Package index • algaware

Launch Application

Start the AlgAware Shiny app

Fetch data from IFCB Dashboard

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
parse_non_bio_classes(): Parse non-biological classes from comma-separated string
compute_unclassified_fractions(): Compute the percentage of unclassified images per station visit
match_bins_to_stations(): Match dashboard metadata to AlgAware stations using spatial join
collect_ferrybox_data(): Collect ferrybox data for station visits

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

Parse CTD profiles and LIMS chlorophyll data for the chlorophyll map

load_chl_statistics(): Load bundled historical Chl-a statistics (1991-2020)
load_station_mapper(): Load station name synonym mapper
load_standard_stations(): Load standard monitoring stations with regional assignments
read_cnv_folder(): Parse all CNV files from a folder tree (AlgAware-matched, for chl map)
read_cnv_folder_all(): Parse all CNV files from a folder tree (all standard stations)
read_lims_data(): Read LIMS discrete chlorophyll data (AlgAware-matched)
read_lims_data_all(): Read LIMS discrete chlorophyll data (all standard stations)
compute_ctd_chl_avg(): Compute 0-20m depth-averaged chlorophyll from CTD data
compute_lims_chl_avg(): Compute 0-20m depth-averaged chlorophyll from LIMS bottle data
compute_lims_hose_avg(): Compute chlorophyll from LIMS hose (integrated 0-10 m) samples

Create plots and maps

create_pie_map(): Pie chart map with displacement and leader lines
create_group_map(): Create a phytoplankton group composition map
create_biomass_maps(): Create biomass and chlorophyll maps
create_chl_map(): Create a standalone chlorophyll map
create_ctd_region_figure(): Create a regional CTD composite figure (all standard stations)
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 concentration map from cruise metadata

Generate Word reports

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
assign_phyto_groups(): Assign phytoplankton groups using the bundled YAML configuration
get_db_path(): Get path to the annotations SQLite database

Image mosaic generation

create_mosaic(): Create an adaptive image mosaic for a taxon
create_region_mosaics(): Create mosaics for top taxa in a region
get_top_taxa(): Get top taxa by total biovolume from a wide summary
get_taxon_rois(): Get ROI information for a specific taxon in a set of samples
extract_random_taxon_image(): Extract a single random image for a taxon

AI-powered report text generation

UI and server module functions

Settings and helper functions