Download SHARK dataset zip archives

Downloads one or more datasets (zip-archives) from the SHARK database (Swedish national marine environmental data archive) and optionally unzips them. The function matches provided dataset names against all available SHARK datasets.

Usage

get_shark_datasets(
  dataset_name,
  save_dir = NULL,
  prod = TRUE,
  utv = FALSE,
  unzip_file = FALSE,
  return_df = FALSE,
  encoding = "latin_1",
  guess_encoding = TRUE,
  verbose = TRUE
)

Arguments

dataset_name

Character vector with one or more dataset names (or partial names). Each entry will be matched against available SHARK dataset identifiers (e.g., "SHARK_Phytoplankton_2023_SMHI_BVVF" for a specific dataset, or "SHARK_Phytoplankton" for all Phytoplankton datasets).

save_dir

Directory where zip files (and optionally their extracted contents) should be stored. Defaults to NULL. If NULL or "", a temporary directory is used.

prod

Logical, whether to download from the production (TRUE, default) or test (FALSE) SHARK server. Ignored if utv is TRUE.

utv

Logical. Select UTV server when TRUE.

unzip_file

Logical, whether to extract downloaded zip archives (TRUE) or only save them (FALSE, default).

return_df

Logical, whether to return a combined data frame with the contents of all downloaded datasets (TRUE) instead of a list of file paths (FALSE, default).

encoding

Character. File encoding of shark_data.txt. Options: "cp1252", "utf_8", "utf_16", "latin_1". Default is "latin_1". If guess_encoding = TRUE, detected encoding overrides this value. Ignored if return_df is FALSE.

guess_encoding

Logical. If TRUE (default), automatically detect file encoding. If FALSE, the function uses only the user-specified encoding. Ignored if return_df is FALSE.

verbose

Logical, whether to show download and extraction progress messages. Default is TRUE.

Value

If return_df = FALSE, a named list of character vectors. Each element corresponds to one matched dataset and contains either the path to the downloaded zip file (if unzip_file = FALSE) or the path to the extraction directory (if unzip_file = TRUE). If return_df = TRUE, a single combined data frame with all dataset contents, including a source column indicating the dataset.

See also

https://shark.smhi.se/en for SHARK database.

get_shark_options() for listing available datasets.

get_shark_data() for downloading tabular data.

Examples

# \donttest{
# Get a specific dataset
get_shark_datasets("SHARK_Phytoplankton_2023_SMHI_BVVF", verbose = FALSE)
#> $`SHARK_Phytoplankton_2023_SMHI_BVVF_version_2025-03-09.zip`
#> [1] "/tmp/RtmpirDMYv/SHARK_Phytoplankton_2023_SMHI_BVVF_version_2025-03-09.zip"
#> 

# Get all Zooplankton datasets from 2022 and unzip them
get_shark_datasets(
  dataset_name = "Zooplankton_2022",
  unzip_file = TRUE,
  verbose = FALSE
)
#> $`SHARK_Zooplankton_2022_DEEP_version_2024-12-17.zip`
#> [1] "/tmp/RtmpirDMYv/SHARK_Zooplankton_2022_DEEP_version_2024-12-17"
#> 
#> $`SHARK_Zooplankton_2022_SMHI_version_2024-12-17.zip`
#> [1] "/tmp/RtmpirDMYv/SHARK_Zooplankton_2022_SMHI_version_2024-12-17"
#> 
#> $`SHARK_Zooplankton_2022_UMSC_version_2024-03-27.zip`
#> [1] "/tmp/RtmpirDMYv/SHARK_Zooplankton_2022_UMSC_version_2024-03-27"
#> 

# Get all Chlorophyll datasets and return as a combined data frame
combined_df <- get_shark_datasets(
  dataset_name = "Chlorophyll",
  return_df = TRUE,
  verbose = FALSE
)
#> Detected encoding 'windows-1252' differs from specified 'latin_1'. Using detected encoding.
head(combined_df)
#> # A tibble: 6 × 73
#>   source delivery_datatype check_status_sv data_checked_by_sv visit_year
#>    <dbl> <chr>             <chr>           <chr>                   <dbl>
#> 1      1 Chlorophyll       Klar            Leverantör               1989
#> 2      1 Chlorophyll       Klar            Leverantör               1989
#> 3      1 Chlorophyll       Klar            Leverantör               1985
#> 4      1 Chlorophyll       Klar            Leverantör               1989
#> 5      1 Chlorophyll       Klar            Leverantör               1989
#> 6      1 Chlorophyll       Klar            Leverantör               1989
#> # ℹ 68 more variables: visit_month <dbl>, station_name <chr>,
#> #   reported_station_name <chr>, sample_location_id <dbl>, station_id <dbl>,
#> #   sample_project_name_en <chr>, sample_orderer_name_en <chr>,
#> #   platform_code <chr>, visit_id <chr>, expedition_id <chr>,
#> #   shark_sample_id_md5 <chr>, sample_date <date>, sample_time <time>,
#> #   sample_enddate <date>, sample_endtime <lgl>, sample_latitude_dm <chr>,
#> #   sample_longitude_dm <chr>, sample_latitude_dd <dbl>, …
# }