Retrieve Data From Nordic Microalgae
Source:vignettes/retrieve_nordic_microalgae_data.Rmd
retrieve_nordic_microalgae_data.RmdNordic Microalgae
Nordic Microalgae is an online platform providing high-quality images, illustrations, and detailed information about aquatic microalgae and related organisms in the Nordic region, including phytoplankton, microzooplankton, and benthic microalgae. It features a comprehensive species checklist, up-to-date taxonomic data linked to WoRMS and AlgaeBase, and supplementary resources such as biovolume lists and occurrence maps. Established in 1996 and supported by long-term funding from the Swedish Research Council through the Swedish Biodiversity Data Infrastructure (SBDI).
All data on Nordic Microalgae is accessible through our API. Below are examples demonstrating how to extract data using the SHARK4R package.
Retrieve Complete Nordic Microalgae Taxon Table
A complete Nordic Microalgae taxa list can be retrieved through the API.
# Get taxa information
taxa <- get_nua_taxa(unparsed = FALSE)
# Print data
tibble(taxa)## # A tibble: 6,852 × 5
## scientific_name authority rank slug nua_url
## <chr> <chr> <chr> <chr> <chr>
## 1 Abollifer Vørs, 1992 Genus abol… https:…
## 2 Abollifer prolabens Vørs, 1992 Spec… abol… https:…
## 3 Acanthoceras Honigm., 1910 Genus acan… https:…
## 4 Acanthoceras zachariasii (Brun) Simonsen, 1979 Spec… acan… https:…
## 5 Acanthocerataceae Round, Crawford & Mann, 1990 Fami… acan… https:…
## 6 Acanthocorbis S.Hara & E.Takahashi, 1984 Genus acan… https:…
## 7 Acanthocorbis apoda (Leadbeater) Hara & Takahashi,… Spec… acan… https:…
## 8 Acanthocorbis asymmetrica (Thomsen) Hara & Takahashi, 19… Spec… acan… https:…
## 9 Acanthocorbis campanula (Espeland) Thomsen, 1991 Spec… acan… https:…
## 10 Acanthocorbis haurakiana Thomsen, 1991 Spec… acan… https:…
## # ℹ 6,842 more rowsThe full taxonomic information can be accessed as an unparsed list by
enabling the unparsed parameter.
Get Nordic Microalgae External Links or Facts
Each taxon sheet on Nordic Microalgae contains facts, such as links to external webpages (e.g. AlgaeBase, WoRMS and Dyntaxa). These links can be retrieved through the API.
# Randomly select 10 taxa from shark_taxon$scientific_name
slugs <- sample(taxa$slug, size = 10)
# Get external links
external_links <- get_nua_external_links(slugs,
verbose = FALSE,
unparsed = FALSE)
# Print list
tibble(external_links)## # A tibble: 56 × 6
## slug provider label external_id external_url collection
## <chr> <chr> <chr> <chr> <chr> <chr>
## 1 ptychocylis-minor AlgaeBase AlgaeBase 141096 https://www… External …
## 2 ptychocylis-minor Dyntaxa Dyntaxa 238510 https://nam… External …
## 3 ptychocylis-minor ENA ENA 1925337 https://www… External …
## 4 ptychocylis-minor GBIF GBIF 7865442 https://www… External …
## 5 ptychocylis-minor NCBI NCBI 1925337 https://www… External …
## 6 ptychocylis-minor WoRMS WoRMS 427510 https://www… External …
## 7 ptychocylis-minor PR2 PR2: Ptycho… Ptychocyli… https://app… External …
## 8 rusalka-fusiformis AlgaeBase AlgaeBase 133790 https://www… External …
## 9 rusalka-fusiformis Dyntaxa Dyntaxa 257549 https://nam… External …
## 10 rusalka-fusiformis ENA ENA 71744 https://www… External …
## # ℹ 46 more rowsThe full list of facts can be accessed as an unparsed list by setting
the unparsed parameter to TRUE.
Get Nordic Microalgae Harmfulness Information
Taxa listed in the IOC-UNESCO Taxonomic Reference List of Harmful Micro Algae contain information about harmfulness. This information can be retrieved through the API.
# Get external links
harmfulness <- get_nua_harmfulness(c("dinophysis-acuta",
"alexandrium-ostenfeldii"),
verbose = FALSE)
# Print list
tibble(harmfulness)## # A tibble: 11 × 6
## slug provider label external_id external_url collection
## <chr> <chr> <chr> <chr> <chr> <chr>
## 1 dinophysis-acuta IOC IOC H… 109604 https://www… Harmful a…
## 2 dinophysis-acuta IOC-UNESCO IOC-U… 6 https://tox… Harmful a…
## 3 dinophysis-acuta IOC-UNESCO IOC-U… 1 https://tox… Harmful a…
## 4 dinophysis-acuta IOC-UNESCO IOC-U… 5 https://tox… Harmful a…
## 5 alexandrium-ostenfeldii IOC IOC H… 109712 https://www… Harmful a…
## 6 alexandrium-ostenfeldii IOC-UNESCO IOC-U… 464 https://tox… Harmful a…
## 7 alexandrium-ostenfeldii IOC-UNESCO IOC-U… 463 https://tox… Harmful a…
## 8 alexandrium-ostenfeldii IOC-UNESCO IOC-U… 462 https://tox… Harmful a…
## 9 alexandrium-ostenfeldii IOC-UNESCO IOC-U… 12 https://tox… Harmful a…
## 10 alexandrium-ostenfeldii IOC-UNESCO IOC-U… 15 https://tox… Harmful a…
## 11 alexandrium-ostenfeldii IOC-UNESCO IOC-U… 17 https://tox… Harmful a…Get Nordic Microalgae Media Links
Links to all images present on Nordic Microalgae can be retrieved through the API. The images are available in four sizes: original (o), small (s), medium (m), and large (l).
# Get all media links
media <- get_nua_media_links(unparsed = FALSE)
# Print list
tibble(media)## # A tibble: 2,413 × 10
## slug image_l_url image_o_url image_s_url image_m_url contributor
## <chr> <chr> <chr> <chr> <chr> <chr>
## 1 NA https://no… https://no… https://no… https://no… Per Wilhel…
## 2 NA https://no… https://no… https://no… https://no… Per Wilhel…
## 3 NA https://no… https://no… https://no… https://no… Per Wilhel…
## 4 dinophysis-odiosa https://no… https://no… https://no… https://no… Susanne Bu…
## 5 ebria-tripartita https://no… https://no… https://no… https://no… Susanne Bu…
## 6 ebria-tripartita https://no… https://no… https://no… https://no… Susanne Bu…
## 7 ebria-tripartita https://no… https://no… https://no… https://no… Susanne Bu…
## 8 ebria-tripartita https://no… https://no… https://no… https://no… Susanne Bu…
## 9 dicroerisma-psil… https://no… https://no… https://no… https://no… Susanne Bu…
## 10 volvox https://no… https://no… https://no… https://no… Per Wilhel…
## # ℹ 2,403 more rows
## # ℹ 4 more variables: photographer_artist <chr>, copyright_holder <chr>,
## # license <chr>, galleries <chr>Complete media information can be retrieved as an unparsed list by
setting the unparsed parameter to TRUE.
Citation
## To cite package 'SHARK4R' in publications use:
##
## Markus Lindh, Anders Torstensson (2025). SHARK4R: Retrieving,
## Analyzing, and Validating Marine Data from SHARK and Nordic
## Microalgae. R package version 0.1.7.9000.
## https://doi.org/10.5281/zenodo.14169399
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {SHARK4R: Retrieving, Analyzing, and Validating Marine Data from SHARK and Nordic Microalgae},
## author = {Markus Lindh and Anders Torstensson},
## year = {2025},
## note = {R package version 0.1.7.9000},
## url = {https://doi.org/10.5281/zenodo.14169399},
## }