add_funguild_info: Add information about Guild for FUNGI the FUNGuild databse

In adrientaudiere/MiscMetabar: Miscellaneous Functions for Metabarcoding Analysis

Add information about Guild for FUNGI the FUNGuild databse

Description

Please cite Nguyen et al. 2016 (\Sexpr[results=rd]{tools:::Rd_expr_doi("doi:10.1016/j.funeco.2015.06.006")})

Usage

add_funguild_info(
  physeq,
  taxLevels = c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species")
)

Arguments

physeq	(required): a phyloseq-class object obtained using the phyloseq package.
taxLevels	Name of the 7 columns in tax_table required by funguild

Details

This function is mainly a wrapper of the work of others. Please make a reference to FUNGuildR package and the associate publication (\Sexpr[results=rd]{tools:::Rd_expr_doi("10.1016/j.funeco.2015.06.006")}) if you use this function.

Value

A new object of class physeq with Guild information added to tax_table slot

Author(s)

Adrien Taudière

See Also

plot_guild_pq()

Examples

if (requireNamespace("httr")) {
  d_fung_mini <- add_funguild_info(data_fungi_mini,
    taxLevels = c(
      "Domain",
      "Phylum",
      "Class",
      "Order",
      "Family",
      "Genus",
      "Species"
    )
  )
  sort(table(d_fung_mini@tax_table[, "guild"]), decreasing = TRUE)
}

adrientaudiere/MiscMetabar documentation built on Oct. 13, 2024, 9:42 p.m.