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Query FishGlob survey data

get_data.Rd

Functions to query the FishGlob database. These functions assume the user has already run install_fishglob_data() once to cache the FishGlob data in a local database on their computer.

get_data(): The main data querying function. Returns a data frame of matching survey catch records with joined haul, survey, and taxon information.

get_surveys(): Return available survey-unit IDs.

get_continents(): Return available continents.

get_sources(): Return available data sources.

get_scientific_names(): Return available accepted scientific names.

get_catch_table(): Return the complete catch table.

get_taxon_table(): Return the complete taxon table.

get_haul_table(): Return the complete haul table.

get_survey_table(): Return the complete survey table.

Usage

get_data(
  scientific_name = NULL,
  regex = FALSE,
  family = NULL,
  survey = NULL,
  continent = NULL,
  source = NULL,
  year = NULL
)

get_surveys()

get_continents()

get_sources()

get_scientific_names()

get_catch_table()

get_taxon_table()

get_haul_table()

get_survey_table()

Arguments

scientific_name

Scientific name(s). See get_scientific_names().

regex

If TRUE, interpret scientific_name as regular expressions. For example, "^hippo*" matches names starting with "hippo".

family

Taxonomic family name(s). See get_taxon_table().

survey

Survey name(s). See get_surveys().

continent

Continent name(s), e.g. "europe". See get_continents().

source

Data source name(s), e.g. "NOAA" or "DATRAS ICES". See get_sources().

year

Vector of years. Defaults to all.

Value

A data frame of matching data.

Details

get_data() is the main querying function to return filtered survey catch records. Not all columns are included by default. Additional columns can be appended by joining (e.g., dplyr::left_join()) the data returned by get_data() with the data from get_taxon_table(), get_haul_table(), or get_survey_table().

See also

install_fishglob_data()

Examples

if (FALSE) { # \dontrun{
# The first time, start by installing the
# database locally:
install_fishglob_data()

# Subsequently, the data does not need to be recached.

# Find available agency data sources
get_sources()

# The full list of available species:
spp <- get_scientific_names()

# All Canary Rockfish data held by DFO
dat <- get_data(
  scientific_name = "sebastes pinniger",
  source = "DFO"
)

# All Sebastes data globally from 2000 to 2021
dat <- get_data(
  scientific_name = "^sebastes*",
  regex = TRUE,
  year = 2000:2021
)
} # }