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Launch Taxonomic Name Standardization App

launch_taxonomic_match_app.Rd

Launch an interactive Shiny application for standardizing taxonomic names against the Central African plant taxonomic backbone. The app provides automatic matching with intelligent fuzzy search, manual review capabilities, and export functionality.

Usage

launch_taxonomic_match_app(
  data = NULL,
  name_column = NULL,
  language = c("fr", "en"),
  min_similarity = 0.7,
  max_suggestions = 10,
  mode = c("interactive", "batch"),
  launch.browser = TRUE
)

Arguments

data

Optional data.frame containing taxonomic names to standardize. If NULL, user will upload an Excel file through the app interface.

name_column

Optional character string specifying the column name containing taxonomic names. If NULL, user will select interactively.

language

Character, initial interface language. Options: - "fr" (French, default) - "en" (English)

min_similarity

Numeric between 0 and 1, minimum similarity threshold for fuzzy matching. Lower values are more permissive. Default: 0.3

max_suggestions

Integer, maximum number of fuzzy match suggestions to show per unmatched name. Default: 10

mode

Character, review mode for unmatched names. Options: - "interactive" (default): Review names one-by-one - "batch": Review all names in table view (not yet implemented)

launch.browser

Logical, whether to launch app in browser. Default: TRUE

Value

Invisibly returns NULL. The app runs until user closes it.

Details

## Workflow

1. **Database Connection**: Login with database credentials (within the app) 2. **Data Input**: Upload Excel file or provide R data.frame 3. **Column Selection**: Choose column containing taxonomic names 4. **Auto Matching**: Automatic matching using hierarchical strategy: - Exact match on full name - Genus-constrained fuzzy match (searches species within matched genera) - Full database fuzzy match (last resort) 5. **Review** (Phase 4): Manually review unmatched names with suggestions 6. **Export**: Download results in Excel, CSV, or RDS format

## Match Quality

The app uses the new `match_taxonomic_names()` function which provides: - Intelligent genus-constrained fuzzy matching - Similarity scoring for match quality assessment - Synonym resolution - Taxonomic hierarchy information

## Data Format

Input data should contain: - One column with taxonomic names (genus + species, optionally with authors) - Other columns with associated data (plots, measurements, etc.)

Output data includes all original columns plus: - `idtax_n`: Matched taxon ID - `idtax_good_n`: Accepted taxon ID (for synonyms) - `matched_name`: Matched name from backbone - `corrected_name`: Final standardized name - `match_method`: How name was matched (exact, genus_constrained, fuzzy) - `match_score`: Similarity score (0-1) - `is_synonym`: Whether matched name is a synonym - `accepted_name`: Accepted name if synonym

See also

- [match_taxonomic_names()] for the underlying matching function - [query_taxa()] for programmatic taxonomic queries - [standardize_taxonomic_batch()] for batch processing without Shiny

Examples

if (FALSE) { # \dontrun{
# Launch with file upload interface
launch_taxonomic_match_app()

# Launch with R data
my_data <- read.csv("tree_inventory.csv")
launch_taxonomic_match_app(
  data = my_data,
  name_column = "species_name"
)

# Launch in French
launch_taxonomic_match_app(language = "fr")

# More strict fuzzy matching
launch_taxonomic_match_app(min_similarity = 0.7)

# Show more suggestions per name
launch_taxonomic_match_app(max_suggestions = 20)
} # }