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Joining identifiers to traits table

Source: R/join_.R
join_identifiers.Rd

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

Usage

join_identifiers(database, format = "single_column_pretty", vars = "all")

Arguments

database

traits.build database (list object)

format

Specifies whether metadata from the identifiers is output in a human readable format ("single_column_pretty"; default), with each location property added as a separate column ("many_columns") or using json syntax ("single_column_json").

vars

Identifier types for which data is to be appended to the traits table, defaulting to all identifier types (vars = "all").

Value

traits.build list object, but with identifiers from the identifiers 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 >=7.0.0 (2025 releases)

  • 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2023 release) see https://github.com/traitecoevo/austraits for how to install old versions of the package or download a newer version of the database.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

# Schulze_2014 records the tree each observation was taken from
(austraits_lite %>% extract_dataset("Schulze_2014") %>%
  join_identifiers(format = "single_column_pretty", vars = "all"))$traits %>%
  dplyr::select(observation_id, trait_name, value, identifier_types)
#> # A tibble: 2,473 × 4
#>    observation_id trait_name                        value       identifier_types
#>    <chr>          <chr>                             <chr>       <chr>           
#>  1 001            leaf_area                         12.201      catalogNumber==…
#>  2 002            leaf_type                         scale       catalogNumber==…
#>  3 002            plant_photosynthetic_organ        cladode     catalogNumber==…
#>  4 003            leaf_area                         17.651      catalogNumber==…
#>  5 004            plant_physical_defence_structures sharp_poin… catalogNumber==…
#>  6 005            leaf_area                         37.2766667  catalogNumber==…
#>  7 006            plant_photosynthetic_organ        leaf        catalogNumber==…
#>  8 007            leaf_area                         3228.84     catalogNumber==…
#>  9 008            plant_photosynthetic_organ        phyllode    catalogNumber==…
#> 10 009            leaf_area                         834.91      catalogNumber==…
#> # ℹ 2,463 more rows