Check for taxa occurrences within a radius around multiple samples using GBIF data

<a href="https://adrientaudiere.github.io/MiscMetabar/articles/Rules.html#lifecycle"> <img src="https://img.shields.io/badge/lifecycle-experimental-orange" alt="lifecycle-experimental"></a>

This function performs a species range check for taxa contained in a phyloseq object, for multiple samples based on their geographic coordinates (longitude and latitude).

Usage

tax_occur_multi_check_pq(
  physeq = NULL,
  taxonomic_rank = "currentCanonicalSimple",
  min_occur = 0,
  verbose = TRUE,
  lon_column = NULL,
  longitudes = NULL,
  lat_column = NULL,
  latitudes = NULL,
  radius_km = 50,
  n_occur = 1000,
  method = c("download", "search"),
  circle_form = TRUE,
  clean_coord = TRUE,
  clean_coord_verbose = FALSE,
  discard_genus_alone = identical(taxonomic_rank, "currentCanonicalSimple"),
  discard_NA = TRUE,
  ...
)

Arguments

physeq

(required) A phyloseq object.

taxonomic_rank

The taxonomic rank to use for the check. Default is "currentCanonicalSimple" which corresponds to the cleaned scientific names in the phyloseq object if [gna_verifier_pq()] was used with default parameter.

min_occur

Minimum number of occurrences in the radius to keep the taxon (default: 0).

verbose

(Logical, default: TRUE). Whether to print progress messages.

lon_column

Column name in sample_data containing longitudes.

longitudes

Vector of longitudes corresponding to samples in the phyloseq object. If provided, it overrides lon_column.

lat_column

Column name in sample_data containing latitudes.

latitudes

Vector of latitudes corresponding to samples in the phyloseq object. If provided, it overrides lat_column.

radius_km

Numeric. Search radius in kilometers (default: 50). See ?[tax_occur_check_pq()].

n_occur

Numeric (default: 1000). Maximum number of occurrences to retrieve from GBIF for each taxon.

method

(character, default `"download"`). How occurrences are fetched. `"download"` issues a **single** [rgbif::occ_download()] covering all taxa over the bounding box of every GPS point (**requires GBIF credentials**); `"search"` uses a per-taxon [rgbif::occ_search()] loop. See [tax_occur_check()].

circle_form

(Logical, default: TRUE). Whether to use a circular search area. If FALSE, a square bounding box is used.

clean_coord

(Logical, default: TRUE). Whether to clean coordinates using `CoordinateCleaner`.

clean_coord_verbose

(Logical, default: FALSE). Whether to print messages from `CoordinateCleaner`.

discard_genus_alone

(logical, default `TRUE` when `taxonomic_rank == "currentCanonicalSimple"`). Passed to [taxonomic_rank_to_taxnames()].

discard_NA

(logical, default `TRUE`). Passed to [taxonomic_rank_to_taxnames()].

...

Additional parameters (currently unused; reserved for forward compatibility).

Value

A list containing: - A tibble resulting from the concatenation of result of function [tax_occur_check()] for each GPS position. - A matrix of samples x taxa with the number of occurrences in the radius for each case of the matrix. - A new phyloseq object with taxa filtered based on min_occur. Be careful, the filtering may be very stringent.

See also

[tax_occur_check()], [tax_occur_multi_pq()]

Author

Adrien Taudiere

Examples

if (FALSE) { # \dontrun{
data_fungi_mini_cleanNames <-
  gna_verifier_pq(data_fungi_mini,
    data_sources = 210
  )
res_occur_check <-
  tax_occur_multi_check_pq(subset_samples(data_fungi_mini_cleanNames, Diameter == 52),
    longitudes = c(8.31, 8.31, 8.64, -1.19, 7.03),
    latitudes = c(47.38, 47.38, 45.83, 43.65, 43.93)
  )
} # }