Skip to contents

Launch Taxonomic Backbone Management App

launch_taxo_backbone_app.Rd

Launches an interactive Shiny application for managing the taxonomic backbone database. This app provides tools for adding new taxa, updating existing records, and managing synonymy relationships.

Usage

launch_taxo_backbone_app(pool_taxa = NULL, language = c("fr", "en"), ...)

Arguments

pool_taxa

Optional database connection pool for the taxa database. If not provided, the app will prompt for login credentials.

language

Character string for UI language. Options:

  • "fr" (French, default)

  • "en" (English)

...

Additional arguments passed to runApp (e.g., launch.browser = TRUE, port = 3838)

Value

NULL (launches the Shiny app)

Details

The app provides an intuitive interface for:

Browse & Search:

  • Search by genus, species, family, order, or taxon ID

  • Filter by synonymy status (all/accepted/synonyms)

  • View database statistics

  • Select taxa for editing

Add New Taxa:

  • Search Tropicos for taxonomic information

  • Manual entry for all taxonomic ranks

  • Duplicate checking and validation

  • Set synonymy relationships

  • Growth form selection

Update Existing Taxa:

  • Edit all taxonomic fields

  • View modification history

  • Automatic backup creation

  • Change validation

Synonymy Management:

  • Set taxa as synonyms

  • Cancel existing synonymy

  • View synonym networks

  • Handle synonym cascades

Hierarchy Viewer:

  • Interactive taxonomic tree

  • Statistics by rank

  • Export capabilities

Database Permissions

The app checks user permissions on startup:

Read Access

All authenticated users can browse and search

Write Access

Only users with INSERT privileges on table_taxa can modify data

Users without write permissions will see a "Read-Only Mode" badge and modification features will be disabled.

Core Functions

The app wraps existing package functions:

Security

All modifications are:

  • Logged in followup_updates_diconames table

  • Backed up before changes

  • Validated for taxonomic consistency

  • Subject to database permissions

See also

add_entry_taxa for adding new taxa programmatically update_dico_name for updating taxa programmatically query_taxa for searching the taxonomic database launch_query_plots_app for the plot query app launch_taxonomic_match_app for the taxonomic matching app

Examples

if (FALSE) { # \dontrun{
# Launch app with default settings
launch_taxo_backbone_app()

# Launch app in English
launch_taxo_backbone_app(language = "en")

# Launch app in browser on specific port
launch_taxo_backbone_app(launch.browser = TRUE, port = 8080)

# Use existing connection pool
pool <- call.mydb.taxa()
launch_taxo_backbone_app(pool_taxa = pool)
} # }