ifcb_match_taxa_names: Retrieve WoRMS Records with Retry Mechanism

In iRfcb: Tools for Managing Imaging FlowCytobot (IFCB) Data

Retrieve WoRMS Records with Retry Mechanism

Description

This function attempts to retrieve WoRMS records using the provided taxa names. It retries the operation if an error occurs, up to a specified number of attempts.

Usage

ifcb_match_taxa_names(
  taxa_names,
  best_match_only = TRUE,
  max_retries = 3,
  sleep_time = 10,
  marine_only = FALSE,
  return_list = FALSE,
  verbose = TRUE,
  fuzzy = deprecated()
)

Arguments

taxa_names	A character vector of taxa names to retrieve records for.
best_match_only	A logical value indicating whether to automatically select the first match and return a single match. Default is TRUE.
max_retries	An integer specifying the maximum number of attempts to retrieve records.
sleep_time	A numeric value indicating the number of seconds to wait between retry attempts.
marine_only	Logical. If TRUE, restricts the search to marine taxa only. Default is FALSE.
return_list	A logical value indicating whether to to return the output as a list. Default is FALSE, where the result is returned as a dataframe.
verbose	A logical indicating whether to print progress messages. Default is TRUE.
fuzzy	The fuzzy argument is no longer available

Value

A data frame (or list if return_list is TRUE) of WoRMS records or NULL if the retrieval fails after the maximum number of attempts.

Examples

## Not run: 
# Example: Retrieve WoRMS records for a list of taxa names
taxa <- c("Calanus finmarchicus", "Thalassiosira pseudonana", "Phaeodactylum tricornutum")

# Call the function
records <- ifcb_match_taxa_names(taxa_names = taxa,
                                 max_retries = 3,
                                 sleep_time = 5,
                                 marine_only = TRUE,
                                 verbose = TRUE)

print(records)

## End(Not run)

iRfcb documentation built on June 8, 2025, 12:43 p.m.