Package: funbiogeo 0.0.1

Nicolas Casajus

funbiogeo: Streamlining Functional Biogeography Analyses

Helps users with analyses in functional biogeography 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_0.0.1.tar.gz
funbiogeo_0.0.1.zip(r-4.7)funbiogeo_0.0.1.zip(r-4.6)funbiogeo_0.0.1.zip(r-4.5)
funbiogeo_0.0.1.tgz(r-4.6-any)funbiogeo_0.0.1.tgz(r-4.5-any)
funbiogeo_0.0.1.tar.gz(r-4.7-any)funbiogeo_0.0.1.tar.gz(r-4.6-any)
funbiogeo_0.0.1.tgz(r-4.6-emscripten)
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:

woodiv_categories - Species x Categories of some Mediterranean Conifers
woodiv_locations - Sites x Locations of some Mediterranean Conifers
woodiv_site_species - Sites x Species of some Mediterranean Conifers
woodiv_traits - Species x Traits of some Mediterranean Conifers

On CRAN:

functional-biogeography functional-diversity functional-trait

5.30 score 12 stars 24 scripts 34 exports 51 dependencies

Last updated from:c9d1fb08a3. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	268
source / vignettes	OK	266
linux-release-x86_64	OK	258
macos-release-arm64	OK	149
macos-oldrel-arm64	OK	146
windows-devel	OK	194
windows-release	OK	189
windows-oldrel	OK	200
wasm-release	OK	184

Exports:fb_aggregate_site_data fb_count_sites_by_species fb_count_species_by_site fb_count_species_by_trait fb_count_traits_by_species fb_cwm fb_filter_sites_by_species_coverage fb_filter_sites_by_trait_coverage fb_filter_species_by_site_coverage fb_filter_species_by_trait_coverage fb_filter_traits_by_species_coverage fb_format_site_locations fb_format_site_species fb_format_species_categories fb_format_species_traits fb_get_all_trait_coverages_by_site fb_get_environment fb_get_trait_combination_coverage fb_get_trait_coverage_by_site fb_make_report fb_map_raster fb_map_site_data fb_map_site_traits_completeness fb_plot_distribution_site_trait_coverage fb_plot_number_sites_by_species fb_plot_number_species_by_trait fb_plot_number_traits_by_species fb_plot_site_environment fb_plot_site_traits_completeness fb_plot_species_traits_completeness fb_plot_species_traits_missingness fb_plot_trait_combination_frequencies fb_plot_trait_correlation fb_table_trait_summary

Dependencies:askpass class classInt cli cpp11 curl DBI dplyr e1071 farver generics ggplot2 glue gtable httr isoband jsonlite KernSmooth labeling lifecycle magrittr MASS mime openssl pillar pkgconfig proxy purrr R6 RColorBrewer Rcpp rlang rnaturalearth s2 S7 scales sf stringi stringr sys terra tibble tidyr tidyselect units utf8 vctrs viridisLite withr wk xfun

Get started with funbiogeo

Rendered fromfunbiogeo.Rmdusingknitr::rmarkdown

Last update: 2026-07-08
Started: 2021-09-08

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Aggregate Site Data Along Coarser Spatial Grid	fb_aggregate_site_data
Count Number of Sites Occupied by Species	fb_count_sites_by_species
Count Number of Species per Site	fb_count_species_by_site
Count Number of Species for Each Trait	fb_count_species_by_trait
Compute Number of Known Trait(s) per Species	fb_count_traits_by_species
Compute community-weighted means (CWM) of trait values	fb_cwm
Filter sites with a given species coverage threshold	fb_filter_sites_by_species_coverage
Filter sites with a given trait coverage threshold	fb_filter_sites_by_trait_coverage
Filter species with a given sites coverage threshold	fb_filter_species_by_site_coverage
Filter species with a given traits coverage threshold	fb_filter_species_by_trait_coverage
Filter traits with a given species coverage threshold	fb_filter_traits_by_species_coverage
Extract site x locations information from long format data	fb_format_site_locations
Extract site x species information from long format data	fb_format_site_species
Extract species x categories information from long format data	fb_format_species_categories
Extract species x traits information from long format data	fb_format_species_traits
Compute Trait Coverage per Site for Each Trait	fb_get_all_trait_coverages_by_site
Extract Raster Values at Location of Sites	fb_get_environment
Compute site trait coverage for each trait combination	fb_get_trait_combination_coverage
Compute Trait Coverage For Each Site Weighted by Abundance	fb_get_trait_coverage_by_site
Create an Rmarkdown Report to Explore User Data	fb_make_report
Map a Single Raster Layer	fb_map_raster
Map Arbitrary Site Data	fb_map_site_data
Map Trait Coverage Per Site	fb_map_site_traits_completeness
Plot Distribution of Trait Coverages across all Sites	fb_plot_distribution_site_trait_coverage
Plot Number of Sites by Species	fb_plot_number_sites_by_species
Plot Number of Species per Trait	fb_plot_number_species_by_trait
Plot Number of Traits per Species	fb_plot_number_traits_by_species
Plot Position of Sites in Environmental Space	fb_plot_site_environment
Plot Trait Coverage per Site for each Trait	fb_plot_site_traits_completeness
Plot Trait Coverage per Species for each Trait	fb_plot_species_traits_completeness
Plot Trait Coverage per Species for each Trait	fb_plot_species_traits_missingness
Plot Present and Missing Trait Combinations Frequencies	fb_plot_trait_combination_frequencies
Plot Trait Correlation Matrix	fb_plot_trait_correlation
Summary Table on Traits (Missingness, Range, etc.)	fb_table_trait_summary
Species x Categories of some Mediterranean Conifers	woodiv_categories
Sites x Locations of some Mediterranean Conifers	woodiv_locations
Sites x Species of some Mediterranean Conifers	woodiv_site_species
Species x Traits of some Mediterranean Conifers	woodiv_traits