Package index • concert

Run the app

run_app(): Launch the CONCERT Shiny Application

Headless curation

Curate a file without the Shiny app, or drive it from an agent loop.

curate_headless(): Run the full curation pipeline headlessly (without Shiny UI)
curate_iterate(): Run one iteration of the agent curation loop
curate_decisions_template(): Write a starter decisions.R for the agent curation loop
stage_clean(): Stage 2: run the cleaning pipeline
stage_curate(): Stage 3: run the CompTox curation search and optional candidate postprocessing
stage_export(): Stage 6: write outputs and build the result list
stage_harmonize(): Stage 5: run numeric, unit, media, and ToxVal harmonization
stage_ingest(): Stage 1: read a file, detect frontmatter, and validate the tag map
stage_review(): Stage 4: apply Review Results edits
run_curation_pipeline(): Orchestrate the full curation pipeline: dedup -> search -> map -> consensus -> resolution
generate_concert_script(): Generate a CONCERT replay script
write_curation_output(): Write Curation Output in a Requested Format
parse_concert_export(): Parse CONCERT Export

Read files and detect frontmatter

safely_read_file(): Safely read a file with multiple fallback strategies
validate_file(): Validate uploaded file before processing
validate_excel_size(): Validate Excel Size Limits
detect_data_start(): Main ensemble detection function combining all methods
detect_data_start_heuristic(): Detect data start using heuristic fill ratio method
detect_pattern_based(): Detect data start using pattern matching for common header keywords
detect_by_type_consistency(): Detect data start by checking column type consistency
extract_clean_data(): Extract clean data based on detection results
handle_merged_cells(): Handle merged cells by filling down first column
calculate_smart_preview_rows(): Calculate smart preview row count based on file size
format_file_size(): Format file size for display

Tag columns

suggest_column_tags(): Suggest Column Tags From Header Names
classify_tags(): Classify Tags into Categories
validate_tag_pairing(): Validate Tag Pairing Requirements
has_required_chemical_tags(): Check for Required Chemical Tags
detect_tag_changes(): Detect Changes Between Tag Sets
find_dtxsid_cols(): Auto-detect DTXSID columns by name pattern

Clean names and identifiers

run_cleaning_pipeline(): Run complete cleaning pipeline with audit trail tracking
apply_value_corrections(): Apply dataset-specific value corrections before cleaning
build_audit_trail(): Build audit trail by comparing two dataframes
clean_text_field(): Clean text field by stripping whitespace and punctuation artifacts
clean_unicode(): Clean Unicode symbols in character strings
perform_unicode_qc(): Perform post-curation Unicode QC (read-only detection)
detect_non_ascii_chars(): Detect non-ASCII characters in a character vector
strip_quality_adjectives(): Strip quality adjectives from name fields
strip_reference_terms(): Strip user-defined reference terms from name fields
strip_salt_references(): Strip salt references from name fields
strip_terminal_enclosures(): Strip terminal enclosures (parentheticals and brackets) from name fields
strip_terminal_unspecified(): Strip terminal "unspecified" suffixes from name fields
normalize_cas_fields(): Normalize CAS fields using ComptoxR
rescue_cas_from_text(): Rescue CAS-RNs from non-CASRN text columns
detect_multi_cas(): Detect rows with multiple CAS-RNs
detect_truncated_compound_names(): Detect likely truncated compound names
detect_bare_formulas(): Detect bare molecular formulas
expand_isotope_shortcodes(): Expand isotope shortcodes to canonical Name-Mass format (vectorized)
protect_chiral_designations(): Protect chiral designations from downstream stripping
restore_chiral_designations(): Restore chiral designation placeholders to original markers
split_synonyms(): Split semicolon-separated synonyms in name fields
extract_cas(): Extracts all valid CASRNs from a character vector
extract_formulas(): Extract molecular formulas from text
extract_mixture(): Detects chemical mixtures by name based on ratio patterns
as_cas(): Coerces and validates a string to a standard CASRN format
is_cas(): Checks if a string is a syntactically and algorithmically valid CASRN
flag_reference_matches(): Flag rows matching reference list entries
dedup_step(): Deduplication wrapper for cleaning step functions
get_dedup_preview(): Get deduplication preview counts before running full pipeline
remap_audit_to_parent(): Remap audit trail row IDs from unique-string slice to parent dataset
inject_row_lineage(): Inject row lineage tracking

Multi-analyte rows

flag_multi_analyte(): Flag rows containing naked multi-analyte expressions
suggest_multi_analyte_parts(): Suggest split parts for a multi-analyte value
resolve_multi_analyte_row(): Resolve one flagged multi-analyte row
apply_multi_analyte_resolutions(): Apply multiple multi-analyte resolutions
is_multi_analyte_review_row(): Identify rows still needing multi-analyte review

Reference lists

load_all_reference_lists(): Load all reference lists
load_block_patterns(): Load block patterns list
load_corrections(): Load one-off corrections table
load_functional_categories(): Load functional use categories
load_isotope_lookup(): Load isotope lookup table
load_media_map(): Load merged media harmonization map (user edits + bundled defaults)
load_or_fetch_reference(): Generic cache-or-fetch function
load_stop_words(): Load stop words list
load_strip_terms(): Load strip terms list
load_toxval_schema(): Load ToxVal schema manifest
load_unit_map(): Load unit conversion map
load_unit_synonyms(): Load unit synonym normalization table
load_user_reference_lists(): Load user reference list overrides
load_wqx_dictionary(): Load WQX dictionary lookup table
merge_reference_lists(): Merge Reference Lists
save_user_reference_lists(): Save user reference list overrides
update_user_reference_list(): Update a user reference list override
validate_reference_list_patterns(): Validate reference-list patterns
reference_list_help_text(): Reference-list help text
refresh_isotope_cache(): Refresh isotope lookup cache
refresh_wqx_cache(): Refresh WQX dictionary cache
clear_starts_with_cache(): Clear the starts-with cache

Resolve identities

CompTox and WQX matching, consensus, and review.

match_wqx(): Match chemical names against WQX Characteristic Name dictionary
classify_consensus(): Classify consensus across tagged columns for each row
classify_auto_resolve(): Classify disagree rows as auto-resolved, suggested, or leave as disagree
compute_similarity_scores(): Compute similarity scores for all disagree rows in resolution_state
score_one_candidate(): Compute similarity score for a single candidate against an input name
enrich_candidates(): Fetch CompTox chemical details for DTXSIDs and return structured cache
enrich_synonyms(): Fetch and cache CompTox synonym data for a set of DTXSIDs
merge_retry_results(): Merge retry curation results back into original resolution state
apply_priority_chain(): Apply en masse column priority to resolve all non-pinned disagree rows
compute_qc_tier(): Compute numeric QC tier for a consensus classification
init_resolution_state(): Initialize resolution state on a classified data frame
get_resolution_options(): Get available resolution options for a disagree row
resolve_row(): Resolve a single disagreement row by choosing a preferred column
resolve_review_row(): Resolve one flagged review row (multi-analyte and/or multi-CAS)
accept_all_suggestions(): Accept all suggested resolutions in bulk
build_review_overrides(): Build content-matched review overrides
apply_review_overrides(): Apply review overrides to a replayed resolution state
apply_review_resolutions(): Apply staged review decisions in one batch
validate_manual_dtxsids(): Validate manually-entered DTXSIDs via CompTox bulk API
set_row_flag(): Set one row flag
set_row_flags(): Set row flags in bulk
normalize_row_flag(): Normalize a row flag value
valid_row_flags(): Valid row flag values
hydrate_session_state(): Hydrate Session State

Review and accept source identities

Capture decision evidence, reconcile changes, and explicitly accept a source identity.

identity_review_state(): Derive accepted identity eligibility from current evidence
apply_identity_decisions(): Apply explicit row-scoped identity decisions
accepted_identity_view(): Return accepted identities with source lineage
source_identifier_evidence(): Validate source DTXSID membership without accepting source identity
unused_source_identifier_diagnostics(): Diagnose retained identifier columns without a source evidence role
build_candidate_review(): Report candidate validation work without changing identity or flags
validate_review_candidates(): Explicitly validate saved candidate IDs with an injected authority
capture_review_decision(): Capture evidence from an explicit review decision
capture_review_state(): Capture evidence currently inspected in a staged review
acknowledge_review_evidence(): Acknowledge current evidence for an existing decision revision
review_decision_key(): Construct a stable content-selector decision ID
review_evidence_scope(): Construct explicit source/content review scope
review_evidence_snapshot(): Construct evidence for an explicit review
identity_evidence_fingerprint(): Capture current row evidence for a scoped identity decision

Harmonize measurements

parse_numeric_results(): Parse messy numeric result strings into a structured tibble
parse_dates(): Parse mixed-format date strings into structured ISO-8601 output
harmonize_units(): Harmonize unit values using a conversion table
harmonize_media(): Harmonize environmental media strings to canonical CONCERT media terms
normalize_uncertainty_to_two_sigma(): Convert reported uncertainty to a two-sigma half-width
classify_detection_events(): Classify row-level detection events
classify_harmonized_detection(): Classify harmonized tagged measurements
map_to_toxval_schema(): Map curated data to ToxVal schema
build_export_sheets(): Build Export Sheets

Dataset context and sites

detect_site_columns(): Detect Site/Location Columns In A Dataset
extract_site_candidates(): Extract Site Candidates
build_site_manifest(): Build A Deterministic Site Manifest
build_chorus_site_manifest(): Build CHORUS Site Manifest Payload
build_site_alias_map(): Build A Deterministic Site Alias Map
normalize_site_manifest(): Normalize A Site Manifest

Shiny modules

mod_clean_data_server(): Clean Data Module - Server
mod_clean_data_ui(): Clean Data Module - UI
mod_data_preview_server(): Data Preview Module - Server
mod_data_preview_ui(): Data Preview Module - UI
mod_dataset_context_server(): Dataset Context Module - Server
mod_dataset_context_ui(): Dataset Context Module - UI
mod_detection_info_server(): Detection Info Module - Server
mod_detection_info_ui(): Detection Info Module - UI
mod_file_upload_server(): File Upload Module - Server
mod_file_upload_ui(): File Upload Module - UI
mod_harmonize_server(): Harmonize Module - Server
mod_harmonize_ui(): Harmonize Module - UI
mod_raw_data_server(): Raw Data Module - Server
mod_raw_data_ui(): Raw Data Module - UI
mod_review_results_server(): Review Results Module - Server
mod_review_results_ui(): Review Results Module - UI
mod_run_curation_server(): Run Curation Module - Server
mod_run_curation_ui(): Run Curation Module - UI
mod_tag_columns_server(): Tag Columns Module - Server
mod_tag_columns_ui(): Tag Columns Module - UI
notify_user(): Show a Shiny notification and mirror important messages to the console
log_condition(): Log a caught condition with structured console context