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Joining taxonomy to traits table

Source: R/join_.R
join_taxa.Rd

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

Usage

join_taxa(
  database,
  vars = c("family", "genus", "taxon_rank", "establishment_means")
)

Arguments

database

traits.build database (list object)

vars

Columns from the taxa table to be joined to the traits table, defaulting to c("family", "genus", "taxon_rank", "establishment_means").

Value

traits.build list object, but with additional fields (columns) for the specified variables from the taxa 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2023 release) see https://github.com/traitecoevo/austraits for how to install old versions of the package or download a newer version of the database.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 details
(austraits_lite %>% extract_dataset("Falster_2003") %>% join_taxa())$traits %>%
  dplyr::select(taxon_name, trait_name, value, family, genus, taxon_rank)
#> # A tibble: 114 × 6
#>    taxon_name        trait_name             value  family    genus    taxon_rank
#>    <chr>             <chr>                  <chr>  <chr>     <chr>    <chr>     
#>  1 Acacia floribunda leaf_area              142    Fabaceae  Acacia   species   
#>  2 Acacia floribunda leaf_inclination_angle 57     Fabaceae  Acacia   species   
#>  3 Acacia floribunda leaf_compoundness      simple Fabaceae  Acacia   species   
#>  4 Acacia myrtifolia leaf_area              319    Fabaceae  Acacia   species   
#>  5 Acacia myrtifolia leaf_inclination_angle 66.1   Fabaceae  Acacia   species   
#>  6 Acacia myrtifolia leaf_compoundness      simple Fabaceae  Acacia   species   
#>  7 Acacia suaveolens leaf_area              562    Fabaceae  Acacia   species   
#>  8 Acacia suaveolens leaf_inclination_angle 71.7   Fabaceae  Acacia   species   
#>  9 Acacia suaveolens leaf_compoundness      simple Fabaceae  Acacia   species   
#> 10 Angophora hispida leaf_area              1590   Myrtaceae Angopho… species   
#> # ℹ 104 more rows