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Get number of occurrences for each taxa of a phyloseq object

Source: R/tax_gbif_occur_pq.R
tax_gbif_occur_pq.Rd

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A wrapper of [rgbif::occ_search()] function to get the number of occurences. Optionally, the number of occurrences can be obtained by years or by country.

Usage

tax_gbif_occur_pq(
  physeq = NULL,
  taxnames = NULL,
  taxonomic_rank = "currentCanonicalSimple",
  add_to_phyloseq = NULL,
  col_prefix = NULL,
  by_country = FALSE,
  by_years = FALSE,
  verbose = TRUE,
  time_to_sleep = 0.3,
  discard_genus_alone = identical(taxonomic_rank, "currentCanonicalSimple"),
  discard_NA = TRUE
)

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")).

add_to_phyloseq

(logical, default TRUE when physeq is provided, FALSE when taxnames is provided) If TRUE, add new column(s) in the tax_table of the phyloseq object. Automatically set to TRUE when a phyloseq object is provided and FALSE when taxnames is provided. Cannot be TRUE if `taxnames` is provided.

col_prefix

A character string to be added as a prefix to the new columns names added to the tax_table slot of the phyloseq object (default: NULL).

by_country

(logical, default FALSE) If TRUE, the number of occurences is computed by country

by_years

(logical, default FALSE) If TRUE, the number of occurences is computed by years

verbose

(logical, default TRUE) If TRUE, prompt some messages.

time_to_sleep

(numeric, default 0.3) Time to sleep between two calls to rgbif::occ_search(). Useful to avoid to be blocked by GBIF. Try to increase this value if you are blocked by the error "To download GBIF occurrence data in bulk, please request..."

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()].

Value

Either a tibble (if add_to_phyloseq = FALSE) or a new phyloseq object, if add_to_phyloseq = TRUE, with new column(s) in the tax_table.

Details

This function is mainly a wrapper of the work of others. Please cite `rgbif` package.

See also

[rgbif::occ_search()], [plot_tax_gbif_pq()], [tax_occurr_pq()]

Author

Adrien Taudiere

Examples

if (FALSE) { # \dontrun{
data_fungi_mini_cleanNames <-
  gna_verifier_pq(data_fungi_mini)

data_fungi_mini_cleanNames <- tax_gbif_occur_pq(data_fungi_mini_cleanNames, by_country = TRUE)

# Get data without adding to phyloseq
tax_gbif_occur_pq(data_fungi_mini_cleanNames, add_to_phyloseq = FALSE)
tax_gbif_occur_pq(data_fungi_mini_cleanNames, by_years = TRUE, add_to_phyloseq = FALSE)

# Using taxnames vector (returns a tibble)
tax_gbif_occur_pq(taxnames = c("Amanita muscaria", "Boletus edulis"))
ggplot(
  data_fungi_mini_cleanNames@tax_table,
  aes(y = log10(as.numeric(Global_occurences)), x = currentCanonicalSimple)
) +
  geom_col() +
  geom_col(aes(y = -log10(as.numeric(FR))), fill = "blue") +
  coord_flip() +
  xlab("Number of occurences (log10 scale) at global (grey) scale and in France (blue)")
} # }