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Download the IOC-UNESCO Taxonomic Reference List of Harmful Micro Algae

Source: R/hab_api_functions.R
get_hab_list.Rd

This function retrieves the IOC-UNESCO Taxonomic Reference List of Harmful Micro Algae (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 the Species column is not NA). Note that this filter is only applied when harmful_non_toxic_only = FALSE; it is ignored when harmful_non_toxic_only = TRUE.

harmful_non_toxic_only

Logical. If TRUE, retrieves only non-toxigenic marine microalgal species flagged with harmful effects. Defaults to FALSE. [Experimental]

aphia_id

Logical. Include the AphiaID field. Defaults to TRUE.

scientific_name

Logical. Include the scientific name field. Defaults to TRUE.

authority

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“`.

Value

A tibble containing the HABs taxonomic list, with columns based on the selected parameters.

Details

This function submits a POST request to the WoRMS database to retrieve the IOC-UNESCO Taxonomic Reference List of Harmful Micro Algae. 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 Micro Algae

Examples

# \donttest{
# Download the default HABs taxonomic list
habs_taxlist_df <- get_hab_list()
head(habs_taxlist_df)
#> # A tibble: 6 × 29
#>   AphiaID ScientificName       Authority AphiaID_accepted ScientificName_accep…¹
#>     <dbl> <chr>                <chr>                <dbl> <chr>                 
#> 1  841664 Aetokthonos hydrill… S.B.Wild…           841664 Aetokthonos hydrillic…
#> 2  232546 Akashiwo sanguinea   (K.Hiras…           232546 Akashiwo sanguinea    
#> 3  109707 Alexandrium affine   (H.Inoue…           109707 Alexandrium affine    
#> 4  231872 Alexandrium anderso… Balech, …           246835 Alexandrium andersonii
#> 5  246835 Alexandrium anderso… Balech, …           246835 Alexandrium andersonii
#> 6  233452 Alexandrium angusti… F.J.R.Ta…           109711 Alexandrium minutum   
#> # ℹ abbreviated name: ¹​ScientificName_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 higer taxa records
habs_taxlist_df <- get_hab_list(species_only = FALSE)
head(habs_taxlist_df)
#> # A tibble: 6 × 29
#>   AphiaID ScientificName       Authority AphiaID_accepted ScientificName_accep…¹
#>     <dbl> <chr>                <chr>                <dbl> <chr>                 
#> 1 1653558 Aerosakkonemataceae  Struneck…          1653558 Aerosakkonemataceae   
#> 2  836651 Aetokthonos          S.B.Wild…           836651 Aetokthonos           
#> 3  841664 Aetokthonos hydrill… S.B.Wild…           841664 Aetokthonos hydrillic…
#> 4  231787 Akashiwo             G.Hansen…           231787 Akashiwo              
#> 5  232546 Akashiwo sanguinea   (K.Hiras…           232546 Akashiwo sanguinea    
#> 6  109470 Alexandrium          Halim, 1…           109470 Alexandrium           
#> # ℹ abbreviated name: ¹​ScientificName_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)
habs_taxlist_df <- get_hab_list(harmful_non_toxic_only = TRUE, verbose = FALSE)
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: ¹​ScientificName_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
habs_taxlist_df <- get_hab_list(aphia_id = TRUE, scientific_name = TRUE, authority = FALSE)
head(habs_taxlist_df)
#> # A tibble: 6 × 28
#>   AphiaID ScientificName               AphiaID_accepted ScientificName_accepted 
#>     <dbl> <chr>                                   <dbl> <chr>                   
#> 1  841664 Aetokthonos hydrillicola               841664 Aetokthonos hydrillicola
#> 2  232546 Akashiwo sanguinea                     232546 Akashiwo sanguinea      
#> 3  109707 Alexandrium affine                     109707 Alexandrium affine      
#> 4  231872 Alexandrium andersoni                  246835 Alexandrium andersonii  
#> 5  246835 Alexandrium andersonii                 246835 Alexandrium andersonii  
#> 6  233452 Alexandrium angustitabulatum           109711 Alexandrium minutum     
#> # 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>
# }