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]

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funbiogeo.pdf |funbiogeo.html✨
funbiogeo/json (API)
NEWS

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

Peer review:

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

Datasets:

On CRAN:

functional-biogeography

34 exports 9 stars 1.69 score 49 dependencies 8 scripts

Last updated 2 months agofrom:3c7d5d1c6e. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKAug 24 2024
R-4.5-winNOTEAug 24 2024
R-4.5-linuxNOTEAug 24 2024
R-4.4-winNOTEAug 24 2024
R-4.4-macNOTEAug 24 2024
R-4.3-winNOTEAug 24 2024
R-4.3-macNOTEAug 24 2024

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:classclassIntclicolorspacecpp11DBIdplyre1071fansifarvergenericsggplot2gluegtableisobandKernSmoothlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigproxypurrrR6RColorBrewerRcpprlangs2scalessfstringistringrterratibbletidyrtidyselectunitsutf8vctrsviridisLitewithrwkxfun

Diagnostic Plots in funbiogeo

Rendered fromdiagnostic-plots.Rmdusingknitr::rmarkdownon Aug 24 2024.

Last update: 2024-07-25
Started: 2022-07-01

Formatting your data

Rendered fromlong-format.Rmdusingknitr::rmarkdownon Aug 24 2024.

Last update: 2023-05-24
Started: 2022-06-21

Get started with funbiogeo

Rendered fromfunbiogeo.Rmdusingknitr::rmarkdownon Aug 24 2024.

Last update: 2024-04-09
Started: 2021-09-08

Upscaling your data

Rendered fromupscaling.Rmdusingknitr::rmarkdownon Aug 24 2024.

Last update: 2023-05-28
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 R Markdown Report on Site/Species/Trait Coverage with Plotsfb_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
Sites x Locations of Western Europe Mammalssite_locations
Sites x Species of Western Europe Mammalssite_species
Species x Categories of Western Europe Mammalsspecies_categories
Species x Traits of Western Europe Mammalsspecies_traits