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Identify Diatoms in Taxa List

Source: R/ifcb_is_diatom.R
ifcb_is_diatom.Rd

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",
  diatom_include = NULL,
  max_retries = 3,
  sleep_time = 10,
  marine_only = FALSE,
  details = FALSE,
  fuzzy = deprecated(),
  verbose = TRUE
)

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".

diatom_include

Optional character vector of taxa (or genera) that should always be treated as diatoms, overriding the WoRMS-based classification. Default is NULL.

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.

details

Logical. If TRUE, return a data frame with the resolved WoRMS class for each taxon instead of a logical vector. This is useful for auditing genus homonyms, i.e. diatom genera (such as Navicula or Actinocyclus) whose names are shared with animals and may therefore resolve to a non-diatom class in WoRMS. Inspect the worms_class column to spot such cases and add the affected taxa to diatom_include. Default is FALSE.

fuzzy

[Deprecated] The fuzzy argument is no longer available

verbose

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

Value

If details = FALSE (the default), a logical vector indicating whether each cleaned taxa name belongs to the specified diatom class. If details = TRUE, a tibble with one row per input taxon and the columns taxa (the original input), genus (the genus name used for matching), worms_class (the class resolved from WoRMS, or NA if no record was found) and is_diatom (the logical classification, including any diatom_include override).

See also

https://www.marinespecies.org/

Examples

# \donttest{
# Example taxa
taxa_list <- c("Nitzschia_sp", "Chaetoceros_sp", "Dinophysis_norvegica", "Thalassiosira_sp")

res <- ifcb_is_diatom(taxa_list)
print(res)
#> [1]  TRUE  TRUE FALSE  TRUE
# }