assign_phytoplankton_group: Assign phytoplankton group to scientific names

Description

This function assigns default phytoplankton groups (Diatoms, Dinoflagellates, Cyanobacteria, or Other) to a list of scientific names or Aphia IDs by retrieving species information from the World Register of Marine Species (WoRMS). The function checks both Aphia IDs and scientific names, handles missing records, and assigns the appropriate plankton group based on taxonomic classification in WoRMS. Additionally, custom plankton groups can be specified using the custom_groups parameter, allowing users to define additional classifications based on specific taxonomic criteria.

Usage

assign_phytoplankton_group(
  scientific_names,
  aphia_ids = NULL,
  diatom_class = c("Bacillariophyceae", "Coscinodiscophyceae", "Mediophyceae",
    "Diatomophyceae"),
  dinoflagellate_class = "Dinophyceae",
  cyanobacteria_class = "Cyanophyceae",
  cyanobacteria_phylum = "Cyanobacteria",
  match_first_word = TRUE,
  marine_only = FALSE,
  return_class = FALSE,
  custom_groups = list(),
  verbose = TRUE
)

Value

A tibble with two columns: scientific_name and plankton_group, where the plankton group is assigned based on taxonomic classification.

Arguments

scientific_names: A character vector of scientific names of marine species.
aphia_ids: A numeric vector of Aphia IDs corresponding to the scientific names. If provided, it improves the accuracy and speed of the matching process. The length of aphia_ids must match the length of scientific_names. Defaults to NULL, in which case the function will attempt to assign plankton groups based only on the scientific names.
diatom_class: A character string or vector representing the diatom class. Default is "Bacillariophyceae", "Coscinodiscophyceae", "Mediophyceae" and "Diatomophyceae".
dinoflagellate_class: A character string or vector representing the dinoflagellate class. Default is "Dinophyceae".
cyanobacteria_class: A character string or vector representing the cyanobacteria class. Default is "Cyanophyceae".
cyanobacteria_phylum: A character string or vector representing the cyanobacteria phylum. Default is "Cyanobacteria".
match_first_word: A logical value indicating whether to match the first word of the scientific name if the Aphia ID is missing. Default is TRUE.
marine_only: A logical value indicating whether to restrict the results to marine taxa only. Default is FALSE.
return_class: A logical value indicating whether to include class information in the result. Default is FALSE.
custom_groups: A named list of additional custom plankton groups (optional). The names of the list correspond to the custom group names (e.g., "Cryptophytes"), and the values should be character vectors specifying one or more of the following taxonomic levels: phylum, class, order, family, genus, or scientific_name. For example: list("Green Algae" = list(class = c("Chlorophyceae", "Ulvophyceae"))). This allows users to extend the default classifications (e.g., Cyanobacteria, Diatoms, Dinoflagellates) with their own groups.
verbose: A logical value indicating whether to print progress messages. Default is TRUE.

Details

The aphia_ids parameter is not necessary but, if provided, will improve the certainty of the matching process. If aphia_ids are available, they will be used directly to retrieve more accurate WoRMS records. If missing, the function will attempt to match the scientific names to Aphia IDs by querying WoRMS using the scientific name(s), with an additional fallback mechanism to match based on the first word of the scientific name.

To skip one of the default plankton groups, you can set the class or phylum of the respective group to an empty string (""). For example, to skip the "Cyanobacteria" group, you can set cyanobacteria_class = "" or cyanobacteria_phylum = "". These taxa will then be placed in Others.

Custom groups are processed in the order they appear in the custom_groups list. If a taxon matches multiple custom groups, it will be assigned to the group that appears last in the list, as later matches overwrite earlier ones. For example, if Teleaulax amphioxeia matches both Cryptophytes (class-based) and a specific group Teleaulax (name-based), it will be assigned to Teleaulax if Teleaulax is listed after Cryptophytes in the custom_groups list.

Examples

Run this code

# \donttest{
# Assign plankton groups to a list of species names
try(result <- assign_phytoplankton_group(
  scientific_names = c("Tripos fusus", "Diatoma", "Nodularia spumigena", "Octactis speculum"),
  verbose = FALSE))

if (exists("result")) print(result)

# Improve classification by explicitly providing Aphia IDs for ambiguous taxa
# Actinocyclus and Navicula are names shared by both diatoms and animals,
# which can lead to incorrect group assignment without an Aphia ID
try(result <- assign_phytoplankton_group(
  scientific_names = c("Actinocyclus", "Navicula", "Nodularia spumigena", "Tripos fusus"),
  aphia_ids = c(148944, 149142, NA, NA),
  verbose = FALSE))

if (exists("result")) print(result)

# Assign plankton groups using additional custom grouping
custom_groups <- list(
    Cryptophytes = list(class = "Cryptophyceae"),
    Ciliates = list(phylum = "Ciliophora")
)

# Assign with custom groups
try(result_custom <- assign_phytoplankton_group(
  scientific_names = c("Teleaulax amphioxeia", "Mesodinium rubrum", "Dinophysis acuta"),
  aphia_ids = c(106306, 232069, 109604),
  custom_groups = custom_groups,         # Adding custom groups
  verbose = FALSE
))

if (exists("result_custom")) print(result_custom)
# }