Package index • CafriplotsR

Database Connections

Connect to and manage PostgreSQL database connections

call.mydb(): Get primary database connection (wrapper)

call.mydb.taxa(): Get taxa database connection (wrapper)

connect_database(): Connect to database

create_pool_main(): Create a connection pool for Shiny apps (main database)

create_pool_taxa(): Create a connection pool for Shiny apps (taxa database)

cleanup_connections(): Cleanup all database connections

db_diagnostic(): Complete database diagnostic

print_connection_status(): Print connection status

get_connection_info(): Get connection information

test_connection(): Test database connection

setup_db_credentials(): Setup credentials storage in environment variables

remove_db_credentials(): Remove stored credentials

create_db_config(): Create local DB config file

func_try_fetch(): Safely execute a SQL query with automatic retry

try_open_postgres_table(): Try to open PostgreSQL table

get_database_fk(): Get database foreign keys

Data Queries

Query plots, individuals, taxa, traits, and specimens from the database

query_plots(): Query plots from database

query_subplots(): Legacy function - wrapper for backward compatibility

query_plot_features(): Query subplot features with improved architecture

query_individual_features(): Query individual features with improved architecture

get_individual_aggregated_features(): Aggregate individual features to individual level

query_taxa(): List, extract taxa

query_taxa_traits(): Query traits at the taxonomic level

query_trait(): Query in taxa trait table

query_traits_measures(): Legacy function - wrapper for backward compatibility

query_traits_measures_features(): Query features associated with trait measurements

query_colnam(): Query in colnam table

query_specimens(): Query Specimens

query_all_specimen_links(): Query All Specimen Links for Individuals

query_citations(): Query citations from table_citations

species_plot_matrix(): Get species-plot data frame

explore_allometric_taxa(): Explore allometric relation

list_individual_features(): List all available individual features

get_linktypes(): Get Link Types from Lookup Table

method_list(): List of method

country_list(): List of countries

subplot_list(): List all available subplot types

traits_list(): List of trait and features potentially liked to individual

traits_taxa_list(): List of trait

PlotFetcher: Fetch plot data

PlotFilterBuilder: Query builder for plot

SpecimenFetcher: Specimen Fetcher

SpecimenFilterBuilder: Specimen Filter Builder

get_user_accessible_plots(): Get plot IDs accessible to a user

match_tax(): Query and standardize taxonomy

match_taxonomic_names(): Match taxonomic names to backbone with intelligent SQL-side strategy

resolve_taxon_synonyms(): Resolve taxonomic synonyms

get_taxon_hierarchy(): Get Full Taxonomy Hierarchy for a Taxon

get_taxon_ancestors(): Get All Ancestors of a Taxon

get_taxon_children(): Get All Children of a Taxon

count_taxon_children(): Count Children at Each Level

get_updates_diconame(): Get backups of modified taxonomic data

get_primary_specimen_link(): Get Primary Specimen for Individuals

get_ref_specimen_ind(): Find Unlinked Individuals with Herbarium Information

Data Adding

Add new plots, individuals, traits, specimens, and taxa to the database

add_plots(): Add new plot metadata

add_individuals(): Add new individuals data

add_plot_features(): Add Plot Features to Existing Plots

add_subplot_features(): Add an observation in subplot_features table

add_subplot_observations_feat(): Add subplot observations features

add_plot_coordinates(): Add 1ha IRd plot coordinates

add_specimens(): Add new specimens data

add_citation(): Add one or more citations to table_citations

add_entry_taxa(): Add new entry to taxonomic table

add_growth_form_taxa(): Add growth forms to a single taxa

add_person_to_db(): Add a person to table_colnam using secure function

add_method(): Add a method in method list

add_sp_traits_measures(): Add an observation in trait measurement table at species level

add_trait(): Add trait

add_trait_taxa(): Add a trait in species trait list

add_traits_measures(): Add an observation in trait measurement table

add_taxa_table_taxa(): Add formatted taxa information

add_subplottype(): Add a type in subplot table

import_plot_metadata(): Import Plot Metadata with Transaction Support

import_individual_data(): Import Individual Data with Transaction Support

Update and Delete

Update existing records and safely delete data with cascade handling

update_records(): Update records with optional single-record comparison display

update_dico_name(): Update taxonomic data

update_dico_name_batch(): Update diconame data based on id of taxa

update_ident_specimens(): Update specimens table

update_link_specimens_batch(): Update plot data data

update_specimens_batch(): Update specimens data data

update_taxa_link_table(): Update table_idtax (Materialized View Version)

update_taxon_parent(): Update Taxon Parent (with consistency check)

update_citation(): Update fields of an existing citation

apply_citation_backfill(): Apply citation backfill from a manually filled data frame

safe_delete_individuals(): Safely delete individual(s) with all related data

safe_delete_plot(): Safely delete plot(s) with all related data

safe_delete_taxa_traits(): Safely delete taxa trait measurements with all related data

safe_delete_individual_features(): Safely delete individual feature measurements with all related data

safe_delete_specimen_links(): Safely delete individual-specimen links

.delete_country(): Delete an entry in country table

.delete_individual_feature_type(): Delete an entry in individual feature table

.delete_specimens(): Delete an entry in specimen table

detect_direct_changes(): Detect changes in direct columns with visual display

Internal Linking & Matching Utilities

Advanced internal functions for data matching and linking

.add_link_specimens(): Add Link Between Specimen and Individual

.add_modif_field(): Query fuzzy match

.add_taxa_noninteractive(): Add taxonomic entry non-interactively (for Shiny apps)

.comp_print_vec(): Compare two row-tibbles and generate HTML with differences

.delete_colnam(): Delete an entry in colnam table

.delete_trait_list(): Delete an entry in trait list

.find_cat(): Internal function

.find_ids(): Internal function

.find_similar_string(): Internal function

.get_trait_individuals_values(): Legacy function - wrapper for backward compatibility

.link_sp_trait(): Internal function

.link_subplotype(): Internal function

.link_table(): Internal function

.link_trait(): Internal function

.pairwise_string_similarity(): Internal function

.query_unmatched_specimens(): Query Unmatched Specimens (Internal)

.rename_data(): Internal function

Data Processing

Process, validate, transform, and aggregate inventory and trait data

compute_growth(): Compute growth rates for permanent plots

compute_mortality(): Compute mortality and recruitment rates

compute_stem_vital_status(): Compute stem vital status for specified individuals

process_trimble_data(): Process trimble data

process_individuals(): Process individuals for query_plots

process_stems(): Process multiple stems

divid_plot(): Divid into quadrats a 1ha plot

extract_corners(): Extract all corners of 1ha plot

approximate_isolated_xy(): Interpolate x y position based on neighnour

proj_rel_xy(): Project stems in geographical space

latlong2UTM(): Get UTM from geographical coordinates

get_plot_rel_xy(): Project stems in geographical space

pivot_categorical_traits_generic(): Pivot categorical trait data to wide format

pivot_numeric_traits_generic(): Pivot numeric trait data to wide format with statistics

summarize_feature(): Get summary statistics for a specific feature

merge_individuals_taxa(): Merge individual records with taxonomic information

replace_NA(): Replace or restore missing values in a data frame

clean_taxonomic_name(): Clean and normalize taxonomic name

parse_taxonomic_name(): Parse taxonomic name into components

standardize_taxonomic_batch(): Standardize taxonomic names in a data frame

validate_plot_metadata(): Validate Plot Metadata Before Import

validate_individual_data(): Validate Individual Data Before Import

map_individual_columns(): Map Individual Data Columns

map_user_columns(): Map User Columns to Database Schema

get_import_column_routing(): Get Import Column Routing Configuration

enrich_traits_with_measurement_features(): Enrich trait data with measurement features (generic)

enrich_with_traits(): Enrich individuals with all traits

print_validation_results(): Print Validation Results

print_individual_validation_results(): Print Individual Validation Results

print_import_result(): Print Import Result

print_template_info(): Print Template Column Information

print_individual_template_info(): Export Individual Template Info

print_mapping_summary(): Print Mapping Summary

get_individual_template(): Generate Individual Data Import Template

get_plot_metadata_template(): Get Plot Metadata Template

export_plot_template(): Export Plot Metadata Template to Excel

describe_columns(): Describe columns in query results

choose_growth_form(): Choose growth forms

choose_prompt(): Choose from prompt

test.order.subplot(): Check the order of subplots in a given data frame

export_taxa_traits_for_citation_backfill(): Export taxa trait measurements for citation backfill

print(<column_documentation>): Print method for column_documentation objects

print(<plot_features_result>): Print method for add_plot_features result

print(<plot_query_list>): Print method for plot_query_list

print(<plot_validation_result>): Print method for validation results

print_table(): print table as html in viewer

Shiny Apps

Launch interactive Shiny applications for data management and exploration

launch_import_wizard(): Launch Import Wizard Shiny App

launch_feature_wizard(): Launch Feature Wizard Shiny App

launch_query_plots_app(): Launch Query Plots Interactive App

launch_individual_specimen_linking_app(): Launch Individual-Specimen Linking App

launch_specimen_import_wizard(): Launch Specimen Import Wizard

launch_taxa_traits_import(): Launch Taxa Traits Import App

launch_taxo_backbone_app(): Launch Taxonomic Backbone Management App

launch_taxonomic_match_app(): Launch Taxonomic Name Standardization App

shiny_app_query_plots(): Query Plots Shiny App

shiny_app_taxo_backbone(): Taxonomic Backbone Management Shiny App

mod_database_login_ui(): Database Login Module - UI

mod_database_login_server(): Database Login Module - Server

Shiny Module Components

Internal Shiny UI and server module components

mod_census_information_server(): Census Information Module - Server

mod_census_information_ui(): Census Information Module - UI

mod_code_preview_server(): Code Preview Module - Server

mod_code_preview_ui(): Code Preview Module - UI

mod_extraction_config_server(): Extraction Configuration Module - Server

mod_extraction_config_ui(): Extraction Configuration Module - UI

mod_feat_step1_select_plots_server(): Feature Wizard Step 1: Select Plots - Server

mod_feat_step1_select_plots_ui(): Feature Wizard Step 1: Select Plots - UI

mod_feat_step2_choose_mode_server(): Feature Wizard Step 2: Choose Mode - Server

mod_feat_step2_choose_mode_ui(): Feature Wizard Step 2: Choose Mode - UI

mod_feat_step3_measurements_server(): Feature Wizard Step 3: Individual Measurements - Server

mod_feat_step3_measurements_ui(): Feature Wizard Step 3: Individual Measurements - UI

mod_feat_step3_multi_stems_server(): Feature Wizard Step 3: Multi-Stems - Server

mod_feat_step3_multi_stems_ui(): Feature Wizard Step 3: Multi-Stems - UI

mod_feat_step3_plot_features_server(): Feature Wizard Step 3: Plot Features - Server

mod_feat_step3_plot_features_ui(): Feature Wizard Step 3: Plot Features - UI

mod_feat_step4_lookup_server(): Feature Wizard Step 4: Lookup Matching - Server

mod_feat_step4_lookup_ui(): Feature Wizard Step 4: Lookup Matching - UI

mod_feat_step5_validation_server(): Feature Wizard Step 5: Validation - Server

mod_feat_step5_validation_ui(): Feature Wizard Step 5: Validation - UI

mod_feat_step6_import_server(): Feature Wizard Step 6: Import - Server

mod_feat_step6_import_ui(): Feature Wizard Step 6: Import - UI

mod_growth_form_selector_server(): Growth Form Selector Module - Server

mod_growth_form_selector_ui(): Growth Form Selector Module - UI

mod_herbarium_parser_server(): Herbarium Parser Module - Server

mod_herbarium_parser_ui(): Herbarium Parser Module - UI

mod_individual_search_server(): Individual Search Module - Server

mod_individual_search_ui(): Individual Search Module - UI

mod_link_executor_server(): Link Executor Module - Server

mod_link_executor_ui(): Link Executor Module - UI

mod_link_preview_server(): Link Preview Module - Server

mod_link_preview_ui(): Link Preview Module - UI

mod_plot_filters_server(): Plot Filters Module - Server

mod_plot_filters_ui(): Plot Filters Module - UI

mod_plot_metadata_viewer_server(): Plot Metadata Viewer Module - Server

mod_plot_metadata_viewer_ui(): Plot Metadata Viewer Module - UI

mod_plot_statistics_server(): Plot Statistics Module - Server

mod_plot_statistics_ui(): Plot Statistics Module - UI

mod_results_display_server(): Results Display Module - Server

mod_results_display_ui(): Results Display Module - UI

mod_specimen_add_server(): Specimen Add Module - Server

mod_specimen_add_ui(): Specimen Add Module - UI

mod_specimen_import_server(): Specimen Import Module - Server

mod_specimen_import_ui(): Specimen Import Module - UI

mod_specimen_lookup_server(): Specimen Lookup Module - Server

mod_specimen_lookup_ui(): Specimen Lookup Module - UI

mod_specimen_mapping_server(): Specimen Mapping Module - Server

mod_specimen_mapping_ui(): Specimen Mapping Module - UI

mod_specimen_retriever_server(): Specimen Retriever Module - Server

mod_specimen_retriever_ui(): Specimen Retriever Module - UI

mod_specimen_search_server(): Specimen Search Module - Server

mod_specimen_search_ui(): Specimen Search Module - UI

mod_specimen_upload_server(): Specimen Upload Module - Server

mod_specimen_upload_ui(): Specimen Upload Module - UI

mod_taxa_add_server(): Taxa Add Module - Server

mod_taxa_add_ui(): Taxa Add Module - UI

mod_taxa_search_server(): Taxa Search & Browser Module - Server

mod_taxa_search_ui(): Taxa Search & Browser Module - UI

mod_taxa_synonymy_server(): Taxa Synonymy Module - Server

mod_taxa_synonymy_ui(): Taxa Synonymy Module - UI

mod_taxa_tree_view_server(): Taxa Tree View Module - Server

mod_taxa_tree_view_ui(): Taxa Tree View Module - UI

mod_taxa_update_server(): Taxa Update Module - Server

mod_taxa_update_ui(): Taxa Update Module - UI

mod_taxonomic_validator_server(): Taxonomic Validator Module - Server

mod_taxonomic_validator_ui(): Taxonomic Validator Module - UI

mod_trait_column_mapping_server(): Trait Column Mapping Module - Server

mod_trait_column_mapping_ui(): Trait Column Mapping Module - UI

mod_trait_metadata_mapping_server(): Trait Metadata Mapping Module - Server

mod_trait_metadata_mapping_ui(): Trait Metadata Mapping Module - UI

mod_trait_preview_import_server(): Trait Preview & Import Module - Server

mod_trait_preview_import_ui(): Trait Preview & Import Module - UI

mod_trait_validation_server(): Trait Validation Module - Server

mod_trait_validation_ui(): Trait Validation Module - UI

model_wd_2: model_wd_1

model_wd_2: model_wd_2

phylo_tree: phylo_tree

Internationalization

Translation and multi-language support utilities for Shiny apps

create_reactive_translator(): Create Reactive Translator

get_available_languages(): Get Available Translation Languages

init_translator(): Initialize Translator for Shiny App

Backbone Cache

Taxonomic backbone cache management for offline use

cache_exists(): Check if valid backbone cache exists

delete_backbone_cache(): Clear backbone cache

get_backbone_cache_path(): Get backbone cache directory path

get_cache_metadata(): Get cache metadata with formatted displays

load_backbone_cache(): Load backbone from cache with validation

save_backbone_cache(): Save backbone data to cache

Administration & Permissions

User management, database permissions, backup, and migration utilities

define_user_policy(): Define user policy for row-level security

define_read_only_policy(): Define read-only policy for a user

define_read_write_policy(): Define read-write policy for a user

define_full_access_policy(): Define full access policy for a user

setup_user_permissions(): Setup user permissions on both databases

setup_import_wizard_permissions(): Setup complete import wizard permissions

list_user_policies(): List user policies

register_user(): Register a user in the registry

deactivate_user(): Deactivate a user

reactivate_user(): Reactivate a user

list_database_users(): List all database users and their permissions

get_registered_users(): Get all registered users

get_user_emails(): Get email addresses of all registered users

create_user_registry(): Create user registry table

grant_all_table_permissions(): Grant permissions on ALL tables and sequences

grant_lookup_table_permissions(): Grant table-level permissions for lookup tables

grant_plot_insert_permissions(): Setup permissions for users to insert plots

backup_database(): Backup PostgreSQL database with timestamp

restore_database(): Restore database from backup

list_backups(): List available database backups

cleanup_old_backups(): Delete old database backups

diagnose_plot_permissions(): Diagnose plot insertion permissions

diagnose_add_person_setup(): Diagnose add_person function and permissions

check_citations_migration(): Check citations migration status

check_created_by_migration(): Check created_by Migration Status

check_taxa_permissions(): Check taxa database permissions

check_hierarchy_consistency(): Check Hierarchy Consistency

check_table_idtax_staleness(): Check table_idtax Staleness

get_table_idtax_metadata(): Get table_idtax Metadata

print_user_access_summary(): Print user access summary

setup_add_person_function(): Grant permissions for adding people to table_colnam

migrate_add_citations_table(): Migration: Add table_citations and id_citation FK to taxa_traits_measures

migrate_add_created_by(): Migration: Add created_by Column for Row-Level Security

migrate_table_idtax_to_materialized_view(): Migrate table_idtax to Materialized View

migration_add_audit_columns(): Add Audit Columns to data_link_specimens

migration_add_id_parent_column(): Add id_parent Column to table_taxa

migration_add_linktype_column(): Add id_linktype Column to data_link_specimens

migration_create_hierarchy_entries(): Create Missing Hierarchy Entries

migration_create_linktypelist(): Create linktypelist Lookup Table

migration_link_hierarchy(): Populate id_parent for Existing Entries

migration_link_infraspecific(): Link Infraspecific Taxa to Species (Step 5 only)

rollback_table_idtax_migration(): Rollback table_idtax Migration

run_hierarchy_migration(): Run Full Hierarchy Migration

run_specimen_links_migration(): Run Full Specimen Links Migration

test_table_idtax_migration(): Test table_idtax Materialized View Setup

verify_hierarchy_integrity(): Verify Hierarchy Integrity

verify_specimen_links_migration(): Verify Specimen Links Migration