Package index • ZooGoN

Survey Data Ingestion

KoboToolbox integration for field survey data collection

ingest_surveys(): Download MC Surveys from Kobotoolbox
get_kobo_data(): Retrieve Data from Kobotoolbox API
preprocess_surveys(): Preprocess MC Surveys

Legacy Data Ingestion

Download, validate, and harmonize legacy zooplankton datasets

ingest_legacy_84_15(): Ingest Legacy Zooplankton Data (1984-2015)
ingest_legacy_16_20(): Ingest Legacy Zooplankton Data (2016-2020)

Data Processing

Merge, harmonize, and convert zooplankton data

format_to_tidy(): Merge all zooplankton datasets into an analysis-ready tidy table
format_to_dc(): Convert legacy LTER-MareChiara zooplankton data to Darwin Core format
build_emof_occurrence(): Build occurrence-level eMoF table
build_emof_events(): Build event-level eMoF sampling metadata

Cloud Storage

SharePoint integration for data storage and retrieval

upload_sharepoint_df(): Upload a data frame to SharePoint
upload_sharepoint_file(): Upload a local file to SharePoint
download_sharepoint_file(): Download a file from SharePoint

Pipeline & Reporting

Orchestrate the full pipeline and render monitoring reports

run_pipeline(): Run the ZooGoN survey-to-report pipeline
render_report(): Render ZooGoN MC Survey Report

Utility Functions

Helper functions for data processing

reshape_kobo_repeat(): Prepare repeat answers from Kobo survey forms
add_version(): Add timestamp and sha string to a file name
read_config(): Read configuration file
load_dotenv(): Load environment variables from .env file

Publishing

Build and register Darwin Core Archives

format_to_DC_archive(): Build a Darwin Core Archive and upload to SharePoint
register_gbif_dataset(): Register a hosted archive on GBIF
register_gbif_dataset_test(): GBIF-Test demo flow (fixed keys and credentials)
add_gbif_license_block(): Add GBIF-style license block to an EML file