mfdb_dplyr: MareFrame DB dplyr interface

In mareframe/mfdb: MareFrame DB Querying Library

MareFrame DB dplyr interface

Description

Use mfdb tables with dplyr

Usage

mfdb_dplyr_table(mdb, table_name, include_cols = all_cols)
mfdb_dplyr_survey_index(mdb, include_cols = all_cols)
mfdb_dplyr_division(mdb, include_cols = all_cols)
mfdb_dplyr_sample(mdb, include_cols = all_cols)
mfdb_dplyr_predator(mdb, include_cols = all_cols)
mfdb_dplyr_prey(mdb, include_cols = all_cols)

Arguments

mdb	An object created by mfdb()
table_name	A table name to query in
include_cols	Any additonal columns to include in output, see details.

Details

Warning: Whilst these might be handy for exploration, there is no guarantee that code using these will continue to work from one version of MFDB to the next.

There is one function for each measurement table. By default every possible taxonomy column is included. However this is somewhat inefficient if you do not require the data, in which case specify the columns requred with include_cols. See mfdb::mfdb_taxonomy_tables for possible values.

To query taxonomy tables, use mfdb_dplyr_table, which works for any supplied table name. See mfdb::mfdb_taxonomy_tables for possible values for table_name.

Value

A dplyr table object, for you to do as you please.

Examples

mdb <- mfdb(tempfile(fileext = '.duckdb'))

# Include as many columns as possible
mfdb_dplyr_sample(mdb)

# Only include 'data_source' and 'species' columns, as well as measurements
mfdb_dplyr_sample(mdb, c('data_source', 'species'))

# Query the sampling_type table
mfdb_dplyr_table(mdb, 'sampling_type')

mfdb_disconnect(mdb)

mareframe/mfdb documentation built on Nov. 17, 2022, 12:51 a.m.