# Retrieve Data From Nordic Microalgae

## 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

#### Installation

You can install the latest version of `SHARK4R` from CRAN using:

    install.packages("SHARK4R")

Load the `SHARK4R` and `dplyr` libraries:

    library(SHARK4R)
    library(dplyr)

## 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: 58 × 6
    ##    slug                       provider label external_id external_url collection
    ##    <chr>                      <chr>    <chr> <chr>       <chr>        <chr>
    ##  1 trachelomonas-armata-var-… AlgaeBa… Alga… 30662       https://www… External …
    ##  2 trachelomonas-armata-var-… Dyntaxa  Dynt… 257735      https://art… External …
    ##  3 trachelomonas-armata-var-… GBIF     GBIF  3208934     https://www… External …
    ##  4 trachelomonas-armata-var-… WoRMS    WoRMS 671172      https://www… External …
    ##  5 oedogonium-oblongum        AlgaeBa… Alga… 27614       https://www… External …
    ##  6 oedogonium-oblongum        Dyntaxa  Dynt… 258191      https://art… External …
    ##  7 oedogonium-oblongum        ENA      ENA   321589      https://www… External …
    ##  8 oedogonium-oblongum        GBIF     GBIF  2640144     https://www… External …
    ##  9 oedogonium-oblongum        NCBI     NCBI  321589      https://www… External …
    ## 10 oedogonium-oblongum        WoRMS    WoRMS 608553      https://www… External …
    ## # ℹ 48 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: 2,420 × 10
    ##    slug              image_l_url image_o_url image_s_url image_m_url contributor
    ##    <chr>             <chr>       <chr>       <chr>       <chr>       <chr>
    ##  1 lennoxia-faveola… https://no… https://no… https://no… https://no… Maria Karl…
    ##  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 <NA>              https://no… https://no… https://no… https://no… Per Wilhel…
    ##  7 pleurosigma       https://no… https://no… https://no… https://no… Maria Karl…
    ##  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 <NA>              https://no… https://no… https://no… https://no… Per Wilhel…
    ## # ℹ 2,410 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 found in cache.

    # 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 1.0.1.
    ##   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 = {2025},
    ##     note = {R package version 1.0.1},
    ##     url = {https://CRAN.R-project.org/package=SHARK4R},
    ##   }