.com/b-cubed-eu/dubicube/issues",
  "license": "https://spdx.org/licenses/MIT",
  "version": "0.9.5",
  "programmingLanguage": {
    "@type": "ComputerLanguage",
    "name": "R",
    "url": "https://r-project.org"
  },
  "runtimePlatform": "R version 4.5.0 (2025-04-11 ucrt)",
  "author": [
    {
      "@type": "Person",
      "givenName": "Ward",
      "familyName": "Langeraert",
      "email": "ward.langeraert@inbo.be",
      "@id": "https://orcid.org/0000-0002-5900-8109"
    },
    {
      "@type": "Person",
      "givenName": "Toon",
      "familyName": "Van Daele",
      "email": "toon.vandaele@inbo.be",
      "@id": "https://orcid.org/0000-0002-1362-853X"
    }
  ],
  "copyrightHolder": [
    {
      "@type": "Organization",
      "name": "Research Institute for Nature and Forest (INBO)"
    }
  ],
  "funder": [
    {
      "@type": "Organization",
      "name": "European Union"
    }
  ],
  "maintainer": [
    {
      "@type": "Person",
      "givenName": "Ward",
      "familyName": "Langeraert",
      "email": "ward.langeraert@inbo.be",
      "@id": "https://orcid.org/0000-0002-5900-8109"
    }
  ],
  "softwareSuggestions": [
    {
      "@type": "SoftwareApplication",
      "identifier": "b3gbi",
      "name": "b3gbi",
      "sameAs": "https://github.com/b-cubed-eu/b3gbi"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "frictionless",
      "name": "frictionless",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=frictionless"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "ggplot2",
      "name": "ggplot2",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=ggplot2"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "testthat",
      "name": "testthat",
      "version": ">= 3.0.0",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=testthat"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "tidyr",
      "name": "tidyr",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=tidyr"
    }
  ],
  "softwareRequirements": {
    "1": {
      "@type": "SoftwareApplication",
      "identifier": "assertthat",
      "name": "assertthat",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=assertthat"
    },
    "2": {
      "@type": "SoftwareApplication",
      "identifier": "data.table",
      "name": "data.table",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=data.table"
    },
    "3": {
      "@type": "SoftwareApplication",
      "identifier": "dplyr",
      "name": "dplyr",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=dplyr"
    },
    "4": {
      "@type": "SoftwareApplication",
      "identifier": "effectclass",
      "name": "effectclass",
      "sameAs": "https://github.com/inbo/effectclass"
    },
    "5": {
      "@type": "SoftwareApplication",
      "identifier": "modelr",
      "name": "modelr",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=modelr"
    },
    "6": {
      "@type": "SoftwareApplication",
      "identifier": "purrr",
      "name": "purrr",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=purrr"
    },
    "7": {
      "@type": "SoftwareApplication",
      "identifier": "rlang",
      "name": "rlang",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=rlang"
    },
    "8": {
      "@type": "SoftwareApplication",
      "identifier": "tibble",
      "name": "tibble",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=tibble"
    },
    "SystemRequirements": null
  },
  "fileSize": "279.37KB",
  "citation": [
    {
      "@type": "SoftwareSourceCode",
      "datePublished": "2025",
      "author": {
        "author1": {
          "@type": "Person",
          "givenName": "Ward",
          "familyName": "Langeraert"
        },
        "author2": {
          "@type": "Person",
          "givenName": "Toon",
          "familyName": "Van Daele"
        }
      },
      "name": "dubicube: Calculation and Interpretation of Data Cube Indicator Uncertainty. Version 0.9.5",
      "identifier": "10.5281/zenodo.14850237",
      "url": "https://b-cubed-eu.github.io/dubicube/",
      "@id": "https://doi.org/10.5281/zenodo.14850237",
      "sameAs": "https://doi.org/10.5281/zenodo.14850237"
    }
  ],
  "releaseNotes": "https://github.com/b-cubed-eu/dubicube/blob/main/NEWS.md",
  "readme": "https://github.com/b-cubed-eu/dubicube/blob/main/README.md",
  "contIntegration": [
    "https://github.com/b-cubed-eu/dubicube/actions/workflows/check_on_different_r_os.yml",
    "https://app.codecov.io/gh/b-cubed-eu/dubicube/"
  ],
  "developmentStatus": "https://www.repostatus.org/#active",
  "keywords": [
    "biodiversity-indicators",
    "data-cubes",
    "r",
    "rpackage",
    "uncertainty-quantification",
    "uncertainty-visualisation"
  ]
}

GitHub Events

Total

Create event: 49
Issues event: 51
Release event: 14
Delete event: 22
Issue comment event: 26
Member event: 1
Push event: 178
Pull request review comment event: 6
Pull request event: 49

Last Year

Create event: 49
Issues event: 51
Release event: 14
Delete event: 22
Issue comment event: 26
Member event: 1
Push event: 178
Pull request review comment event: 6
Pull request event: 49

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 34
Total pull requests: 26
Average time to close issues: 13 days
Average time to close pull requests: 3 days
Total issue authors: 1
Total pull request authors: 2
Average comments per issue: 0.32
Average comments per pull request: 0.12
Merged pull requests: 18
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 34
Pull requests: 26
Average time to close issues: 13 days
Average time to close pull requests: 3 days
Issue authors: 1
Pull request authors: 2
Average comments per issue: 0.32
Average comments per pull request: 0.12
Merged pull requests: 18
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

wlangera (34)

Pull Request Authors

wlangera (26)
ToonVanDaele (1)

Top Labels

Issue Labels

documentation (17) enhancement (4) invalid (3) bug (1) good first issue (1)

Pull Request Labels

Dependencies

.github/workflows/check_on_branch.yml actions

inbo/actions/check_pkg main 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 main composite

.github/workflows/release.yml actions

actions/checkout v3 composite
ncipollo/release-action v1 composite

DESCRIPTION cran

testthat >= 3.0.0 suggests

ecosyste.ms

Data

Tools

Indexes

Applications

Experiments

Open Source Science

dubicube

Science Score: 67.0%

Keywords

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

dubicube

Installation

install.packages("remotes")

Key Features

🔍 1. Data Exploration & Variability Assessment

📈 2. Estimating Indicator Uncertainty

🧠 3. Interpretation & Visualisation

Owner

Citation (CITATION.cff)

CodeMeta (codemeta.json)

GitHub Events

Total

Last Year

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Dependencies