Package index • plotsdatabase

All functions

PlotFetcher: Fetch plot data

PlotFilterBuilder: Query builder for plot

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_plot_coordinates(): Add 1ha IRd plot coordinates

add_plots(): Add new plot metadata

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

add_specimens(): Add new specimens data

add_subplot_features(): List of subplot features

add_subplot_observations_feat(): #' Add a type in subplot table #' #' Add feature and associated descriptors in subplot list table #' #' @return nothing #' #' @author Gilles Dauby, gilles.dauby@ird.fr #' @param new_type string value with new type descritors - try to avoid space #' @param new_valuetype string one of following 'numeric', 'integer', 'categorical', 'ordinal', 'logical', 'character' #' @param new_maxallowedvalue numeric if valuetype is numeric, indicate the maximum allowed value #' @param new_minallowedvalue numeric if valuetype is numeric, indicate the minimum allowed value #' @param new_typedescription string full description of trait #' @param new_factorlevels string a vector of all possible value if valuetype is categorical or ordinal #' @param new_expectedunit string expected unit (unitless if none) #' @param new_comments string any comments #' #' @export add_subplottype <- function(new_type = NULL, new_valuetype = NULL, new_maxallowedvalue = NULL, new_minallowedvalue = NULL, new_typedescription = NULL, new_factorlevels = NULL, new_expectedunit = NULL, new_comments = NULL) if(is.null(new_type)) stop("define new type") if(try_open_postgres_table(table = "subplotype_list", con = mydb) dplyr::distinct(type) dplyr::filter(type == !!new_type) dplyr::collect() nrow()>0) stop("new type already in table") if (is.null(new_valuetype)) stop("define new_valuetype") if (!any(new_valuetype==c('numeric', 'integer', 'categorical', 'ordinal', 'logical', 'character', 'table_colnam'))) stop("valuetype should one of following 'numeric', 'integer', 'categorical', 'ordinal', 'logical', 'character' or 'table_colnam'") if (new_valuetype=="numeric" | new_valuetype=="integer") if (!is.numeric(new_maxallowedvalue) & !is.integer(new_maxallowedvalue)) stop("valuetype numeric of integer and max value not of this type") if (new_valuetype=="numeric" | new_valuetype=="integer") if (!is.numeric(new_minallowedvalue) & !is.integer(new_minallowedvalue)) stop("valuetype numeric of integer and min value not of this type") mydb <- call.mydb() new_data_renamed <- tibble(type = new_type, valuetype = new_valuetype, maxallowedvalue = ifelse(is.null(new_maxallowedvalue), NA, new_maxallowedvalue), minallowedvalue = ifelse(is.null(new_minallowedvalue), NA, new_minallowedvalue), typedescription = ifelse(is.null(new_typedescription), NA, new_typedescription), factorlevels = ifelse(is.null(new_factorlevels), NA, new_factorlevels), expectedunit = ifelse(is.null(new_expectedunit), NA, new_expectedunit), comments = ifelse(is.null(new_comments), NA, new_comments)) print(new_data_renamed) Q <- choose_prompt(message = "confirm adding this type?") if(Q) DBI::dbWriteTable(mydb, "subplotype_list", new_data_renamed, append = TRUE, row.names = FALSE)

add_taxa_table_taxa(): Add formatted taxa information

add_trait(): Add trait

add_trait_taxa(): Add a trait in species trait list

add_traits_measures(): Add an observation in trait measurement table

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_taxa_permissions(): Check taxa database permissions

choose_growth_form(): Choose growth forms

choose_prompt(): Choose from prompt

cleanup_connections(): Cleanup all database connections

connect_database(): Connect to database

country_list(): List of countries

create_db_config(): Create local DB config file

db_diagnostic(): Complete database diagnostic

define_read_only_policy(): Helper functions for common policy scenarios

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

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

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

.delete_colnam(): Delete an entry in colnam 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_individual_feature_type(): Delete an entry in individual feature table

.delete_individuals(): Delete an entry in individuals table

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

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

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

.delete_specimens(): Delete an entry in specimen table

.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

.split_censuses(): Split plot data into census

.time_diff(): Add time difference in number of days for two census

.trim.growth(): Identify potential errors for estimating growth

enrich_with_traits(): Enrich individuals with all traits

explore_allometric_taxa(): Explore allometric relation

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_individual_aggregated_features(): Aggregate individual features to individual level

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

growth_computing(): Growth computing for multiple census

latlong2UTM(): Get UTM from geographical coordinates

launch_stand_tax_app(): Launch shiny app for taxonomic standardization

launch_taxonomic_match_app(): Launch Taxonomic Name Standardization App

list_individual_features(): List all available individual features

list_user_policies(): List user policies

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

model_wd_2: model_wd_1

phylo_tree model_wd_2: phylo_tree

print(<plot_query_list>): Print method for plot_query_list

print_connection_status(): Print connection status

print_table(): print table as html in viewer

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_plot_features(): Query subplot features with improved architecture

query_plots(): Query plots from database

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(): Query fuzzy match

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

table_taxa_tb: Table taxa

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