Retrieve WoRMS records

This function retrieves records from the WoRMS (World Register of Marine Species) database using the worrms R package for a given list of Aphia IDs. If the retrieval fails, it retries a specified number of times before stopping.

Usage

get_worms_records(
  aphia_ids,
  max_retries = 3,
  sleep_time = 10,
  verbose = TRUE,
  aphia_id = deprecated()
)

Arguments

aphia_ids

A vector of Aphia IDs for which records should be retrieved.

max_retries

An integer specifying the maximum number of retry attempts for each Aphia ID in case of failure. Default is 3.

sleep_time

A numeric value specifying the time (in seconds) to wait between retry attempts. Default is 10 seconds.

verbose

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

aphia_id

Use aphia_ids instead.

Value

A tibble containing the retrieved WoRMS records for the provided Aphia IDs. Each row corresponds to one Aphia ID.

Details

The function attempts to fetch records for each Aphia ID in the provided vector. If a retrieval fails, it retries up to the specified max_retries, with a pause of sleep_time seconds between attempts. If all retries fail for an Aphia ID, the function stops with an error message.

See also

https://marinespecies.org/ for WoRMS website.

https://CRAN.R-project.org/package=worrms

Examples

# \donttest{
# Example usage with a vector of Aphia IDs
aphia_ids <- c(12345, 67890, 112233)
worms_records <- get_worms_records(aphia_ids, verbose = FALSE)

print(worms_records)
#> # A tibble: 3 × 28
#>   AphiaID status url   scientificname authority unacceptreason taxonRankID rank 
#>     <dbl> <chr>  <chr> <chr>          <chr>     <lgl>                <int> <chr>
#> 1   12345 no co… NA    NA             NA        NA                      NA NA   
#> 2   67890 no co… NA    NA             NA        NA                      NA NA   
#> 3  112233 accep… http… Nonionella     Cushman,… NA                     180 Genus
#> # ℹ 20 more variables: 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 <lgl>,
#> #   isFreshwater <int>, isTerrestrial <int>, isExtinct <int>, match_type <chr>,
#> #   modified <chr>
# }