
Retrieve Data From Nordic Microalgae
Source:vignettes/retrieve_nordic_microalgae_data.Rmd
retrieve_nordic_microalgae_data.Rmd
Nordic 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.
Getting Started
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: 6,860 × 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 6,850 more rows
The 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: 52 × 6
## slug provider label external_id external_url collection
## <chr> <chr> <chr> <chr> <chr> <chr>
## 1 pterosperma-vanhoeffenii AlgaeBase Algae… 56416 https://www… External …
## 2 pterosperma-vanhoeffenii Dyntaxa Dynta… 238959 https://nam… External …
## 3 pterosperma-vanhoeffenii GBIF GBIF 2688130 https://www… External …
## 4 pterosperma-vanhoeffenii WoRMS WoRMS 345881 https://www… External …
## 5 rosenvingiellopsis AlgaeBase Algae… 52010 https://www… External …
## 6 rosenvingiellopsis Dyntaxa Dynta… 6046635 https://nam… External …
## 7 rosenvingiellopsis ENA ENA 1936980 https://www… External …
## 8 rosenvingiellopsis GBIF GBIF 9916441 https://www… External …
## 9 rosenvingiellopsis NCBI NCBI 1936980 https://www… External …
## 10 rosenvingiellopsis WoRMS WoRMS 1312598 https://www… External …
## # ℹ 42 more rows
The 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: 2,419 × 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 NA https://no… https://no… https://no… https://no… Per Wilhel…
## 5 NA https://no… https://no… https://no… https://no… Per Wilhel…
## 6 pleurosigma https://no… https://no… https://no… https://no… Maria Karl…
## 7 NA https://no… https://no… https://no… https://no… Per Wilhel…
## 8 NA https://no… https://no… https://no… https://no… Per Wilhel…
## 9 NA https://no… https://no… https://no… https://no… Per Wilhel…
## 10 dinophysis-odiosa https://no… https://no… https://no… https://no… Susanne Bu…
## # ℹ 2,409 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
.
Get NOMP and EG Phyto Biovolume lists
To standardize phytoplankton monitoring efforts in the Baltic Sea,
Skagerrak, and the North Sea, various lists containing size class
information for each taxon have been established. These lists can be
retrieved directly in R using SHARK4R
:
# Get EG Phyto Biovolume list
peg_list <- get_peg_list()
## Reading PEG biovolume Excel file for year: 2025
# Print list
tibble(peg_list)
## # A tibble: 3,527 × 36
## Division Class Order Genus Species SFLAG STAGE Author AphiaID AphiaID_link
## <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <dbl> <chr>
## 1 CYANOBACTE… Cyan… CHRO… Apha… Aphano… NA NA West … 146563 http://www.…
## 2 CYANOBACTE… Cyan… CHRO… Apha… Aphano… NA NA West … 146563 http://www.…
## 3 CYANOBACTE… Cyan… CHRO… Apha… Aphano… NA NA West … 146563 http://www.…
## 4 CYANOBACTE… Cyan… CHRO… Apha… Aphano… NA NA West … 146563 http://www.…
## 5 CYANOBACTE… Cyan… CHRO… Apha… Aphano… NA NA West … 146563 http://www.…
## 6 CYANOBACTE… Cyan… CHRO… Apha… Aphano… NA NA West … 146563 http://www.…
## 7 CYANOBACTE… Cyan… CHRO… Apha… Aphano… NA NA West … 146563 http://www.…
## 8 CYANOBACTE… Cyan… CHRO… Apha… Aphano… NA NA W. & … 146564 http://www.…
## 9 CYANOBACTE… Cyan… CHRO… Apha… Aphano… NA NA W. & … 146564 http://www.…
## 10 CYANOBACTE… Cyan… CHRO… Apha… Aphano… NA NA W. & … 146564 http://www.…
## # ℹ 3,517 more rows
## # ℹ 26 more variables: Trophy <chr>, Geometric_shape <chr>, FORMULA <chr>,
## # SizeClassNo <dbl>, Nonvalid_SIZCL <lgl>, Not_accepted_name <lgl>,
## # Unit <chr>, SizeRange <chr>, `Length(l1)µm` <dbl>, `Length(l2)µm` <dbl>,
## # `Width(w)µm` <dbl>, `Height(h)µm` <dbl>, `Diameter(d1)µm` <dbl>,
## # `Diameter(d2)µm` <dbl>, `No_of_cells/counting_unit` <dbl>,
## # `Calculated_volume_µm3 (with formula) - NOT IMPORTED, NOT handled by ICES` <dbl>, …
# Get NOMP Biovolume list
nomp_list <- get_nomp_list()
## File for year 2025 not available. Trying previous year...
## File for year 2024 downloaded and cached.
# Print list
tibble(nomp_list)
## # A tibble: 3,846 × 39
## List `HELCOM area` `OSPAR area` Division Class Order Genus Species SFLAG
## <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
## 1 PEG_BVOL… x NA CYANOBA… Cyan… CHRO… Apha… Aphano… NA
## 2 PEG_BVOL… x NA CYANOBA… Cyan… CHRO… Apha… Aphano… NA
## 3 PEG_BVOL… x NA CYANOBA… Cyan… CHRO… Apha… Aphano… NA
## 4 PEG_BVOL… x NA CYANOBA… Cyan… CHRO… Apha… Aphano… NA
## 5 PEG_BVOL… x NA CYANOBA… Cyan… CHRO… Apha… Aphano… NA
## 6 PEG_BVOL… x NA CYANOBA… Cyan… CHRO… Apha… Aphano… NA
## 7 PEG_BVOL… x NA CYANOBA… Cyan… CHRO… Apha… Aphano… NA
## 8 PEG_BVOL… x NA CYANOBA… Cyan… CHRO… Apha… Aphano… NA
## 9 PEG_BVOL… x NA CYANOBA… Cyan… CHRO… Apha… Aphano… NA
## 10 PEG_BVOL… x NA CYANOBA… Cyan… CHRO… Apha… Aphano… NA
## # ℹ 3,836 more rows
## # ℹ 30 more variables: STAGE <chr>, Author <chr>, AphiaID <dbl>,
## # AphiaID_link <chr>, Trophy <chr>, Geometric_shape <chr>, FORMULA <chr>,
## # SizeClassNo <dbl>, Nonvalid_SIZCL <lgl>, Not_accepted_name <chr>,
## # Unit <chr>, SizeRange <chr>, `Length(l1)µm` <dbl>, `Length(l2)µm` <dbl>,
## # `Width(w)µm` <dbl>, `Height(h)µm` <dbl>, `Diameter(d1)µm` <dbl>,
## # `Diameter(d2)µm` <dbl>, `No_of_cells/counting_unit` <dbl>, …
Please note that SHARK4R
also includes a useful function
for reading exported Plankton
Toolbox data files: read_ptbx()
.
Citation
## To cite package 'SHARK4R' in publications use:
##
## Lindh, M. and Torstensson, A. (2025). SHARK4R: Accessing and
## Validating Marine Environmental Data from SHARK and Related
## Databases. R package version 0.1.7.9000.
## https://doi.org/10.5281/zenodo.14169399
##
## 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 = {2025},
## note = {R package version 0.1.7.9000},
## url = {https://doi.org/10.5281/zenodo.14169399},
## }