Launch Individual-Specimen Linking App — launch_individual_specimen_linking

Launches interactive Shiny application for creating links between individual trees and herbarium specimens based on herbarium information in the individuals dataset.

Usage

launch_individual_specimen_linking_app(lang = "en")

Arguments

lang: Character, initial language ("en" or "fr"). Default "en".

Value

Launches Shiny app (does not return until app closes)

Details

**Workflow:**

1. **Select Individuals**: Filter individuals by plot, country, tag, etc. 2. **Parse Herbarium Info**: Extract collector names and specimen numbers from `herbarium_nbe_char` and `herbarium_nbe_type` columns 3. **Match Collectors**: Interactively match extracted collector names to entries in `table_colnam` 4. **Retrieve Specimens**: Find matching specimens in database by collector + number 5. **Validate Taxonomy**: Review taxonomic matches between individuals and specimens 6. **Create Links**: Execute link creation for validated matches

**Understanding the Two Column Types:**

The system uses two columns to track different specimen-individual relationships:

- **`herbarium_nbe_type`**: The ACTUAL tree where the specimen was physically collected - Direct evidence (high confidence) - Creates `type_individual` link

- **`herbarium_nbe_char`**: Trees field-identified as the SAME SPECIES as the specimen tree - Indirect evidence based on field identification (lower confidence) - Creates `referenced_individual` link - Extends specimen utility to more trees without collecting additional specimens

**Link Type Logic:** - If `herbarium_nbe_type` is non-empty → `type_individual` (specimen from THIS tree) - If only `herbarium_nbe_char` is non-empty → `referenced_individual` (tree believed to be same species) - If both columns have the SAME value → `type_individual` (confirms this is the specimen tree)

Examples

if (FALSE) { # \dontrun{
launch_individual_specimen_linking_app()
launch_individual_specimen_linking_app(lang = "fr")
} # }