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Retrieve WoRMS Records with Retry Mechanism

Source: R/ifcb_match_taxa_names.R
ifcb_match_taxa_names.Rd

[Superseded]

This function has been superseded by SHARK4R::match_worms_taxa() or worrms::wm_records_names(). It will not receive new features, but will continue to receive critical bug fixes as needed.

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

[Deprecated] 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

# \donttest{
# 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 as tibble
print(records)
#> # A tibble: 3 × 29
#>   name  AphiaID url   scientificname authority status unacceptreason taxonRankID
#>   <chr>   <int> <chr> <chr>          <chr>     <chr>  <lgl>                <int>
#> 1 Cala…  104464 http… Calanus finma… (Gunneru… accep… NA                     220
#> 2 Thal…  148934 http… Thalassiosira… Hasle & … unass… NA                     220
#> 3 Phae…  175584 http… Phaeodactylum… Bohlin, … unass… NA                     220
#> # ℹ 21 more variables: rank <chr>, valid_AphiaID <int>, valid_name <chr>,
#> #   valid_authority <chr>, parentNameUsageID <int>, originalNameUsageID <int>,
#> #   kingdom <chr>, phylum <chr>, class <chr>, order <chr>, family <chr>,
#> #   genus <chr>, citation <chr>, lsid <chr>, isMarine <int>, isBrackish <int>,
#> #   isFreshwater <int>, isTerrestrial <int>, isExtinct <int>, match_type <chr>,
#> #   modified <chr>
# }