Retrieve Taxonomic Data From AlgaeBase
Source:vignettes/retrieve_algaebase_data.Rmd
retrieve_algaebase_data.RmdAlgaeBase
AlgaeBase is a comprehensive database containing information on a
wide variety of algae species, including terrestrial, marine, and
freshwater organisms, with an emphasis on marine botany. AlgaeBase is
continually updated and funded by various phycological societies, with
contributions from researchers and institutions worldwide. It can be
accessed via a web interface or
through the API, as
demonstrated in this tutorial using SHARK4R. Please note
that the authors of SHARK4R are not affiliated with
AlgaeBase.
Getting Started
Installation
You can install the latest version of SHARK4R from CRAN
using:
install.packages("SHARK4R")Load the SHARK4R and dplyr libraries:
AlgaeBase API Key
AlgaeBase requires a subscription key to access its API. To obtain your own key, please visit the API documentation. In the example below, the key is retrieved from an environment variable.
# Retrieve the API key
algaebase_key <- Sys.getenv("ALGAEBASE_KEY")Match Genus Name
Taxonomic records can be retrieved for individual genera names using
the match_algaebase_genus() function.
# Match a genus name with AlgaeBase API
genus_records <- match_algaebase_genus(genus = "Gymnodinium",
subscription_key = algaebase_key)
# Print the result
print(genus_records)## # A tibble: 2 × 20
## kingdom phylum class order family id genus species infrasp taxonomic_status
## <chr> <chr> <chr> <chr> <chr> <int> <chr> <lgl> <lgl> <chr>
## 1 Chromi… Dinof… Dino… Gymn… Gymno… 43632 Gymn… NA NA currently accep…
## 2 Chromi… Dinof… Dino… Gymn… Gymno… 51372 Para… NA NA currently accep…
## # ℹ 10 more variables: nomenclatural_status <lgl>, currently_accepted <dbl>,
## # accepted_name <lgl>, genus_only <dbl>, input_name <chr>, input_match <dbl>,
## # taxon_rank <chr>, mod_date <date>, long_name <chr>, authorship <chr>Match Species Name
Taxonomic records can be retrieved for individual species names using
the match_algaebase_species() function.
# Match a species with AlgaeBase API
species_records <- match_algaebase_species(genus = "Tripos",
species = "muelleri",
subscription_key = algaebase_key)
# Print the result
print(species_records)## # A tibble: 1 × 20
## id accepted_name input_name input_match currently_accepted genus_only
## <int> <chr> <chr> <dbl> <dbl> <dbl>
## 1 65254 Tripos muelleri Tripos muelle… 1 1 0
## # ℹ 14 more variables: kingdom <chr>, phylum <chr>, class <chr>, order <chr>,
## # family <chr>, genus <chr>, species <chr>, infrasp <lgl>, long_name <chr>,
## # taxonomic_status <chr>, nomenclatural_status <chr>, taxon_rank <chr>,
## # mod_date <date>, authorship <chr>Match Multiple Scientific Names
Multiple names can be matched with the
match_algaebase_taxa() function. The scientific names need
to be parsed into genus and species names
before being passed to the API, which can be achieved by the
parse_scientific_names() function.
# Retrieve all phytoplankton data from April 2015
shark_data <- get_shark_data(fromYear = 2015,
toYear = 2015,
months = 4,
dataTypes = "Phytoplankton",
verbose = FALSE)
# Randomly select 10 rows from the shark_data dataframe
random_rows <- shark_data[sample(nrow(shark_data), 10), ]
# Parse scientific names into genus and species names
parsed_taxa <- parse_scientific_names(random_rows$scientific_name)
# Print the parsed data
print(parsed_taxa)## # A tibble: 10 × 2
## genus species
## <chr> <chr>
## 1 Guinardia "delicatula"
## 2 Monoraphidium "contortum"
## 3 Flagellates ""
## 4 Thalassiosira "baltica"
## 5 Amylax "triacantha"
## 6 Flagellates ""
## 7 Karlodinium "micrum"
## 8 Cryptomonadales ""
## 9 Octactis "speculum"
## 10 Mesodinium "rubrum"
# Match the taxa with AlgaeBase
algaebase_match <- match_algaebase_taxa(genera = parsed_taxa$genus,
species = parsed_taxa$species,
subscription_key = algaebase_key,
verbose = FALSE)
# Print the result
print(algaebase_match)## # A tibble: 9 × 20
## genus species id accepted_name input_name input_match currently_accepted
## <chr> <chr> <int> <chr> <chr> <dbl> <dbl>
## 1 Guinar… delica… NA NA NA NA NA
## 2 Monora… contor… 27719 Monoraphidiu… Monoraphi… 1 1
## 3 Flagel… NA NA NA NA NA NA
## 4 Thalas… baltica 39921 Thalassiosir… Thalassio… 1 1
## 5 Amylax triaca… 52120 Amylax triac… Amylax tr… 1 1
## 6 Karlod… micrum 44335 Karlodinium … Karlodini… 1 0
## 7 Crypto… NA NA NA NA NA NA
## 8 Octact… specul… 164546 Octactis spe… Octactis … 1 1
## 9 Mesodi… rubrum 56539 Mesodinium r… Mesodiniu… 1 1
## # ℹ 13 more variables: genus_only <dbl>, kingdom <chr>, phylum <chr>,
## # class <chr>, order <chr>, family <chr>, infrasp <lgl>, long_name <chr>,
## # taxonomic_status <chr>, nomenclatural_status <lgl>, taxon_rank <chr>,
## # mod_date <date>, authorship <chr>Citation
## To cite package 'SHARK4R' in publications use:
##
## Lindh, M. and Torstensson, A. (2026). SHARK4R: Accessing and
## Validating Marine Environmental Data from 'SHARK' and Related
## Databases. R package version 1.0.3.
## https://CRAN.R-project.org/package=SHARK4R
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {SHARK4R: Accessing and Validating Marine Environmental Data from 'SHARK' and Related Databases},
## author = {Markus Lindh and Anders Torstensson},
## year = {2026},
## note = {R package version 1.0.3},
## url = {https://CRAN.R-project.org/package=SHARK4R},
## }