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Pivot wide format traits table into long format

Source: R/trait_pivot_longer.R
trait_pivot_longer.Rd

[Deprecated] trait_pivot_longer "gathers" wide format data into a "tidy" format This function converts the data into long format where observations are on different rows and the type of observation is denoted by trait name. In other words, trait_pivot_longer reverts the actions of trait_pivot_wider

Usage

trait_pivot_longer(wide_data)

Arguments

wide_data

output from trait_pivot_wider.

Value

A tibble in long format

A tibble in long format

Details

  • If bind_trait_values was applied prior to trait_pivot_wider for AusTraits <= v3.0.2, trait_pivot_longer will return a tibble with fewer observations than the original traits table.

  • For AusTraits version >3.0.2, trait_pivot_longer will return a tibble with fewer columns than that original traits table

    • The excluded columns include: "unit", "replicates", "measurement_remarks", "basis_of_record", "basis_of_value"

This function reverts the actions of the function traits.use::trait_pivot_wider.

It begins with a derivation of a traits.build traits table, where multiple measurements that comprise a single observation are displayed on a single row,with a column for each trait. It then converts the table into long format where measurements of multiple traits that comprise a single observation are on different rows and a column specifying the trait names is added.

trait_pivot_longer has been developed to pivot the traits table for a database build 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2023 release) see https://github.com/traitecoevo/austraits for how to install old versions of the package or download a newer version of the database.

Author

Daniel Falster - daniel.falster@unsw.edu.au

Fonti Kar - fonti.kar@unsw.edu.au

Examples

# trait_pivot_longer() is deprecated, and gives an error. Pivot the output
# of trait_pivot_wider() back with tidyr::pivot_longer() instead:
data <- austraits_lite$traits %>%
  dplyr::filter(dataset_id == "Falster_2003")
traits_wide <- trait_pivot_wider(data)
tidyr::pivot_longer(traits_wide, cols = dplyr::all_of(unique(data$trait_name)),
  names_to = "trait_name", values_to = "value", values_drop_na = TRUE)
#> # A tibble: 114 × 21
#>    dataset_id   taxon_name observation_id entity_type basis_of_record life_stage
#>    <chr>        <chr>      <chr>          <chr>       <chr>           <chr>     
#>  1 Falster_2003 Acacia fl… 01             population  field           adult     
#>  2 Falster_2003 Acacia fl… 01             population  field           adult     
#>  3 Falster_2003 Acacia fl… 02             species     field           adult     
#>  4 Falster_2003 Acacia my… 03             population  field           adult     
#>  5 Falster_2003 Acacia my… 03             population  field           adult     
#>  6 Falster_2003 Acacia my… 04             species     field           adult     
#>  7 Falster_2003 Acacia su… 05             population  field           adult     
#>  8 Falster_2003 Acacia su… 05             population  field           adult     
#>  9 Falster_2003 Acacia su… 06             species     field           adult     
#> 10 Falster_2003 Angophora… 07             population  field           adult     
#> # ℹ 104 more rows
#> # ℹ 15 more variables: 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>, method_id <chr>,
#> #   method_context_id <chr>, original_name <chr>, trait_name <chr>, value <chr>