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 (Torstensson et al. 2024). 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
Installation
You can install the latest version of SHARK4R from CRAN
using:
install.packages("SHARK4R")Load the SHARK4R and dplyr libraries:
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
print(taxa)## # A tibble: 6,867 × 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 6,857 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
print(external_links)## # A tibble: 59 × 6
## slug provider label external_id external_url collection
## <chr> <chr> <chr> <chr> <chr> <chr>
## 1 pterosperma-polygonum AlgaeBase AlgaeBase 56414 https://www… External …
## 2 pterosperma-polygonum Dyntaxa Dyntaxa 238955 https://art… External …
## 3 pterosperma-polygonum GBIF GBIF 2688134 https://www… External …
## 4 pterosperma-polygonum ITIS ITIS 9590 http://www.… External …
## 5 pterosperma-polygonum WoRMS WoRMS 341610 https://www… External …
## 6 romeria-gracilis AlgaeBase AlgaeBase 65685 https://www… External …
## 7 romeria-gracilis Dyntaxa Dyntaxa 263585 https://art… External …
## 8 romeria-gracilis ENA ENA 1744976 https://www… External …
## 9 romeria-gracilis GBIF GBIF 7644679 https://www… External …
## 10 romeria-gracilis NCBI NCBI 1744976 https://www… External …
## # ℹ 49 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 Microalgae 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
print(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
print(media)## # A tibble: 2,423 × 10
## slug image_l_url image_o_url image_s_url image_m_url contributor
## <chr> <chr> <chr> <chr> <chr> <chr>
## 1 odontella-sinens… https://no… https://no… https://no… https://no… Ann-Turi S…
## 2 odontella-aurita https://no… https://no… https://no… https://no… Ann-Turi S…
## 3 octactis-speculum https://no… https://no… https://no… https://no… SMHI
## 4 lennoxia-faveola… https://no… https://no… https://no… https://no… Maria Karl…
## 5 NA https://no… https://no… https://no… https://no… Per Wilhel…
## 6 NA https://no… https://no… https://no… https://no… Per Wilhel…
## 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 pleurosigma https://no… https://no… https://no… https://no… Maria Karl…
## # ℹ 2,413 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 Nordic Microalgae Media Metadata
Detailed metadata for all media items on Nordic Microalgae can be retrieved through the API. This includes information such as location, sampling date, geographic coordinates, imaging technique, and contributor details.
# Get all media metadata
media_metadata <- get_nua_media_metadata(unparsed = FALSE)
# Print list
print(media_metadata)## # A tibble: 2,423 × 26
## slug taxon_slug scientific_name file type title caption license location
## <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
## 1 odonte… odontella… Odontella sine… odon… imag… Odon… "O. si… Creati… Kosterf…
## 2 odonte… odontella… Odontella auri… odon… imag… Odon… "Live … Creati… Havsten…
## 3 octact… octactis-… Octactis specu… octa… imag… Octa… "Two c… Creati… Danafjo…
## 4 lennox… lennoxia-… Lennoxia faveo… lenn… imag… Lenn… "" Creati… Danafjo…
## 5 bolmen… NA NA bolm… imag… Bolm… "Taken… Creati… Bolmen,…
## 6 bolmen… NA NA bolm… imag… Bolm… "Taken… Creati… Bolmen,…
## 7 bolmen… NA NA bolm… imag… Bolm… "Taken… Creati… Bolmen,…
## 8 hassle… NA NA hass… imag… Hass… "Taken… Creati… Hasslem…
## 9 hassle… NA NA hass… imag… Hass… "Taken… Creati… Hasslem…
## 10 pleuro… pleurosig… Pleurosigma pleu… imag… Pleu… "" Creati… Byttelo…
## # ℹ 2,413 more rows
## # ℹ 17 more variables: contributor <chr>, photographer_artist <chr>,
## # copyright_holder <chr>, copyright_stamp <chr>, galleries <chr>,
## # technique <list>, contrast_enhancement <list>, preservation <list>,
## # stain <list>, sampling_date <chr>, geographic_area <chr>,
## # latitude_degree <chr>, longitude_degree <chr>, institute <chr>,
## # contributing_organisation <chr>, created_at <chr>, updated_at <chr>Get Nordic Microalgae Image Labeling Links
Nordic Microalgae hosts images from automated imaging instruments
(e.g., IFCB) used for image labeling. Links to these images can be
retrieved through the API, similar to
get_nua_media_links().
# Get all image labeling media links
il_links <- get_nua_image_labeling_links(unparsed = FALSE)
# Print list
print(il_links)## # A tibble: 796 × 10
## slug image_l_url image_o_url image_s_url image_m_url contributor
## <chr> <chr> <chr> <chr> <chr> <chr>
## 1 tripos-muelleri https://nord… https://no… https://no… https://no… Anders Tor…
## 2 tripos-muelleri https://nord… https://no… https://no… https://no… Anders Tor…
## 3 tripos-muelleri https://nord… https://no… https://no… https://no… Anders Tor…
## 4 tripos-muelleri https://nord… https://no… https://no… https://no… Anders Tor…
## 5 tripos-muelleri https://nord… https://no… https://no… https://no… Anders Tor…
## 6 tripos-lineatus https://nord… https://no… https://no… https://no… Anders Tor…
## 7 tripos-lineatus https://nord… https://no… https://no… https://no… Anders Tor…
## 8 tripos-lineatus https://nord… https://no… https://no… https://no… Anders Tor…
## 9 tripos-lineatus https://nord… https://no… https://no… https://no… Anders Tor…
## 10 tripos-lineatus https://nord… https://no… https://no… https://no… Anders Tor…
## # ℹ 786 more rows
## # ℹ 4 more variables: copyright_holder <chr>, license <chr>,
## # imaging_instrument <chr>, priority <int>Get Nordic Microalgae Image Labeling Metadata
Detailed metadata for automated imaging images can be retrieved through the API. This includes information about the imaging instrument, training dataset, location, and taxonomic details.
# Get all image labeling metadata
il_metadata <- get_nua_image_labeling_metadata(unparsed = FALSE)
# Print list
print(il_metadata)## # A tibble: 796 × 22
## slug taxon_slug scientific_name file type title caption license location
## <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
## 1 tripos… tripos-mu… Tripos muelleri trip… imag… Trip… "" Creati… Tångesu…
## 2 tripos… tripos-mu… Tripos muelleri trip… imag… Trip… "" Creati… Tångesu…
## 3 tripos… tripos-mu… Tripos muelleri trip… imag… Trip… "" Creati… Tångesu…
## 4 tripos… tripos-mu… Tripos muelleri trip… imag… Trip… "" Creati… Tångesu…
## 5 tripos… tripos-mu… Tripos muelleri trip… imag… Trip… "" Creati… Tångesu…
## 6 tripos… tripos-li… Tripos lineatus trip… imag… Trip… "" Creati… Tångesu…
## 7 tripos… tripos-li… Tripos lineatus trip… imag… Trip… "" Creati… Tångesu…
## 8 tripos… tripos-li… Tripos lineatus trip… imag… Trip… "" Creati… Tångesu…
## 9 tripos… tripos-li… Tripos lineatus trip… imag… Trip… "" Creati… Tångesu…
## 10 tripos… tripos-li… Tripos lineatus trip… imag… Trip… "" Creati… Tångesu…
## # ℹ 786 more rows
## # ℹ 13 more variables: contributor <chr>, copyright_holder <chr>,
## # imaging_instrument <chr>, training_dataset <chr>, sampling_date <lgl>,
## # geographic_area <chr>, latitude_degree <chr>, longitude_degree <chr>,
## # institute <chr>, contributing_organisation <chr>, priority <int>,
## # created_at <chr>, updated_at <chr>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
print(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 2026 not available. Trying previous year...## File for year 2025 downloaded and cached.
# Print list
print(nomp_list)## # A tibble: 3,852 × 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 3,842 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. (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},
## }