Get data for animals, with options to filter results. Associated tag
information is available in columns starting with tag and
acoustic_tag_id. If multiple tags are associated with a single animal,
the information is comma-separated.
Usage
get_animals(
connection = con,
animal_id = NULL,
tag_serial_number = NULL,
animal_project_code = NULL,
scientific_name = NULL
)Arguments
- connection
A connection to the ETN database. Defaults to
con.- animal_id
Integer (vector). One or more animal identifiers.
- tag_serial_number
Character (vector). One or more tag serial numbers.
- animal_project_code
Character (vector). One or more animal project codes. Case-insensitive.
- scientific_name
Character (vector). One or more scientific names.
Value
A tibble with animals data, sorted by animal_project_code,
release_date_time and tag_serial_number. See also
field definitions.
Examples
# Set default connection variable
con <- connect_to_etn()
# Get all animals
get_animals(con)
#> # A tibble: 22,786 × 66
#> animal_id animal_project_code tag_serial_number tag_type tag_subtype
#> <int> <chr> <chr> <chr> <chr>
#> 1 5923 2004_Gudena 1208 acoustic animal
#> 2 5924 2004_Gudena 1209 acoustic animal
#> 3 5915 2004_Gudena 7416 acoustic animal
#> 4 5916 2004_Gudena 7417 acoustic animal
#> 5 5917 2004_Gudena 7418 acoustic animal
#> 6 5918 2004_Gudena 7419 acoustic animal
#> 7 5919 2004_Gudena 7420 acoustic animal
#> 8 5920 2004_Gudena 7421 acoustic animal
#> 9 5921 2004_Gudena 7422 acoustic animal
#> 10 5922 2004_Gudena 7423 acoustic animal
#> # ℹ 22,776 more rows
#> # ℹ 61 more variables: acoustic_tag_id <chr>,
#> # acoustic_tag_id_alternative <chr>, scientific_name <chr>,
#> # common_name <chr>, aphia_id <int>, animal_label <chr>,
#> # animal_nickname <chr>, tagger <chr>, capture_date_time <dttm>,
#> # capture_location <chr>, capture_latitude <dbl>, capture_longitude <dbl>,
#> # capture_method <chr>, capture_depth <chr>, …
# Get specific animals
get_animals(con, animal_id = 305) # Or string value "305"
#> # A tibble: 1 × 66
#> animal_id animal_project_code tag_serial_number tag_type tag_subtype
#> <int> <chr> <chr> <chr> <chr>
#> 1 305 2014_demer 1187450 acoustic animal
#> # ℹ 61 more variables: acoustic_tag_id <chr>,
#> # acoustic_tag_id_alternative <chr>, scientific_name <chr>,
#> # common_name <chr>, aphia_id <int>, animal_label <chr>,
#> # animal_nickname <chr>, tagger <chr>, capture_date_time <dttm>,
#> # capture_location <chr>, capture_latitude <dbl>, capture_longitude <dbl>,
#> # capture_method <chr>, capture_depth <chr>,
#> # capture_temperature_change <chr>, release_date_time <dttm>, …
get_animals(con, animal_id = c(304, 305, 2827))
#> # A tibble: 3 × 66
#> animal_id animal_project_code tag_serial_number tag_type tag_subtype
#> <int> <chr> <chr> <chr> <chr>
#> 1 304 2014_demer 1187449 acoustic animal
#> 2 305 2014_demer 1187450 acoustic animal
#> 3 2827 2015_phd_verhelst_cod 1271054,1271054 acoustic-archiv… animal,ani…
#> # ℹ 61 more variables: acoustic_tag_id <chr>,
#> # acoustic_tag_id_alternative <chr>, scientific_name <chr>,
#> # common_name <chr>, aphia_id <int>, animal_label <chr>,
#> # animal_nickname <chr>, tagger <chr>, capture_date_time <dttm>,
#> # capture_location <chr>, capture_latitude <dbl>, capture_longitude <dbl>,
#> # capture_method <chr>, capture_depth <chr>,
#> # capture_temperature_change <chr>, release_date_time <dttm>, …
# Get animals from specific animal project(s)
get_animals(con, animal_project_code = "2014_demer")
#> # A tibble: 16 × 66
#> animal_id animal_project_code tag_serial_number tag_type tag_subtype
#> <int> <chr> <chr> <chr> <chr>
#> 1 304 2014_demer 1187449 acoustic animal
#> 2 384 2014_demer 1157781 acoustic animal
#> 3 385 2014_demer 1157782 acoustic animal
#> 4 386 2014_demer 1157783 acoustic animal
#> 5 305 2014_demer 1187450 acoustic animal
#> 6 383 2014_demer 1157780 acoustic animal
#> 7 369 2014_demer 1171781 acoustic animal
#> 8 370 2014_demer 1171782 acoustic animal
#> 9 365 2014_demer 1171775 acoustic animal
#> 10 366 2014_demer 1171776 acoustic animal
#> 11 368 2014_demer 1171780 acoustic animal
#> 12 382 2014_demer 1157779 acoustic animal
#> 13 371 2014_demer 1171783 acoustic animal
#> 14 372 2014_demer 1171784 acoustic animal
#> 15 367 2014_demer 1171777 acoustic animal
#> 16 306 2014_demer 1187468 acoustic animal
#> # ℹ 61 more variables: acoustic_tag_id <chr>,
#> # acoustic_tag_id_alternative <chr>, scientific_name <chr>,
#> # common_name <chr>, aphia_id <int>, animal_label <chr>,
#> # animal_nickname <chr>, tagger <chr>, capture_date_time <dttm>,
#> # capture_location <chr>, capture_latitude <dbl>, capture_longitude <dbl>,
#> # capture_method <chr>, capture_depth <chr>,
#> # capture_temperature_change <chr>, release_date_time <dttm>, …
get_animals(con, animal_project_code = c("2014_demer", "2015_dijle"))
#> # A tibble: 42 × 66
#> animal_id animal_project_code tag_serial_number tag_type tag_subtype
#> <int> <chr> <chr> <chr> <chr>
#> 1 304 2014_demer 1187449 acoustic animal
#> 2 384 2014_demer 1157781 acoustic animal
#> 3 385 2014_demer 1157782 acoustic animal
#> 4 386 2014_demer 1157783 acoustic animal
#> 5 305 2014_demer 1187450 acoustic animal
#> 6 383 2014_demer 1157780 acoustic animal
#> 7 369 2014_demer 1171781 acoustic animal
#> 8 370 2014_demer 1171782 acoustic animal
#> 9 365 2014_demer 1171775 acoustic animal
#> 10 366 2014_demer 1171776 acoustic animal
#> # ℹ 32 more rows
#> # ℹ 61 more variables: acoustic_tag_id <chr>,
#> # acoustic_tag_id_alternative <chr>, scientific_name <chr>,
#> # common_name <chr>, aphia_id <int>, animal_label <chr>,
#> # animal_nickname <chr>, tagger <chr>, capture_date_time <dttm>,
#> # capture_location <chr>, capture_latitude <dbl>, capture_longitude <dbl>,
#> # capture_method <chr>, capture_depth <chr>, …
# Get animals associated with a specific tag_serial_number
get_animals(con, tag_serial_number = "1187450")
#> # A tibble: 1 × 66
#> animal_id animal_project_code tag_serial_number tag_type tag_subtype
#> <int> <chr> <chr> <chr> <chr>
#> 1 305 2014_demer 1187450 acoustic animal
#> # ℹ 61 more variables: acoustic_tag_id <chr>,
#> # acoustic_tag_id_alternative <chr>, scientific_name <chr>,
#> # common_name <chr>, aphia_id <int>, animal_label <chr>,
#> # animal_nickname <chr>, tagger <chr>, capture_date_time <dttm>,
#> # capture_location <chr>, capture_latitude <dbl>, capture_longitude <dbl>,
#> # capture_method <chr>, capture_depth <chr>,
#> # capture_temperature_change <chr>, release_date_time <dttm>, …
# Get animals of specific species (across all projects)
get_animals(con, scientific_name = c("Rutilus rutilus", "Silurus glanis"))
#> # A tibble: 66 × 66
#> animal_id animal_project_code tag_serial_number tag_type tag_subtype
#> <int> <chr> <chr> <chr> <chr>
#> 1 304 2014_demer 1187449 acoustic animal
#> 2 384 2014_demer 1157781 acoustic animal
#> 3 385 2014_demer 1157782 acoustic animal
#> 4 386 2014_demer 1157783 acoustic animal
#> 5 305 2014_demer 1187450 acoustic animal
#> 6 369 2014_demer 1171781 acoustic animal
#> 7 370 2014_demer 1171782 acoustic animal
#> 8 365 2014_demer 1171775 acoustic animal
#> 9 366 2014_demer 1171776 acoustic animal
#> 10 368 2014_demer 1171780 acoustic animal
#> # ℹ 56 more rows
#> # ℹ 61 more variables: acoustic_tag_id <chr>,
#> # acoustic_tag_id_alternative <chr>, scientific_name <chr>,
#> # common_name <chr>, aphia_id <int>, animal_label <chr>,
#> # animal_nickname <chr>, tagger <chr>, capture_date_time <dttm>,
#> # capture_location <chr>, capture_latitude <dbl>, capture_longitude <dbl>,
#> # capture_method <chr>, capture_depth <chr>, …
# Get animals of a specific species from a specific project
get_animals(con, animal_project_code = "2014_demer", scientific_name = "Rutilus rutilus")
#> # A tibble: 2 × 66
#> animal_id animal_project_code tag_serial_number tag_type tag_subtype
#> <int> <chr> <chr> <chr> <chr>
#> 1 304 2014_demer 1187449 acoustic animal
#> 2 305 2014_demer 1187450 acoustic animal
#> # ℹ 61 more variables: acoustic_tag_id <chr>,
#> # acoustic_tag_id_alternative <chr>, scientific_name <chr>,
#> # common_name <chr>, aphia_id <int>, animal_label <chr>,
#> # animal_nickname <chr>, tagger <chr>, capture_date_time <dttm>,
#> # capture_location <chr>, capture_latitude <dbl>, capture_longitude <dbl>,
#> # capture_method <chr>, capture_depth <chr>,
#> # capture_temperature_change <chr>, release_date_time <dttm>, …