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GDRarity GDRarity logo

An R package for the Global Model of Discretized Rarity

Overview

The Global Model of Discretized Rarity (GDR) integrates geographic, functional, and phylogenetic dimensions of rarity at regional and local scales. GDRarity is an R package that characterizes the GDR and its 63 restrictions.

Its webpage is at https://anytko.github.io/GDRarity/; its source code is at https://github.com/anytko/GDRarity.

Installation

You can install the development version of GDRarity like so:

devtools::install_github("anytko/GDRarity")

Features

  • Automates restriction selection based on available data.
  • Characterizes the rarity of species using multiple restrictions simultaneously.
  • Tests various methods of calculating geographic, functional, and phylogenetic dimensions of rarity and rarity thresholding.
  • Analyzes restriction performance in explaining a response variable (i.e. biological processes).
  • Accepts additional, user specified dimensions of rarity to create or augment new restrictions of the GDR.

Caveats

  • Only pulls plant trait data from the LEDA and BIEN plant trait databases.
  • Certain methods, such as calculating regional geographic rarity using extent of occurrence (range size) requires an internet connection and can be computationally intensive.
  • Does not incorporate Rabinowitz Rarity as a GDR restriction, but habitat specificity can be added as an additional, user specified dimension of rarity.

Example

The 63 restrictions of the GDR can be applied using phylogeny, species, abundance, and trait data within one function.

species_70_path <- system.file("extdata", "species_70.csv", package = "GDRarity")
abundance_70_path <- system.file("extdata", "abundance_70.csv", package = "GDRarity")

species_70 <- read.csv(species_70_path)
abundance_70 <- read.csv(abundance_70_path)

all_restrictions <- gdrare_pipeline(
      species_df = species_70,
      abundance_df = abundance_70,
      trait_cols = c("SLA", "seed_mass", "canopy_height"),
      geo_rarity_method = "taxonomic",
      fun_rarity_method = "min_distance")

Results of Restriction GRFLPR

all_restrictions %>%
  select(species, GR_raw, FL_raw, PR_raw, GRFLPR) %>%
  head(6) %>%
  mutate(across(where(is.numeric), ~ round(., 3))) %>%  
  knitr::kable()
species GR_raw FL_raw PR_raw GRFLPR
Acer_campestre 0.656 0.409 2.193 GR-FL+PR-
Alnus_glutinosa 0.447 0.237 2.442 GR-FL-PR-
Alopecurus_myosuroides 0.825 0.144 -1.178 GR-FL-PR-
Anthemis_cotula 0.871 0.134 -0.008 GR-FL-PR-
Arum_maculatum 0.565 0.423 3.105 GR-FL+PR+
Calluna_vulgaris 0.446 0.129 -0.564 GR-FL-PR-