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gcube:
- source: https://raw.githubusercontent.com/b-cubed-eu/gcube/refs/heads/main/README.Rmd
title: "gcube: Simulating Biodiversity Data Cubes"
sidebar_label: Introduction
replace:
- "# gcube ": ""
- "man/figures/logo.png": "https://b-cubed-eu.github.io/gcube/logo.png"
dependencies: sf, dplyr, ggplot2
- source: https://raw.githubusercontent.com/b-cubed-eu/gcube/refs/heads/main/vignettes/articles/occurrence-process.Rmd
title: Simulating the occurrence process
sidebar_label: Occurrence process
dependencies: sf, dplyr, ggplot2, tidyterra
- source: https://raw.githubusercontent.com/b-cubed-eu/gcube/refs/heads/main/vignettes/articles/detection-process.Rmd
title: Simulating the detection process
sidebar_label: Detection process
dependencies: sf dplyr ggplot2
- source: https://raw.githubusercontent.com/b-cubed-eu/gcube/refs/heads/main/vignettes/articles/grid-designation-process.Rmd
title: Specifying the grid designation process
sidebar_label: Grid designation process
dependencies: sf dplyr ggplot2 ggExtra
- source: https://raw.githubusercontent.com/b-cubed-eu/gcube/refs/heads/main/vignettes/articles/multi-species-approach.Rmd
title: Creating cubes for multiple species
sidebar_label: Multi-species approach
dependencies: sf dplyr ggplot2
- source: https://raw.githubusercontent.com/b-cubed-eu/gcube/refs/heads/main/vignettes/articles/cube-for-virtual-species.Rmd
title: Create occurrence cubes for virtual species
sidebar_label: Cube for virtual species
dependencies: geodata virtualspecies sf terra ggplot2
- source: https://raw.githubusercontent.com/b-cubed-eu/gcube/refs/heads/main/vignettes/articles/custom-grid-designation.Rmd
title: Grid designation for custom datasets
sidebar_label: Custom grid designation
dependencies: frictionless ggplot2 dplyr sf
dubicube:
- source: https://raw.githubusercontent.com/b-cubed-eu/dubicube/refs/heads/main/README.md
title: "dubicube: Calculation and Interpretation of Data Cube Indicator Uncertainty"
sidebar_label: Introduction
replace:
- "# dubicube ": ""
- "man/figures/logo.png": "https://b-cubed-eu.github.io/dubicube/logo.png"
- "https://b-cubed-eu.github.io/dubicube/articles/group-level-sensitivity.html": "https://docs.b-cubed.eu/software/dubicube/group-level-sensitivity/"
- "https://b-cubed-eu.github.io/dubicube/articles/bootstrap-method-cubes.html": "https://docs.b-cubed.eu/software/dubicube/bootstrap-method-cubes/"
- "https://b-cubed-eu.github.io/dubicube/articles/bootstrap-interval-calculation.html": "https://docs.b-cubed.eu/software/dubicube/bootstrap-interval-calculation/"
- "https://b-cubed-eu.github.io/dubicube/articles/whole-cube-versus-group-specific-bootstrap.html": "https://docs.b-cubed.eu/software/dubicube/whole-cube-versus-group-specific-bootstrap/"
- "https://b-cubed-eu.github.io/dubicube/articles/effect-classification.html": "https://docs.b-cubed.eu/software/dubicube/effect-classification/"
- "https://b-cubed-eu.github.io/dubicube/articles/visualising-temporal-trends.html": "https://docs.b-cubed.eu/software/dubicube/visualising-temporal-trends/"
- "https://b-cubed-eu.github.io/dubicube/articles/visualising-spatial-trends.html": "https://docs.b-cubed.eu/software/dubicube/visualising-spatial-trends/"
- source: https://raw.githubusercontent.com/b-cubed-eu/dubicube/refs/heads/main/vignettes/articles/group-level-sensitivity.Rmd
title: Group-level sensitivity analysis
sidebar_label: Group-level sensitivity analysis
dependencies: frictionless b3gbi ggplot2 dplyr
replace:
- "https://b-cubed-eu.github.io/dubicube/articles/group-level-sensitivity.html": "https://docs.b-cubed.eu/software/dubicube/group-level-sensitivity/"
- "https://b-cubed-eu.github.io/dubicube/articles/bootstrap-method-cubes.html": "https://docs.b-cubed.eu/software/dubicube/bootstrap-method-cubes/"
- "https://b-cubed-eu.github.io/dubicube/articles/bootstrap-interval-calculation.html": "https://docs.b-cubed.eu/software/dubicube/bootstrap-interval-calculation/"
- "https://b-cubed-eu.github.io/dubicube/articles/whole-cube-versus-group-specific-bootstrap.html": "https://docs.b-cubed.eu/software/dubicube/whole-cube-versus-group-specific-bootstrap/"
- "https://b-cubed-eu.github.io/dubicube/articles/effect-classification.html": "https://docs.b-cubed.eu/software/dubicube/effect-classification/"
- "https://b-cubed-eu.github.io/dubicube/articles/visualising-temporal-trends.html": "https://docs.b-cubed.eu/software/dubicube/visualising-temporal-trends/"
- "https://b-cubed-eu.github.io/dubicube/articles/visualising-spatial-trends.html": "https://docs.b-cubed.eu/software/dubicube/visualising-spatial-trends/"
- source: https://raw.githubusercontent.com/b-cubed-eu/dubicube/refs/heads/main/vignettes/articles/bootstrap-method-cubes.Rmd
title: Bootstrap method for data cubes
sidebar_label: Bootstrapping data cubes
dependencies: frictionless b3gbi ggplot2 dplyr tidyr
replace:
- "figures/bootstrapping.png": "https://b-cubed-eu.github.io/dubicube/articles/figures/bootstrapping.png"
- "https://b-cubed-eu.github.io/dubicube/articles/group-level-sensitivity.html": "https://docs.b-cubed.eu/software/dubicube/group-level-sensitivity/"
- "https://b-cubed-eu.github.io/dubicube/articles/bootstrap-method-cubes.html": "https://docs.b-cubed.eu/software/dubicube/bootstrap-method-cubes/"
- "https://b-cubed-eu.github.io/dubicube/articles/bootstrap-interval-calculation.html": "https://docs.b-cubed.eu/software/dubicube/bootstrap-interval-calculation/"
- "https://b-cubed-eu.github.io/dubicube/articles/whole-cube-versus-group-specific-bootstrap.html": "https://docs.b-cubed.eu/software/dubicube/whole-cube-versus-group-specific-bootstrap/"
- "https://b-cubed-eu.github.io/dubicube/articles/effect-classification.html": "https://docs.b-cubed.eu/software/dubicube/effect-classification/"
- "https://b-cubed-eu.github.io/dubicube/articles/visualising-temporal-trends.html": "https://docs.b-cubed.eu/software/dubicube/visualising-temporal-trends/"
- "https://b-cubed-eu.github.io/dubicube/articles/visualising-spatial-trends.html": "https://docs.b-cubed.eu/software/dubicube/visualising-spatial-trends/"
- source: https://raw.githubusercontent.com/b-cubed-eu/dubicube/refs/heads/main/vignettes/articles/bootstrap-interval-calculation.Rmd
title: Calculating bootstrap confidence intervals
sidebar_label: Bootstrap confidence intervals
dependencies: frictionless b3gbi ggplot2 dplyr tidyr
replace:
- "https://b-cubed-eu.github.io/dubicube/articles/group-level-sensitivity.html": "https://docs.b-cubed.eu/software/dubicube/group-level-sensitivity/"
- "https://b-cubed-eu.github.io/dubicube/articles/bootstrap-method-cubes.html": "https://docs.b-cubed.eu/software/dubicube/bootstrap-method-cubes/"
- "https://b-cubed-eu.github.io/dubicube/articles/bootstrap-interval-calculation.html": "https://docs.b-cubed.eu/software/dubicube/bootstrap-interval-calculation/"
- "https://b-cubed-eu.github.io/dubicube/articles/whole-cube-versus-group-specific-bootstrap.html": "https://docs.b-cubed.eu/software/dubicube/whole-cube-versus-group-specific-bootstrap/"
- "https://b-cubed-eu.github.io/dubicube/articles/effect-classification.html": "https://docs.b-cubed.eu/software/dubicube/effect-classification/"
- "https://b-cubed-eu.github.io/dubicube/articles/visualising-temporal-trends.html": "https://docs.b-cubed.eu/software/dubicube/visualising-temporal-trends/"
- "https://b-cubed-eu.github.io/dubicube/articles/visualising-spatial-trends.html": "https://docs.b-cubed.eu/software/dubicube/visualising-spatial-trends/"
- source: https://raw.githubusercontent.com/b-cubed-eu/dubicube/refs/heads/main/vignettes/articles/whole-cube-versus-group-specific-bootstrap.Rmd
title: Whole-cube bootstrap versus group-specific bootstrap
sidebar_label: Bootstrap methods
dependencies: frictionless b3gbi ggplot2 dplyr tidyr
replace:
- "https://b-cubed-eu.github.io/dubicube/articles/group-level-sensitivity.html": "https://docs.b-cubed.eu/software/dubicube/group-level-sensitivity/"
- "https://b-cubed-eu.github.io/dubicube/articles/bootstrap-method-cubes.html": "https://docs.b-cubed.eu/software/dubicube/bootstrap-method-cubes/"
- "https://b-cubed-eu.github.io/dubicube/articles/bootstrap-interval-calculation.html": "https://docs.b-cubed.eu/software/dubicube/bootstrap-interval-calculation/"
- "https://b-cubed-eu.github.io/dubicube/articles/whole-cube-versus-group-specific-bootstrap.html": "https://docs.b-cubed.eu/software/dubicube/whole-cube-versus-group-specific-bootstrap/"
- "https://b-cubed-eu.github.io/dubicube/articles/effect-classification.html": "https://docs.b-cubed.eu/software/dubicube/effect-classification/"
- "https://b-cubed-eu.github.io/dubicube/articles/visualising-temporal-trends.html": "https://docs.b-cubed.eu/software/dubicube/visualising-temporal-trends/"
- "https://b-cubed-eu.github.io/dubicube/articles/visualising-spatial-trends.html": "https://docs.b-cubed.eu/software/dubicube/visualising-spatial-trends/"
- source: https://raw.githubusercontent.com/b-cubed-eu/dubicube/refs/heads/main/vignettes/articles/effect-classification.Rmd
title: Classifying effects using confidence limits
sidebar_label: Effect classification
dependencies: ggplot2
replace:
- "https://b-cubed-eu.github.io/dubicube/articles/group-level-sensitivity.html": "https://docs.b-cubed.eu/software/dubicube/group-level-sensitivity/"
- "https://b-cubed-eu.github.io/dubicube/articles/bootstrap-method-cubes.html": "https://docs.b-cubed.eu/software/dubicube/bootstrap-method-cubes/"
- "https://b-cubed-eu.github.io/dubicube/articles/bootstrap-interval-calculation.html": "https://docs.b-cubed.eu/software/dubicube/bootstrap-interval-calculation/"
- "https://b-cubed-eu.github.io/dubicube/articles/whole-cube-versus-group-specific-bootstrap.html": "https://docs.b-cubed.eu/software/dubicube/whole-cube-versus-group-specific-bootstrap/"
- "https://b-cubed-eu.github.io/dubicube/articles/effect-classification.html": "https://docs.b-cubed.eu/software/dubicube/effect-classification/"
- "https://b-cubed-eu.github.io/dubicube/articles/visualising-temporal-trends.html": "https://docs.b-cubed.eu/software/dubicube/visualising-temporal-trends/"
- "https://b-cubed-eu.github.io/dubicube/articles/visualising-spatial-trends.html": "https://docs.b-cubed.eu/software/dubicube/visualising-spatial-trends/"
- source: https://raw.githubusercontent.com/b-cubed-eu/dubicube/refs/heads/main/vignettes/articles/visualising-temporal-trends.Rmd
title: Visualising temporal trends
sidebar_label: Visualising temporal trends
dependencies: frictionless b3gbi ggplot2 dplyr tidyr effectclass
replace:
- "https://b-cubed-eu.github.io/dubicube/articles/group-level-sensitivity.html": "https://docs.b-cubed.eu/software/dubicube/group-level-sensitivity/"
- "https://b-cubed-eu.github.io/dubicube/articles/bootstrap-method-cubes.html": "https://docs.b-cubed.eu/software/dubicube/bootstrap-method-cubes/"
- "https://b-cubed-eu.github.io/dubicube/articles/bootstrap-interval-calculation.html": "https://docs.b-cubed.eu/software/dubicube/bootstrap-interval-calculation/"
- "https://b-cubed-eu.github.io/dubicube/articles/whole-cube-versus-group-specific-bootstrap.html": "https://docs.b-cubed.eu/software/dubicube/whole-cube-versus-group-specific-bootstrap/"
- "https://b-cubed-eu.github.io/dubicube/articles/effect-classification.html": "https://docs.b-cubed.eu/software/dubicube/effect-classification/"
- "https://b-cubed-eu.github.io/dubicube/articles/visualising-temporal-trends.html": "https://docs.b-cubed.eu/software/dubicube/visualising-temporal-trends/"
- "https://b-cubed-eu.github.io/dubicube/articles/visualising-spatial-trends.html": "https://docs.b-cubed.eu/software/dubicube/visualising-spatial-trends/"
- source: https://raw.githubusercontent.com/b-cubed-eu/dubicube/refs/heads/main/vignettes/articles/visualising-spatial-trends.Rmd
title: Visualising spatial trends
sidebar_label: Visualising spatial trends
dependencies: frictionless b3gbi ggplot2 dplyr sf
replace:
- "figures/blur-spatial-uncertainty.png": "https://b-cubed-eu.github.io/dubicube/articles/figures/blur-spatial-uncertainty.png"
- "https://b-cubed-eu.github.io/dubicube/articles/group-level-sensitivity.html": "https://docs.b-cubed.eu/software/dubicube/group-level-sensitivity/"
- "https://b-cubed-eu.github.io/dubicube/articles/bootstrap-method-cubes.html": "https://docs.b-cubed.eu/software/dubicube/bootstrap-method-cubes/"
- "https://b-cubed-eu.github.io/dubicube/articles/bootstrap-interval-calculation.html": "https://docs.b-cubed.eu/software/dubicube/bootstrap-interval-calculation/"
- "https://b-cubed-eu.github.io/dubicube/articles/whole-cube-versus-group-specific-bootstrap.html": "https://docs.b-cubed.eu/software/dubicube/whole-cube-versus-group-specific-bootstrap/"
- "https://b-cubed-eu.github.io/dubicube/articles/effect-classification.html": "https://docs.b-cubed.eu/software/dubicube/effect-classification/"
- "https://b-cubed-eu.github.io/dubicube/articles/visualising-temporal-trends.html": "https://docs.b-cubed.eu/software/dubicube/visualising-temporal-trends/"
- "https://b-cubed-eu.github.io/dubicube/articles/visualising-spatial-trends.html": "https://docs.b-cubed.eu/software/dubicube/visualising-spatial-trends/"
b3doc:
- source: https://raw.githubusercontent.com/b-cubed-eu/b3doc/refs/heads/main/README.Rmd
title: "b3doc: Tools for the B-Cubed Documentation Website"
sidebar_label: Introduction
replace:
- "# b3doc": ""
b3gbi:
- source: https://raw.githubusercontent.com/b-cubed-eu/b3gbi/refs/heads/main/README.Rmd
title: "b3gbi: General Biodiversity Indicators for Biodiversity Data Cubes"
sidebar_label: Introduction
replace:
- "# b3gbi ": ""
- "man/figures/logo.png": "https://b-cubed-eu.github.io/b3gbi/logo.png"
- "the tutorial: https://b-cubed-eu.github.io/b3gbi/articles/b3gbi.html": "[this tutorial](/software/b3gbi/b3gbi/)"
- source: https://raw.githubusercontent.com/b-cubed-eu/b3gbi/refs/heads/main/vignettes/b3gbi.Rmd
title: Get started
sidebar_label: Get started
replace:
- "The package is publicly available at <https://www.github.com/b-cubed-eu/b3gbi>.": ""
impIndicator:
- source: https://raw.githubusercontent.com/b-cubed-eu/impIndicator/refs/heads/main/README.Rmd
title: "impIndicator: Impact Indicators of Alien Taxa"
sidebar_label: Introduction
replace:
- "# impIndicator ": ""
- "man/figures/logo.png": "https://b-cubed-eu.github.io/impIndicator/logo.png"
dependencies: b3gbi ggplot2 tidyr
- source: https://raw.githubusercontent.com/b-cubed-eu/impIndicator/refs/heads/main/vignettes/background.Rmd
sidebar_label: Background
- source: https://raw.githubusercontent.com/b-cubed-eu/impIndicator/refs/heads/main/vignettes/prepare_data.Rmd
sidebar_labe: Prepare data
dependencies: b3gbi dplyr knitr
trias:
- source: https://raw.githubusercontent.com/trias-project/trias/refs/heads/main/README.Rmd
title: "trias: Functionality for TrIAS and LIFE RIPARIAS"
sidebar_label: Introduction
replace:
- "# trias ": ""
- "man/figures/logo.png": https://trias-project.github.io/trias/logo.png
rgbif:
- source: https://raw.githubusercontent.com/ropensci/rgbif/refs/heads/master/README.md
title: "rgbif: Interface to the Global Biodiversity Information Facility API"
sidebar_label: Introduction
replace:
- "# rgbif ": ""
- "man/figures/logo.png": "https://docs.ropensci.org/rgbif/logo.png"
ebvcube:
- source: https://raw.githubusercontent.com/EBVcube/ebvcube/refs/heads/main/README.Rmd
title: "EBVcube: Working with netCDF for Essential Biodiversity Variables"
sidebar_label: Introduction
replace:
- "# ebvcube package": ""
dependencies: BiocManager rhdf5 DelayedArray HDF5Array terra ggplot2 tidyterra
pdindicatoR:
- source: https://raw.githubusercontent.com/b-cubed-eu/pdindicatoR/refs/heads/main/README.Rmd
title: "pdindicatoR: Calculate and visualize a phylogenetic diversity indicators based
on species occurrence data cubes"
sidebar_label: Introduction
replace:
- "# pdindicatoR ": ""
- "man/figures/logo.png": "https://b-cubed-eu.github.io/pdindicatoR/logo.png"
dependencies: sf dplyr
vscube:
- source: https://raw.githubusercontent.com/b-cubed-eu/vscube/refs/heads/main/README.Rmd
title: "vscube: Virtual Suitability Cube"
sidebar_label: Introduction
dependencies: terra stars ggplot2 viridis
replace:
- "# Virtual Suitability Cube": ""
- "## Inspect species ": "\n## Inspect species " # Remove if origin has empty line above