Package: funbiogeo 0.0.0.9000

Nicolas Casajus

funbiogeo: Functional Biogeography Analyses

Helps users with analyses in functional biogeogeography by loading and combining data, computing trait coverage, as well as computing functional diversity indices, drawing maps, correlating them with the environment, and upscaling assemblages.

Authors:Nicolas Casajus [aut, cre, cph], Matthias Grenié [aut]

funbiogeo_0.0.0.9000.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
funbiogeo/json (API)

# Install 'funbiogeo' in R:
install.packages('funbiogeo', repos = c('https://frbcesab.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/frbcesab/funbiogeo/issues

Pkgdown/docs site:https://frbcesab.github.io

Datasets:

On CRAN:

Conda:

functional-biogeographyfunctional-diversityfunctional-trait

5.94 score 12 stars 24 scripts 34 exports 51 dependencies

Last updated from:19591c5c17. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK259
source / vignettesOK416
linux-release-x86_64OK232
macos-release-arm64OK152
macos-oldrel-arm64OK158
windows-develOK196
windows-releaseOK193
windows-oldrelOK202
wasm-releaseOK168

Exports:fb_aggregate_site_datafb_count_sites_by_speciesfb_count_species_by_sitefb_count_species_by_traitfb_count_traits_by_speciesfb_cwmfb_filter_sites_by_species_coveragefb_filter_sites_by_trait_coveragefb_filter_species_by_site_coveragefb_filter_species_by_trait_coveragefb_filter_traits_by_species_coveragefb_format_site_locationsfb_format_site_speciesfb_format_species_categoriesfb_format_species_traitsfb_get_all_trait_coverages_by_sitefb_get_environmentfb_get_trait_combination_coveragefb_get_trait_coverage_by_sitefb_make_reportfb_map_rasterfb_map_site_datafb_map_site_traits_completenessfb_plot_distribution_site_trait_coveragefb_plot_number_sites_by_speciesfb_plot_number_species_by_traitfb_plot_number_traits_by_speciesfb_plot_site_environmentfb_plot_site_traits_completenessfb_plot_species_traits_completenessfb_plot_species_traits_missingnessfb_plot_trait_combination_frequenciesfb_plot_trait_correlationfb_table_trait_summary

Dependencies:askpassclassclassIntclicpp11curlDBIdplyre1071farvergenericsggplot2gluegtablehttrisobandjsonliteKernSmoothlabelinglifecyclemagrittrMASSmimeopensslpillarpkgconfigproxypurrrR6RColorBrewerRcpprlangrnaturalearths2S7scalessfstringistringrsysterratibbletidyrtidyselectunitsutf8vctrsviridisLitewithrwkxfun

Diagnostic plots in funbiogeo
Naming Convention | Regular Plots | Distribution of Trait Coverage Across Sites | Plotting the Number of Sites by Species | Plotting the Number of Species per Trait | Plotting the Number of Traits per Species | Plotting Environmental Position of Sites | Plotting Trait Coverage for All Sites | Plotting Trait Coverage per Species | Plotting Number of Species with Missing Traits | Displaying Trait Combinations | Displaying Trait Correlations | Maps | Mapping Trait Coverage of Sites | Mapping Arbitrary Site Data | Mapping Site Rasters
Rendered fromdiagnostic-plots.Rmdusingknitr::rmarkdown

Last update: 2026-06-11
Started: 2022-07-01

Formatting your data
Wide vs. Long Format | The fb_format_*() functions | Usage | Extracting Species x Traits Data | Extracting Site x Species Data | Extracting Site x Locations Data | Extracting Species x Categories Data
Rendered fromlong-format.Rmdusingknitr::rmarkdown

Last update: 2026-06-11
Started: 2022-06-21

Get started with funbiogeo
Types of Data | Provided Dataset | Species x Traits | Site x Species | Site x Locations | Species x Categories | Visualizing the Data (Diagnostic plots) | Trait Completeness per Species | Number of Traits per Species | Filtering the Data | Filter trait by Species Coverage | Filter Species by Trait Coverage | Filter Sites by Trait Coverage | Computing Functional Diversity Metrics | Community-Weighted Mean (CWM) | Compute Functional Diversity Indices | Putting Variables on a Map | Mapping Diversity Indices | Mapping an Environmental Raster | Map of Average Environmental Variables in Site | Conclusion | References
Rendered fromfunbiogeo.Rmdusingknitr::rmarkdown

Last update: 2026-06-11
Started: 2021-09-08

Special cases in funbiogeo
Working with Categorical Traits | Considering Intraspecific Variation | Sites of Arbitrary Shapes
Rendered fromspecial_cases.Rmdusingknitr::rmarkdown

Last update: 2026-06-11
Started: 2026-04-11

Upscaling your data: aggregating at coarser scales
Preamble: Getting Site-Level Data | Aggregating Through a Square Grid | Aggregating Through Irregular Polygons | Aggregating Through a SpatRaster Grid | Specific Examples | Coarsening Site x Species Data | Obtaining Back a Site x Species data.frame | Upscaling Functional Diversity Data | Coarsen CWM of Plant Height | Coarser FRic Through fundiversity
Rendered fromupscaling.Rmdusingknitr::rmarkdown

Last update: 2026-06-11
Started: 2022-06-21

Readme and manuals

Help Manual

Help pageTopics
Aggregate Site Data Along Coarser Spatial Gridfb_aggregate_site_data
Count Number of Sites Occupied by Speciesfb_count_sites_by_species
Count Number of Species per Sitefb_count_species_by_site
Count Number of Species for Each Traitfb_count_species_by_trait
Compute Number of Known Trait(s) per Speciesfb_count_traits_by_species
Compute community-weighted means (CWM) of trait valuesfb_cwm
Filter sites with a given species coverage thresholdfb_filter_sites_by_species_coverage
Filter sites with a given trait coverage thresholdfb_filter_sites_by_trait_coverage
Filter species with a given sites coverage thresholdfb_filter_species_by_site_coverage
Filter species with a given traits coverage thresholdfb_filter_species_by_trait_coverage
Filter traits with a given species coverage thresholdfb_filter_traits_by_species_coverage
Extract site x locations information from long format datafb_format_site_locations
Extract site x species information from long format datafb_format_site_species
Extract species x categories information from long format datafb_format_species_categories
Extract species x traits information from long format datafb_format_species_traits
Compute Trait Coverage per Site for Each Traitfb_get_all_trait_coverages_by_site
Extract Raster Values at Location of Sitesfb_get_environment
Compute site trait coverage for each trait combinationfb_get_trait_combination_coverage
Compute Trait Coverage For Each Site Weighted by Abundancefb_get_trait_coverage_by_site
Create an Rmarkdown Report to Explore User Datafb_make_report
Map a Single Raster Layerfb_map_raster
Map Arbitrary Site Datafb_map_site_data
Map Trait Coverage Per Sitefb_map_site_traits_completeness
Plot Distribution of Trait Coverages across all Sitesfb_plot_distribution_site_trait_coverage
Plot Number of Sites by Speciesfb_plot_number_sites_by_species
Plot Number of Species per Traitfb_plot_number_species_by_trait
Plot Number of Traits per Speciesfb_plot_number_traits_by_species
Plot Position of Sites in Environmental Spacefb_plot_site_environment
Plot Trait Coverage per Site for each Traitfb_plot_site_traits_completeness
Plot Trait Coverage per Species for each Traitfb_plot_species_traits_completeness
Plot Trait Coverage per Species for each Traitfb_plot_species_traits_missingness
Plot Present and Missing Trait Combinations Frequenciesfb_plot_trait_combination_frequencies
Plot Trait Correlation Matrixfb_plot_trait_correlation
Summary Table on Traits (Missingness, Range, etc.)fb_table_trait_summary
Species x Categories of some Mediterranean Coniferswoodiv_categories
Sites x Locations of some Mediterranean Coniferswoodiv_locations
Sites x Species of some Mediterranean Coniferswoodiv_site_species
Species x Traits of some Mediterranean Coniferswoodiv_traits