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Joining taxonomic updates information to traits table

Source: R/join_.R
join_taxonomic_updates.Rd

Function to merge metadata from the taxonomic_updates table of a traits.build database into the core traits table.

Usage

join_taxonomic_updates(database, vars = c("aligned_name"))

Arguments

database

traits.build database (list object)

vars

Columns from the taxa table to be joined to the traits table, defaulting to c("aligned_name").

Value

traits.build list object, but with additional fields (columns) for the specified variables from the taxonomic_updates table appended to the traits table.

Details

the join_ functions have been developed to join relational tables for databases built using the traits.build workflow. Learn more at: https://github.com/traitecoevo/traits.build & https://github.com/traitecoevo/traits.build-book

Note to AusTraits users:

  • This function works with AusTraits version >= 5.0.0 (from Nov 2023 release)

  • For AusTraits versions <= 4.2.0 (up to Sept 2023 release) see https://github.com/traitecoevo/austraits for how to install old versions of the package or download a newer version of the database.

Examples

# Append taxonomic update details
(austraits_lite %>% extract_dataset("Falster_2003") %>% join_taxonomic_updates())$traits
#> # A tibble: 114 × 27
#>    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 20 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>, …