MareFrame Taxonomy import functions — mfdb_import

Functions to import taxonomy data into MareFrame DB

mfdb_import_area(mdb, data_in)
    mfdb_import_division(mdb, data_in)
    mfdb_import_sampling_type(mdb, data_in)
    mfdb_import_bait_type_taxonomy(mdb, data_in)
    mfdb_import_population_taxonomy(mdb, data_in)
    mfdb_import_port_taxonomy(mdb, data_in)
    mfdb_import_tow_taxonomy(mdb,  data_in)
    mfdb_import_net_type_taxonomy(mdb, data_in)
    mfdb_import_trip_taxonomy(mdb, data_in)
    mfdb_import_vessel_taxonomy(mdb,  data_in)
    mfdb_import_vessel_owner_taxonomy(mdb,  data_in)

    mfdb_empty_taxonomy(mdb, taxonomy_name)

    mfdb_import_cs_taxonomy(mdb, taxonomy_name, data_in)

Arguments

mdb: Database connection created by mfdb().
taxonomy_name: The name of the taxonomy to import, if there isn't a special function for it. See mfdb:::mfdb_taxonomy_tables for possible values.
data_in: A data.frame of data to import, see details.

Details

MFDB taxonomies define the values you can use when importing / querying for data. They need to be populated with the values you need before data is imported. Most taxonomies are pre-populated by the MFDB package, so you should use the predefined values. Others however this does not make sense, so should be done separately. This is what these functions do.

mfdb_import_division is a special case, which imports groupings of areacells into divisions, if you haven't already done this with mfdb_import_area or your divisions are too complicated to represent this way. The data_in should be a list of areacell vectors, with division names. For example, list(divA = c('45G01', '45G02', '45G03'))

Beyond this, all functions accept the following columns:

id: Optional. A numeric ID to use internally, defaults to 1..n
name: Required. A vector of short names to use in data, e.g. "SEA"
t_group: Optional. A vector of the that groups together a set of values

Note that the database doesn't use your short names internally. This means you can rename items by changing what name is set to. t_group allows taxonomy values to be grouped together. For example, giving all vessels in a fleet the same t_group you can then query the entire fleet as well as individually.

mfdb_import_area imports areacell information for your case study. Beyond the above, you can also provide the following:

size: The size of the areacell
depth: The depth of the areacell
division: The name of the division this areacell is part of

mfdb_import_vessel_taxonomy imports names of vessels into the taxonomy table, so they can be used when importing samples. As well as the above, you can also specify:

full_name: Optional. The full name of this vessel
length: Optional. The length of the vessel in meters
power: Optional. The vessel's engine power in KW
tonnage: Optional. The vessel's gross tonnage
vessel_owner: Optional. The short name of the vessel owner (see mfdb_import_vessel_owner_taxonomy)

mfdb_import_vessel_owner_taxonomy imports names of vessels owners into a taxonomy table, to be used when importing vessels. As well as name/t_group, you can also specify:

full_name: Optional. The full name of the owning organisation

mfdb_import_tow_taxonomy imports names of vessels into the taxonomy table, so they can be used when importing samples. As well as the above, you can also specify:

latitude: Optional.
longitude: Optional.
depth: Optional. Depth in meters
length: Optional. Length in meters

mfdb_import_port_taxonomy imports names of ports that trips can start/finish at. As well as id/name, you can provide:

latitude: Optional. Latitutde as real number
longitude: Optional. Latitutde as real number
institute: Optional. Institute (from institute taxonomy, could be country) responsible for port

mfdb_import_trip_taxonomy imports names of trips that samples can be labelled part of. As well as id/name, you can provide:

latitude: Optional. Latitutde as real number
longitude: Optional. Latitutde as real number
start_date: Optional. Start date-time, as YYYY-MM-DD or YYYY-MM-DD HH:MM:SS
end_date: Optional. End date-time, as YYYY-MM-DD or YYYY-MM-DD HH:MM:SS
crew: Optional. Number of crew on-board
oil_consumption: Optional. Total oil consumption for trip
start_port: Optional. Name of port (from port taxonomy) trip started
end_port: Optional. Name of port (from port taxonomy) trip finished

mfdb_import_sampling_type imports sampling types so that you can then use these against records in the sample table. You can also provide:

description: Optional. A vector of descriptive names, e.g. "sea sampling"

mfdb_empty_taxonomy allows you to empty out a taxonomy of previous data. The import functions insert or update values that already exist, based on the numeric ID for these values. They do not delete anything, as it may be impossible to remove rows without destroying existing data.

However, if e.g. you want to replace the species taxonomy with an entirely different one you will need to flush it first, before you import any data. Use this function, then mfdb_import_species_taxonomy to import the new taxonomy.

NB: This won't be possible if there is some data already using any of the terms. It is best used before your database is populated.

Value

NULL