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Joining references to traits table

Source: R/join_.R
join_sources.Rd

Function to merge the references each observation cites into the core traits table of a traits.build database: the dataset's own citation, the citation of the source the observation was taken from, and the dataset's secondary references.

Usage

join_sources(database, vars = "all")

Arguments

database

traits.build database (list object)

vars

Columns to be joined to the traits table, defaulting to all of them (vars = "all"):

  • dataset_id_type: BibTeX type of the dataset's own reference (Article, Book, Thesis, ...)

  • dataset_id_citation: citation for the dataset's own reference

  • source_id_citation: citation for the reference the observation was taken from, sources[[source_id]]

  • secondary_id: keys, separated by ; , of the dataset's secondary references (later publications that re-used the data)

  • secondary_citation: citations, separated by ; , for those references

Value

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

Details

Each observation's source_id holds the key of the reference in sources that it was taken from: the dataset's own reference (keyed by the dataset_id), or, for a dataset compiled from several studies, the study the observation came from. source_id_citation formats that reference; the other columns come from the methods table and are the same for every observation of a dataset. A source_id with no entry in sources gets NA. In databases built with traits.build before 2.3, an observation collected in the dataset's own study has no source_id, and its dataset_id is used in its place.

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

Examples

(austraits_lite %>% extract_dataset("Yang_2023") %>%
  join_sources(vars = c("dataset_id_citation", "source_id_citation")))$traits %>%
  dplyr::select(trait_name, value, source_id, dataset_id_citation, source_id_citation)
#> # A tibble: 2,635 × 5
#>    trait_name            value  source_id dataset_id_citation source_id_citation
#>    <chr>                 <chr>  <chr>     <chr>               <chr>             
#>  1 resprouting_capacity  fire_… ABRS_2022 S. Yang. “Unpublis… Australian Biolog…
#>  2 post_fire_recruitment post_… ABRS_2022 S. Yang. “Unpublis… Australian Biolog…
#>  3 post_fire_recruitment post_… ABRS_2022 S. Yang. “Unpublis… Australian Biolog…
#>  4 resprouting_capacity  fire_… ABRS_2022 S. Yang. “Unpublis… Australian Biolog…
#>  5 resprouting_capacity  fire_… ABRS_2022 S. Yang. “Unpublis… Australian Biolog…
#>  6 bud_bank_location     basal… ABRS_2022 S. Yang. “Unpublis… Australian Biolog…
#>  7 resprouting_capacity  respr… ABRS_2022 S. Yang. “Unpublis… Australian Biolog…
#>  8 post_fire_recruitment post_… ABRS_2022 S. Yang. “Unpublis… Australian Biolog…
#>  9 resprouting_capacity  fire_… ABRS_2022 S. Yang. “Unpublis… Australian Biolog…
#> 10 bud_bank_location     basal… ABRS_2022 S. Yang. “Unpublis… Australian Biolog…
#> # ℹ 2,625 more rows