Package index • CafriplotsR

All functions

add_entry_taxa(): Add new entry to taxonomic table

add_growth_form_taxa(): Add growth forms to a single taxa

add_individuals(): Add new individuals data

add_method(): Add a method in method list

add_plots(): Add new plot metadata

add_plot_coordinates(): Add 1ha IRd plot coordinates

add_plot_features(): Add Plot Features to Existing Plots

add_specimens(): Add new specimens data

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

add_subplot_features(): Add an observation in subplot_features table

add_subplot_observations_feat(): Add subplot observations features

add_taxa_table_taxa(): Add formatted taxa information

add_trait(): Add trait

add_traits_measures(): Add an observation in trait measurement table

add_trait_taxa(): Add a trait in species trait list

approximate_isolated_xy(): Interpolate x y position based on neighnour

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

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

check_created_by_migration(): Check created_by Migration Status

check_taxa_permissions(): Check taxa database permissions

choose_growth_form(): Choose growth forms

choose_prompt(): Choose from prompt

cleanup_connections(): Cleanup all database connections

compute_growth(): Compute growth rates for permanent plots

compute_mortality(): Compute mortality and recruitment rates

connect_database(): Connect to database

country_list(): List of countries

create_db_config(): Create local DB config file

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

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

db_diagnostic(): Complete database diagnostic

define_full_access_policy(): Define full access policy for a user

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

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

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

delete_backbone_cache(): Clear backbone cache

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

divid_plot(): Divid into quadrats a 1ha plot

.add_link_specimens(): Add link between specimen and individual

.add_modif_field(): Query fuzzy match

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

.delete_colnam(): Delete an entry in colnam table

.delete_country(): Delete an entry in country table

.delete_entry_sp_trait_measure(): Delete an entry in traits measurements table

.delete_entry_trait_measure(): Delete an entry in trait measurement table (individuals features)

.delete_entry_trait_measure_features(): Delete an entry in trait measurement features table

.delete_individuals(): Delete an entry in individuals table

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

.delete_link_individual_specimen(): Delete an entry in trait measurement table

.delete_plot(): Delete an entry in plot meta-data

.delete_specimens(): Delete an entry in specimen table

.delete_sp_trait_list(): Delete an entry in species trait list

.delete_subplotfeature(): Delete an entry in data_liste_sub_plots features

.delete_subplotfeature_feat(): Delete an entry in data_liste_sub_plots features

.delete_subplottype(): Delete an entry in subplotype_list table

.delete_trait_list(): Delete an entry in trait list

.find_cat(): Internal function

.find_ids(): Internal function

.find_similar_string(): Internal function

.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(): Internal function

.rename_data(): Internal function

enrich_with_traits(): Enrich individuals with all traits

explore_allometric_taxa(): Explore allometric relation

export_plot_template(): Export Plot Metadata Template to Excel

extract_corners(): Extract all corners of 1ha plot

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

get_connection_info(): Get connection information

get_database_fk(): Get database foreign keys

get_import_column_routing(): Get Import Column Routing Configuration

get_individual_aggregated_features(): Aggregate individual features to individual level

get_individual_template(): Generate Individual Data Import Template

get_plot_metadata_template(): Get Plot Metadata Template

get_plot_rel_xy(): Project stems in geographical space

get_ref_specimen_ind(): Find unlinked individual

get_updates_diconame(): Get backups of modified taxonomic data

get_user_accessible_plots(): Get plot IDs accessible to a user

import_individual_data(): Import Individual Data with Transaction Support

import_plot_metadata(): Import Plot Metadata with Transaction Support

latlong2UTM(): Get UTM from geographical coordinates

launch_import_wizard(): Launch Import Wizard Shiny App

launch_query_plots_app(): Launch Query Plots Interactive App

launch_taxonomic_match_app(): Launch Taxonomic Name Standardization App

list_database_users(): List all database users and their permissions

list_individual_features(): List all available individual features

list_user_policies(): List user policies

map_individual_columns(): Map Individual Data Columns

map_user_columns(): Map User Columns to Database Schema

match_tax(): Query and standardize taxonomy

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

merge_individuals_taxa(): Merge individual records with taxonomic information

method_list(): List of method

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

model_wd_2: model_wd_1

model_wd_2: model_wd_2

mod_auto_matching_server(): Auto Matching Module - Server

phylo_tree: phylo_tree

PlotFetcher: Fetch plot data

PlotFilterBuilder: Query builder for plot

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_connection_status(): Print connection status

print_import_result(): Print Import Result

print_individual_template_info(): Export Individual Template Info

print_individual_validation_results(): Print Individual Validation Results

print_mapping_summary(): Print Mapping Summary

print_table(): print table as html in viewer

print_template_info(): Print Template Column Information

print_user_access_summary(): Print user access summary

print_validation_results(): Print Validation Results

process_individuals(): Process individuals for query_plots

process_stems(): Process multiple stems

process_trimble_data(): Process trimble data

proj_rel_xy(): Project stems in geographical space

query_colnam(): Query in colnam table

query_individual_features(): Query individual features with improved architecture

query_link_individual_specimen(): Query link between specimens and individuals

query_plots(): Query plots from database

query_plot_features(): Query subplot features with improved architecture

query_specimens(): Exploring specimens data

query_taxa(): List, extract taxa

query_taxa_traits(): Query traits at the taxonomic level

query_trait(): Query in taxa trait table

query_traits_measures_features(): Query features associated with trait measurements

remove_db_credentials(): Remove stored credentials

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

setup_db_credentials(): Setup credentials storage in environment variables

species_plot_matrix(): Get species-plot data frame

standardize_taxonomic_batch(): Standardize taxonomic names in a data frame

subplot_list(): List all available subplot types

summarize_feature(): Get summary statistics for a specific feature

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

test_connection(): Test database connection

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

traits_taxa_list(): List of trait

try_open_postgres_table(): Try to open PostgreSQL table

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

update_specimens_batch(): Update specimens data data

update_taxa_link_table(): Update local taxonomy link table

validate_individual_data(): Validate Individual Data Before Import

validate_plot_metadata(): Validate Plot Metadata Before Import