Function reference • funbiogeo

Included Datasets

species_traits: Species x Traits of Western Europe Mammals

site_species: Sites x Species of Western Europe Mammals

site_locations: Sites x Locations of Western Europe Mammals

species_categories: Species x Categories of Western Europe Mammals

Formatting Functions

Transform your raw dataset to the expected format by funbiogeo

fb_format_site_locations(): Extract site x locations information from long format data

fb_format_site_species(): Extract site x species information from long format data

fb_format_species_categories(): Extract species x categories information from long format data

fb_format_species_traits(): Extract species x traits information from long format data

Coverage functions

Count species, traits, sites by trait/species coverage (proportion of species with known traits/present). Also filter datasets based on their coverages.

Count functions

fb_count_sites_by_species(): Count Number of Sites Occupied by Species

fb_count_species_by_site(): Count Number of Species per Site

fb_count_species_by_trait(): Count Number of Species for Each Trait

fb_count_traits_by_species(): Compute Number of Known Trait(s) per Species

Trait coverage functions

fb_get_trait_combination_coverage(): Compute site trait coverage for each trait combination

fb_get_trait_coverage_by_site(): Compute Trait Coverage For Each Site Weighted by Abundance

fb_get_all_trait_coverages_by_site(): Compute Trait Coverage per Site for Each Trait

Filtering functions

fb_filter_sites_by_species_coverage(): Filter sites with a given species coverage threshold

fb_filter_sites_by_trait_coverage(): Filter sites with a given trait coverage threshold

fb_filter_species_by_site_coverage(): Filter species with a given sites coverage threshold

fb_filter_species_by_trait_coverage(): Filter species with a given traits coverage threshold

fb_filter_traits_by_species_coverage(): Filter traits with a given species coverage threshold

Functional Diversity Functions

fb_cwm(): Compute community-weighted means (CWM) of trait values

Upscaling functions

Aggregate your site data over a coarser spatial grid

fb_get_environment(): Extract Raster Values at Location of Sites

fb_aggregate_site_data(): Aggregate Site Data Along Coarser Spatial Grid

Visualization & Summary functions

Maps

fb_map_raster(): Map a Single Raster Layer

fb_map_site_data(): Map Arbitrary Site Data

fb_map_site_traits_completeness(): Map Trait Coverage Per Site

Regular plots and summary

fb_plot_distribution_site_trait_coverage(): Plot Distribution of Trait Coverages across all Sites

fb_plot_number_sites_by_species(): Plot Number of Sites by Species

fb_plot_number_species_by_trait(): Plot Number of Species per Trait

fb_plot_number_traits_by_species(): Plot Number of Traits per Species

fb_plot_site_environment(): Plot Position of Sites in Environmental Space

fb_plot_site_traits_completeness(): Plot Trait Coverage per Site for each Trait

fb_plot_species_traits_completeness(): Plot Trait Coverage per Species for each Trait

fb_plot_trait_combination_frequencies(): Plot Present and Missing Trait Combinations Frequencies

fb_plot_trait_correlation(): Plot Trait Correlation Matrix

fb_table_trait_summary(): Summary Table on Traits (Missingness, Range, etc.)

Pre-analysis R Markdown report

fb_make_report(): Create an R Markdown Report on Site/Species/Trait Coverage with Plots