In sharksmhi/SHARK4R: Retrieving, Analyzing, and Validating Marine Data from SHARK and Nordic Microalgae

AlgaeBase

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 package from GitHub using the devtools package:

# install.packages("devtools")
devtools::install_github("sharksmhi/SHARK4R",
                         dependencies = TRUE)

Load the SHARK4R and tibble libraries:

library(SHARK4R)
library(tibble)

suppressPackageStartupMessages({
  library(SHARK4R)
  library(tibble)
})

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 get_algaebase_genus function.

# Match a genus name with AlgaeBase API
genus_records <- get_algaebase_genus(genus = "Gymnodinium",
                                     apikey = algaebase_key)

# Print the result
print(genus_records)

Match Species Name

Taxonomic records can be retrieved for individual species names using the get_algaebase_species function.

# Match a species with AlgaeBase API
species_records <- get_algaebase_species(genus = "Tripos",
                                         species = "muelleri",
                                         apikey = algaebase_key)

# Print the result
print(species_records)

Match Multiple Scientific Names

Multiple names can be matched with the match_algaebase 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 = c("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)

# Match the taxa with AlgaeBase
algaebase_match <- match_algaebase(genus = parsed_taxa$genus,
                                   species = parsed_taxa$species,
                                   apikey = algaebase_key,
                                   verbose = FALSE)

# Print the result
tibble(algaebase_match)