Package index • algaware

Launch Application

Start the AlgAware Shiny app

launch_app(): Launch the AlgAware Shiny Application

Data Download

Fetch data from IFCB Dashboard

fetch_dashboard_metadata(): Fetch metadata from the IFCB Dashboard
fetch_image_counts(): Fetch image count metadata from the IFCB Dashboard
filter_metadata(): Filter metadata by cruise number or date range
download_raw_data(): Download raw IFCB files for selected bins
download_features(): Download feature files for selected bins

Data Processing

Process and aggregate IFCB data

aggregate_station_data(): Aggregate biovolume data per station visit
summarize_biovolumes(): Summarize biovolumes for classified bins
create_wide_summary(): Create wide-format summary for a region
match_bins_to_stations(): Match dashboard metadata to AlgAware stations using spatial join
collect_ferrybox_data(): Collect ferrybox data for station visits

Classification

Read and resolve classifier data

read_h5_classifications(): Read classifications from H5 files
read_classifier_name(): Read classifier name from an H5 classification file
resolve_class_list(): Resolve the active class list
copy_classification_files(): Copy classification H5 files for selected bins

Visualization

Create plots and maps

create_biomass_maps(): Create biomass and chlorophyll maps
create_heatmap(): Create a heatmap of biovolume by species and station
create_stacked_bar(): Create a stacked bar chart of relative biovolume
create_image_count_map(): Create an image count map from cruise metadata

Reports

Generate Word reports

generate_report(): Generate the AlgAware Word report
generate_english_summary(): Generate the English summary text
generate_swedish_summary(): Generate the Swedish summary text
generate_station_description(): Generate a station description

Database

SQLite database operations

load_annotations_db(): Load annotations from SQLite
save_annotations_db(): Save selected annotations to SQLite
load_global_class_list_db(): Load global class list from SQLite
save_global_class_list_db(): Save global class list to SQLite
load_algaware_stations(): Load AlgAware station definitions
load_taxa_lookup(): Load the bundled taxa lookup table
get_db_path(): Get path to the annotations SQLite database

Mosaics

Image mosaic generation

create_mosaic(): Create an adaptive image mosaic for a taxon
create_region_mosaics(): Create mosaics for top taxa in a region

LLM Support

AI-powered report text generation

llm: LLM Text Generation for AlgAware Reports
llm_available(): Check if LLM text generation is available
llm_provider(): Detect the default LLM provider
llm_providers(): List available LLM providers
llm_model_name(): Get the model name for a provider

Shiny Modules

UI and server module functions

mod_data_loader_server(): Data Loader Module Server
mod_data_loader_ui(): Data Loader Module UI
mod_gallery_server(): Gallery Module Server
mod_gallery_ui(): Gallery Module UI
mod_report_server(): Report Module Server
mod_report_ui(): Report Module UI
mod_settings_server(): Settings Module Server
mod_settings_ui(): Settings Module UI
mod_validation_server(): Validation Module Server
mod_validation_ui(): Validation Module UI

Utilities

Settings and helper functions

load_settings(): Load persistent settings
save_settings(): Save settings to disk