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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 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(
  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
)

Arguments

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.

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.

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 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>

# 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 1653558 Aerosakkonemataceae               1653558 Aerosakkonemataceae     
#> 2  836651 Aetokthonos                        836651 Aetokthonos             
#> 3  841664 Aetokthonos hydrillicola           841664 Aetokthonos hydrillicola
#> 4  231787 Akashiwo                           231787 Akashiwo                
#> 5  232546 Akashiwo sanguinea                 232546 Akashiwo sanguinea      
#> 6  109470 Alexandrium                        109470 Alexandrium             
#> # 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>
# }