iRfcb (version 0.5.1)

ifcb_is_diatom: Identify Diatoms in Taxa List

Description

This function takes a list of taxa names, cleans them, retrieves their corresponding classification records from the World Register of Marine Species (WoRMS), and checks if they belong to the specified diatom class. The function only uses the first name (genus name) of each taxa for classification.

Usage

ifcb_is_diatom(
  taxa_list,
  diatom_class = "Bacillariophyceae",
  max_retries = 3,
  sleep_time = 10,
  marine_only = FALSE,
  fuzzy = deprecated(),
  verbose = TRUE
)

Value

A logical vector indicating whether each cleaned taxa name belongs to the specified diatom class.

Arguments

taxa_list

A character vector containing the list of taxa names.

diatom_class

A character string or vector specifying the class name(s) to be identified as diatoms, according to WoRMS. Default is "Bacillariophyceae".

max_retries

An integer specifying the maximum number of attempts to retrieve WoRMS records in case of an error. Default is 3.

sleep_time

A numeric value indicating the number of seconds to wait between retry attempts. Default is 10 seconds.

marine_only

Logical. If TRUE, restricts the search to marine taxa only. Default is FALSE.

fuzzy

The fuzzy argument is no longer available

verbose

A logical indicating whether to print progress messages. Default is TRUE.

See Also

https://www.marinespecies.org/

Examples

if (FALSE) {
taxa_list <- c("Nitzschia_sp", "Chaetoceros_sp", "Dinophysis_norvegica", "Thalassiosira_sp")
ifcb_is_diatom(taxa_list)
}