fg_assign: Assign FUNGuild data

In hjsimpso/fungarium: An R package for enabling the use of fungaria collection data in comprehensive trait analyses

Assign FUNGuild data

Description

Assigns FUNGuild data (e.g. trophic mode, functional guild, etc) to taxa listed in a dataframe using the FUNGuild database (PLEASE CITE:Nguyen et al. 2016).

Usage

fg_assign(
  tax_table,
  url = "http://www.stbates.org/funguild_db.php",
  tax_cols = c("new_phylum", "new_class", "new_order", "new_family", "new_genus",
    "new_species")
)

Arguments

tax_table	Data.frame of taxonomic classifications (e.g. phylum, class, order, family, genus, and species names)
url	URL where FUNGuild database lives. Current default: http://www.stbates.org/funguild_db.php.
tax_cols	Character vector specifying the column names containing taxonomic variables. Names must be in descending order of taxonomic rank. Default is c("new_phylum", "new_class", "new_order", "new_family", "new_genus", "new_species").

Value

      Returns the input data.frame with FUNGuild assignments appended.

References

1. Nguyen NH, Song Z, Bates ST, Branco S, Tedersoo L, Menke J, Schilling JS, Kennedy PG. 2016. FUNGuild: An open annotation tool for parsing fungal community datasets by ecological guild. Fungal Ecology, 20: 241-248. doi:10.1016/j.funeco.2015.06.006

Examples

library(fungarium)
data(agaricales_updated) #import sample dataset with updated taxon names

#get funguild assignments
agaricales_fg <- fg_assign(agaricales_updated)

hjsimpso/fungarium documentation built on Aug. 23, 2023, 3:59 p.m.