Download the IOC-UNESCO Taxonomic Reference List of Harmful Microalgae
Source:R/hab_api_functions.R
get_hab_list.RdThis function retrieves the IOC-UNESCO Taxonomic Reference List of Harmful Microalgae (Lundholm et al. 2009) from the World Register of Marine Species (WoRMS). The data is returned as a dataframe, with options to customize the fields included in the download.
Usage
get_hab_list(
species_only = TRUE,
harmful_non_toxic_only = FALSE,
aphia_id = TRUE,
scientific_name = TRUE,
authority = TRUE,
fossil = TRUE,
rank_name = TRUE,
status_name = TRUE,
qualitystatus_name = TRUE,
modified = TRUE,
lsid = TRUE,
parent_id = TRUE,
stored_path = TRUE,
citation = TRUE,
classification = TRUE,
environment = TRUE,
accepted_taxon = TRUE,
verbose = TRUE
)Arguments
- species_only
Logical. If
TRUE, only species-level records are returned (i.e., rows where theSpeciescolumn is notNA). Note that this filter is only applied whenharmful_non_toxic_only = FALSE; it is ignored whenharmful_non_toxic_only = TRUE.- harmful_non_toxic_only
Logical. If
TRUE, retrieves only non-toxigenic marine microalgal species flagged with harmful effects. Defaults toFALSE.![[Experimental]](figures/lifecycle-experimental.svg)
- aphia_id
Logical. Include the AphiaID field. Defaults to
TRUE.- scientific_name
Logical. Include the scientific name field. Defaults to
TRUE.Logical. Include the authority field. Defaults to
TRUE.- fossil
Logical. Include information about fossil status. Defaults to
TRUE.- rank_name
Logical. Include the taxonomic rank (e.g., species, variety, forma). Defaults to
TRUE.- status_name
Logical. Include the taxonomic status field. Defaults to
TRUE.- qualitystatus_name
Logical. Include the quality status field. Defaults to
TRUE.- modified
Logical. Include the date of last modification field. Defaults to
TRUE.- lsid
Logical. Include the Life Science Identifier (LSID) field. Defaults to
TRUE.- parent_id
Logical. Include the parent AphiaID field. Defaults to
TRUE.- stored_path
Logical. Include the stored path field. Defaults to
TRUE.- citation
Logical. Include citation information. Defaults to
TRUE.- classification
Logical. Include the full taxonomic classification (e.g., kingdom, phylum, class). Defaults to
TRUE.- environment
Logical. Include environmental data (e.g., marine, brackish, freshwater, terrestrial). Defaults to
TRUE.- accepted_taxon
Logical. Include information about the accepted taxon (e.g., scientific name and authority). Defaults to
TRUE.- verbose
Logical. Whether to display progress information. Default is
TRUE.
Details
This function submits a POST request to the WoRMS database to retrieve the IOC-UNESCO Taxonomic Reference List of Harmful Microalgae.
The downloaded data can include various fields, which are controlled by the input parameters.
If a field is not required, set the corresponding parameter to FALSE to exclude it from the output.
References
Lundholm, N.; Bernard, C.; Churro, C.; Escalera, L.; Hoppenrath, M.; Iwataki, M.; Larsen, J.; Mertens, K.; Murray, S.; Probert, I.; Salas, R.; Tillmann, U.; Zingone, A. (Eds) (2009 onwards). IOC-UNESCO Taxonomic Reference List of Harmful Microalgae. https://www.marinespecies.org/hab/. doi:10.14284/362
See also
https://www.marinespecies.org/hab/ for IOC-UNESCO Taxonomic Reference List of Harmful Microalgae
Examples
# \donttest{
# Download the default HABs taxonomic list
try(habs_taxlist_df <- get_hab_list())
if (exists("habs_taxlist_df")) head(habs_taxlist_df)
#> # A tibble: 6 × 29
#> AphiaID ScientificName Authority AphiaID_accepted ScientificName_accep…¹
#> <dbl> <chr> <chr> <dbl> <chr>
#> 1 418135 Acanthogonyaulax sp… (Murray … 418135 Acanthogonyaulax spin…
#> 2 639809 Achomosphaera hyper… (Defland… 110041 Gonyaulax spinifera
#> 3 841664 Aetokthonos hydrill… S.B.Wild… 841664 Aetokthonos hydrillic…
#> 4 232546 Akashiwo sanguinea (K.Hiras… 232546 Akashiwo sanguinea
#> 5 233407 Alexandrium acatene… (Whedon … 231873 Alexandrium catenella
#> 6 109707 Alexandrium affine (H.Inoue… 109707 Alexandrium affine
#> # ℹ abbreviated name: ¹ScientificName_accepted
#> # ℹ 24 more variables: Authority_accepted <chr>, Fossil <dbl>, Kingdom <chr>,
#> # Phylum <chr>, Class <chr>, Order <chr>, Family <chr>, taxonRank <chr>,
#> # Genus <chr>, Subgenus <lgl>, Species <chr>, Subspecies <lgl>, Marine <dbl>,
#> # Brackish <dbl>, Fresh <dbl>, Terrestrial <dbl>, taxonomicStatus <chr>,
#> # Qualitystatus <chr>, Unacceptreason <chr>, DateLastModified <date>,
#> # LSID <chr>, `Parent AphiaID` <dbl>, Storedpath <chr>, Citation <chr>
# Include higher taxa records
try(habs_taxlist_df <- get_hab_list(species_only = FALSE))
if (exists("habs_taxlist_df")) head(habs_taxlist_df)
#> # A tibble: 6 × 29
#> AphiaID ScientificName Authority AphiaID_accepted ScientificName_accep…¹
#> <dbl> <chr> <chr> <dbl> <chr>
#> 1 415000 Acanthogonyaulax (Kofoid)… 415000 Acanthogonyaulax
#> 2 418135 Acanthogonyaulax sp… (Murray … 418135 Acanthogonyaulax spin…
#> 3 601319 Achomosphaera Evitt, 1… 601319 Achomosphaera
#> 4 639809 Achomosphaera hyper… (Defland… 110041 Gonyaulax spinifera
#> 5 1653558 Aerosakkonemataceae Struneck… 1653558 Aerosakkonemataceae
#> 6 836651 Aetokthonos S.B.Wild… 836651 Aetokthonos
#> # ℹ abbreviated name: ¹ScientificName_accepted
#> # ℹ 24 more variables: Authority_accepted <chr>, Fossil <dbl>, Kingdom <chr>,
#> # Phylum <chr>, Class <chr>, Order <chr>, Family <chr>, taxonRank <chr>,
#> # Genus <chr>, Subgenus <lgl>, Species <chr>, Subspecies <lgl>, Marine <dbl>,
#> # Brackish <dbl>, Fresh <dbl>, Terrestrial <dbl>, taxonomicStatus <chr>,
#> # Qualitystatus <chr>, Unacceptreason <chr>, DateLastModified <date>,
#> # LSID <chr>, `Parent AphiaID` <dbl>, Storedpath <chr>, Citation <chr>
# Retrieve only non-toxigenic harmful species (experimental stage)
try(habs_taxlist_df <- get_hab_list(harmful_non_toxic_only = TRUE, verbose = FALSE))
if (exists("habs_taxlist_df")) head(habs_taxlist_df)
#> # A tibble: 6 × 24
#> AphiaID ScientificName Authority AphiaID_accepted ScientificName_accep…¹
#> <int> <chr> <chr> <int> <chr>
#> 1 109708 Alexandrium balechii (Steidin… 109708 Alexandrium balechii
#> 2 375699 Aureococcus anophag… Hargrave… 375699 Aureococcus anophagef…
#> 3 375701 Aureoumbra lagunens… D.A.Stoc… 375701 Aureoumbra lagunensis
#> 4 1360848 Blixaea quinquecorn… (T.H.Abé… 1360848 Blixaea quinquecornis
#> 5 149619 Cerataulina pelagica (Cleve) … 149619 Cerataulina pelagica
#> 6 163013 Chaetoceros calcitr… (Paulsen… 163015 Chaetoceros simplex v…
#> # ℹ abbreviated name: ¹ScientificName_accepted
#> # ℹ 19 more variables: Authority_accepted <chr>, Fossil <int>, Kingdom <chr>,
#> # Phylum <chr>, Class <chr>, Order <chr>, Family <chr>, taxonRank <chr>,
#> # Genus <chr>, Marine <int>, Brackish <int>, Fresh <int>, Terrestrial <int>,
#> # taxonomicStatus <chr>, Unacceptreason <chr>, DateLastModified <dttm>,
#> # LSID <chr>, `Parent AphiaID` <int>, Citation <chr>
# Include only specific fields in the output
try(habs_taxlist_df <- get_hab_list(aphia_id = TRUE, scientific_name = TRUE, authority = FALSE))
if (exists("habs_taxlist_df")) head(habs_taxlist_df)
#> # A tibble: 6 × 28
#> AphiaID ScientificName AphiaID_accepted ScientificName_accepted
#> <dbl> <chr> <dbl> <chr>
#> 1 418135 Acanthogonyaulax spinifera 418135 Acanthogonyaulax spinifera
#> 2 639809 Achomosphaera hyperacantha 110041 Gonyaulax spinifera
#> 3 841664 Aetokthonos hydrillicola 841664 Aetokthonos hydrillicola
#> 4 232546 Akashiwo sanguinea 232546 Akashiwo sanguinea
#> 5 233407 Alexandrium acatenella 231873 Alexandrium catenella
#> 6 109707 Alexandrium affine 109707 Alexandrium affine
#> # ℹ 24 more variables: Authority_accepted <chr>, Fossil <dbl>, Kingdom <chr>,
#> # Phylum <chr>, Class <chr>, Order <chr>, Family <chr>, taxonRank <chr>,
#> # Genus <chr>, Subgenus <lgl>, Species <chr>, Subspecies <lgl>, Marine <dbl>,
#> # Brackish <dbl>, Fresh <dbl>, Terrestrial <dbl>, taxonomicStatus <chr>,
#> # Qualitystatus <chr>, Unacceptreason <chr>, DateLastModified <date>,
#> # LSID <chr>, `Parent AphiaID` <dbl>, Storedpath <chr>, Citation <chr>
# }