Package index • STOPeData

Summarise

Summarise session data into text strings for CREED quality assessment reporting.

summarise_CREED_details(): summarise user-entered data for the CREED dataset details reporting
summarise_CREED_relevance(): summarise user-entered data for the CREED relevance criteria reporting
summarise_CREED_reliability(): summarise user-entered data for the CREED reliability criteria reporting
summarise_biota(): Summarise biota data
summarise_compartments(): Summarise compartments data
summarise_date_range(): Calculate Date Range
summarise_lod_loq(): Summarise LOD/LOQ data
summarise_measured_units(): Generate Units Summary by Parameter
summarise_multiple(): Summarise Multiple Values
summarise_protocols(): Summarise protocols data
summarise_reference(): Summarise mod_reference data into a single string
summarise_sig_figs(): Summarise significant figures in numeric column
summarise_sites(): Summarise sites data
summarise_uncertainty_comments(): Summarise uncertainty and measurement comments
calculate_coordinate_precision(): Calculate coordinate precision
manual_completion_message(): Return manual completion message

Validate data formats and structures.

validate_and_lookup_identifier(): Validate and lookup DOI/PMID with comprehensive error handling
validate_and_parse_bibtex(): Validate and parse BibTeX string with error handling
validate_dataset_structure(): Validate dataset structure
validate_doi_format(): Validate DOI format
validate_pmid_format(): Validate PMID format

Helpers for preparing and submitting datasets to Zenodo.

Create new data rows and structures.

create_compartment_combination(): Create new compartment combination row
create_dummy_session_data(): Create Dummy Session Data
create_existing_parameter(): Create parameter row from existing parameter data
create_metadata_tibble(): Create metadata tibble
create_new_parameter(): Create new blank parameter row
create_new_site(): Create a new site record

Build and download session data as ZIP archives and metadata files.

write_metadata_txt(): Create readable metadata text file
get_git_commit(): Get git commit hash
get_export_metadata(): Get export metadata
get_dataset_display_name(): Get dataset display name
object_to_text(): Convert object to human-readable text
build_session_zip(): Build a session ZIP archive
download_all_data(): Download all data as CSV and TXT files in a ZIP archive
write_creed_report_txt(): Write CREED report as human-readable text file

Import session data from exported ZIP archives.

Parse BibTeX, look up DOIs and PMIDs, and manage bibliographic references.

bib_string2df_alt(): Convert BibTeX string to data frame using temporary file
map_bibtex_to_reference_fields(): Map BibTeX fields to reference input fields
map_crossref_to_reference_fields(): Map Crossref data to reference input fields
clean_bibtex_text(): Clean BibTeX text formatting
extract_clean_doi(): Extract clean DOI from input string
extract_clean_pmid(): Extract clean PMID from input string
pmid_to_doi(): Convert PMID to DOI using PubMed API
lookup_crossref_doi(): Lookup publication data using Crossref
validate_and_lookup_identifier(): Validate and lookup DOI/PMID with comprehensive error handling
reference_character_limits(): Reference field character limits

Look up and generate IDs for parameters, samples, and protocols.

get_parameters_of_types(): Get parameter names for a specific parameter type
get_parameters_filtered(): Get parameter names filtered by type and optionally subtype

Configuration and helper functions for CREED quality assessment criteria.

collect_CREED_data(): Collect CREED Scores from Input
CREED_reliability_criteria_config(): CREED Reliability Criteria Configuration
CREED_relevance_criteria_config(): CREED Relevance Criteria Configuration
copper_CREED_purpose_statement(): Load copper CREED purpose statement

Generate dummy data for development and testing.

populate_session_with_dummy_data(): Populate session data directly with dummy data
creed_tibble_to_mock_input(): Convert CREED Tibble to Mock Input List

General-purpose helpers for the Shiny app.

printreactiveValues(): Print content of reactiveValues object
info_accordion(): Create a collapsible single-panel accordion containing a markdown file
get_session_data_safe(): Safely retrieve data from session reactive values

Run the STOPeData Shiny application.