Create combined traits.build table — flatten

Create a single database output that merges together the information in all relational tables within a traits.build database. Trait measurements are still output in long format (1 row per trait value), but all measurement-related metadata (methods, location properties, context properties, contributors, references) are now included as additional columns in a single table. References are joined by join_sources(), so vars$sources selects among its columns, and the reference columns of the methods table are not repeated.

Usage

flatten_database(database, format, vars, include_description)

Arguments

database: traits.build database (list object)
format: A parameter for the locations, contexts and data contributors tables specifying how data are packed. All three can be formatted as a single compacted column(s) will have a human readable column ("single_column_pretty") or using json ("single_column_json") syntax. For location properties or context properties there is also the option to add each location_property or context_property to the traits table as its own column ("many_columns"); the contributors column defaults to "single_column_pretty" when this option is selected.
vars: List specifying which columns or properties to include from each table. The detail is for all columns/properties to be included.
include_description: A logical indicating whether to include (TRUE) or omit (FALSE) the context_property descriptions; defaults to TRUE.

Value

A table combining information in 8 traits.build relational tables: traits, locations, contexts, methods, taxa, taxonomic_updates, contributors, and identifiers

Examples

flat <- austraits_lite %>%
  extract_dataset("Falster_2003") %>%
  flatten_database()
flat
#> # A tibble: 114 × 66
#>    dataset_id   taxon_name     observation_id trait_name value unit  entity_type
#>    <chr>        <chr>          <chr>          <chr>      <chr> <chr> <chr>      
#>  1 Falster_2003 Acacia florib… 01             leaf_area  142   mm2   population 
#>  2 Falster_2003 Acacia florib… 01             leaf_incl… 57    deg   population 
#>  3 Falster_2003 Acacia florib… 02             leaf_comp… simp… NA    species    
#>  4 Falster_2003 Acacia myrtif… 03             leaf_area  319   mm2   population 
#>  5 Falster_2003 Acacia myrtif… 03             leaf_incl… 66.1  deg   population 
#>  6 Falster_2003 Acacia myrtif… 04             leaf_comp… simp… NA    species    
#>  7 Falster_2003 Acacia suaveo… 05             leaf_area  562   mm2   population 
#>  8 Falster_2003 Acacia suaveo… 05             leaf_incl… 71.7  deg   population 
#>  9 Falster_2003 Acacia suaveo… 06             leaf_comp… simp… NA    species    
#> 10 Falster_2003 Angophora his… 07             leaf_area  1590  mm2   population 
#> # ℹ 104 more rows
#> # ℹ 59 more variables: value_type <chr>, basis_of_value <chr>,
#> #   replicates <chr>, basis_of_record <chr>, life_stage <chr>,
#> #   population_id <chr>, individual_id <chr>, repeat_measurements_id <chr>,
#> #   temporal_context_id <chr>, source_id <chr>, location_id <chr>,
#> #   entity_context_id <chr>, plot_context_id <chr>, treatment_context_id <chr>,
#> #   collection_date <chr>, measurement_remarks <chr>, method_id <chr>, …