Function to merge metadata from the contexts table of a traits.build database into the core traits table.
Usage
join_context_properties(
database,
format = "single_column_pretty",
vars = "all",
include_description = TRUE
)Arguments
- database
traits.build database (list object)
- format
Specifies whether metadata from the contexts is output in a human readable format ("single_column_pretty"; default), with each context property added as a separate column ("many_columns") or using json syntax ("single_column_json").
- vars
Location properties for which data is to be appended to the traits table, defaulting to all context properties (vars = "all").
- include_description
A logical indicating whether to include (TRUE) or omit (FALSE) the context_property descriptions.
Value
traits.build list object, but context properties from the contexts 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2023 release) see https://github.com/traitecoevo/austraits for how to install old versions of the package or download a newer version of the database.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
(austraits_lite %>% extract_dataset("Crous_2013") %>%
join_context_properties(format = "many_columns", vars = "all",
include_description = TRUE))$traits %>%
dplyr::select(trait_name, value, dplyr::contains("_context: "))
#> # A tibble: 391 × 7
#> trait_name value treatment_context: t…¹ treatment_context: C…²
#> <chr> <chr> <chr> <chr>
#> 1 leaf_N_per_area 1.43 elevated <<Plants gro… 400 ppm <<Plants grow…
#> 2 leaf_N_per_dry_mass 30.3… elevated <<Plants gro… 400 ppm <<Plants grow…
#> 3 leaf_light_respiration_p… 2690 elevated <<Plants gro… 400 ppm <<Plants grow…
#> 4 leaf_light_respiration_p… 2270 elevated <<Plants gro… 400 ppm <<Plants grow…
#> 5 leaf_mass_per_area 47.02 elevated <<Plants gro… 400 ppm <<Plants grow…
#> 6 leaf_photosynthesis_Jmax… 183.… elevated <<Plants gro… 400 ppm <<Plants grow…
#> 7 leaf_photosynthesis_Jmax… 168.… elevated <<Plants gro… 400 ppm <<Plants grow…
#> 8 leaf_photosynthesis_Vcma… 94.48 elevated <<Plants gro… 400 ppm <<Plants grow…
#> 9 leaf_photosynthesis_Vcma… 112.… elevated <<Plants gro… 400 ppm <<Plants grow…
#> 10 leaf_photosynthetic_rate… 27.7… elevated <<Plants gro… 400 ppm <<Plants grow…
#> # ℹ 381 more rows
#> # ℹ abbreviated names: ¹`treatment_context: temperature treatment`,
#> # ²`treatment_context: CO2 treatment`
#> # ℹ 3 more variables: `plot_context: plots` <chr>,
#> # `temporal_context: sampling season` <chr>,
#> # `method_context: measurement temperature` <chr>