Get and plot the range of taxa within a bioregion using gbif.range package

A wrapper of [gbif.range::get_gbif()] and [gbif.range::get_range()] functions to get and plot the range of taxa using ggplot2. The function takes a phyloseq object as input and extracts the taxonomic names from the specified taxonomic rank. The occurrences are plotted as points on a map, along with the range of the taxon within a specified bioregion. The bioregion used is "eco_terra", which corresponds to terrestrial ecoregions defined by the World Wildlife Fund (WWF).

Usage

range_bioreg_pq(
  physeq = NULL,
  taxnames = NULL,
  taxonomic_rank = "currentCanonicalSimple",
  occ_samp = 5000,
  verbose = TRUE,
  verbose_gbif_range = FALSE,
  make_plot = FALSE,
  crop_plot = TRUE,
  remove_legend = TRUE,
  discard_genus_alone = taxonomic_rank == "currentCanonicalSimple",
  discard_NA = TRUE,
  ...
)

plot_range_bioreg_pq(...)

Arguments

physeq: (optional) A phyloseq object. Either `physeq` or `taxnames` must be provided, but not both.
taxnames: (optional) A character vector of taxonomic names.
taxonomic_rank: (Character, default "currentCanonicalSimple") The column(s) present in the @tax_table slot of the phyloseq object. Can be a vector of two columns (e.g. c("Genus", "Species")).
occ_samp: (Numeric, default 5000) Number of occurrences to sample from GBIF. See [gbif.range::get_gbif()] for more details.
verbose: (logical, default TRUE) If TRUE, prompt some messages.
verbose_gbif_range: (logical, default TRUE) If TRUE, prompt some messages from gbif.range functions.
make_plot: (logical, default TRUE) If TRUE, return a list of ggplot objects. Else return a list of range outputs from [gbif.range::get_range()].
crop_plot: (logical, default TRUE) If TRUE, crop the plot to the extent of the bioregion.
remove_legend: (logical, default TRUE) If TRUE, remove the legend from the plot.
...: Additional arguments to pass to [gbif.range::get_gbif()].

Value

If make_plot = TRUE (default), a list of ggplot objects, one for each taxon. If make_plot = FALSE, a list of range outputs from [gbif.range::get_range()].

Details

[plot_range_bioreg_pq()] is a wrapper of just a shortcut for `range_bioreg_pq(..., make_plot = TRUE)`.

Author

Adrien Taudiere

Examples

if (FALSE) { # \dontrun{

data_fungi_mini_cleanNames <- gna_verifier_pq(data_fungi_mini, data_source = 210)

res_range <- range_bioreg_pq(subset_taxa(
  data_fungi_mini_cleanNames,
  currentCanonicalSimple %in% c("Xylodon flaviporus", "Basidiodendron eyrei")
), occ_samp = 100)

p <- plot_range_bioreg_pq(subset_taxa(
  data_fungi_mini_cleanNames,
  currentCanonicalSimple %in% c("Xylodon flaviporus", "Basidiodendron eyrei")
), occ_samp = 100)

requireNamespace("patchwork")
p[[1]] / p[[2]]

p <- plot_range_bioreg_pq(subset_taxa_pq(
  data_fungi_mini_cleanNames,
  taxa_sums(data_fungi_mini) > 20000
), occ_samp = 500)

p[[1]] / p[[2]]
} # }