Add Link Between Specimen and Individual — .add_link

Creates links between herbarium specimens and individual trees in the database. Includes validation to ensure foreign key references exist.

Usage

.add_link_specimens(
  new_data,
  col_names_select = NULL,
  col_names_corresp = c("id_specimen", "id_n", "id_linktype"),
  launch_adding_data = FALSE,
  validate = TRUE,
  con = NULL
)

Arguments

new_data: Tibble with column id_specimen, either id_linktype or type, and - depending on the scope of that link type - id_n (individual-level) or id_liste_plots (plot-level).
col_names_select: Character vector of column names in new_data to use. If NULL, uses all columns of new_data.
col_names_corresp: Character vector of target column names. Default: c("id_specimen", "id_n", "id_linktype")
launch_adding_data: Logical. If TRUE, links are actually added to database. Default FALSE for safety.
validate: Logical. If TRUE, validates FK references before adding. Default TRUE.
con: Database connection. If NULL, calls call.mydb()

Value

Invisibly returns the data that was (or would be) added

Details

Link types, and the column each one fills: - type_individual: specimen collected from this specific individual (id_n) - referenced_individual: specimen of the same species from a different individual (id_n) - reference_plot: specimen collected within a plot, the individual tree unknown (id_liste_plots)

Which of the two a type expects is `linktypelist.scope`, checked here.

The function: 1. Renames columns to standard names 2. Checks for duplicate links (same specimen, individual, type and plot) 3. Validates FK references and link scope if validate=TRUE 4. Sets audit columns (created_by, created_at) 5. Adds links if launch_adding_data=TRUE

Author

Gilles Dauby, gilles.dauby@ird.fr