Package index • calcofi4r

Read

functions reading data, particularly from the CalCOFI API

cc_describe_table(): Describe a CalCOFI database table
cc_list_measurement_types(): List available measurement types
cc_list_tables(): List tables in CalCOFI database
cc_query(): Execute SQL query on CalCOFI database
cc_read_bottle(): Read CalCOFI bottle data
cc_read_casts() cc_read_cast(): Read CalCOFI cast data
cc_read_cruise(): Read CalCOFI cruise data
cc_read_ichthyo() cc_read_larvae(): Read CalCOFI ichthyoplankton (larvae) data
cc_read_measurements(): Read CalCOFI bottle measurements
cc_read_site(): Read CalCOFI site data
cc_read_species(): Read CalCOFI species data
cc_read_tow(): Read CalCOFI tow data
get_cruises() deprecated: Get cruises from CalCOFI API
get_env(): Retrieve Environmental Data from Database
get_raster() deprecated: Get raster of interpolated values from CalCOFI API
get_sp(): Retrieve Species Larval Abundance Data from Database
get_timeseries() deprecated: Get timeseries summary from CalCOFI API
get_variables() deprecated: Get variables from CalCOFI API

functions for analyzing data

buffer_transect(): Create Buffer Around Line Segment with Dateline Handling
get_oceano_var_aoi() deprecated: Get oceanographic variable for area of interest
prep_env_hex(): Aggregate Environmental Data into H3 Hexagons
prep_filter_summary(): Build Filter Summary for Display
prep_sp_hex(): Aggregate Species Data into H3 Hexagons
prep_splot(): Prepare Data for Species-Environment Scatterplot
prep_ts_env(): Build Environmental Time Series Data
prep_ts_sp(): Build Species Time Series Data
pts_to_contours_gam(): Interpolate points to contours using a Generalized Additive Model (GAM)
pts_to_rast_idw(): Interpolate points to raster using Inverse-Distance Weighting (IDW)
rast_to_contours(): Raster to contour polygons

functions for visualizing data

map_env(): Create Interactive Environmental Map with Hexagonal Binning
map_raster(): Map raster interactively
map_sp(): Create Interactive Species Distribution Map with Hexagonal Binning
modal_data(): Data Selection Modal Dialog
modal_depth_profile(): Depth Profile Modal Dialog
plot_depth(): Plot interactive depth of an oceanographic variable
plot_timeseries(): Plot interactive time series of an oceanographic variable
plot_ts(): Create Dual-Panel Time Series Plot
ui_placeholder(): Create Placeholder Message UI

small lookup and example datasets not requiring API access

bottle_temp_depth: Bottle data of temperature with depth (m)
bottle_temp_lonlat: Bottle data of temperature in space (latitude, longitude)
cc_bottle: Bottle data in space and time
cc_grid: CalCOFI Grid for Extracting Effort
cc_grid_ctrs: CalCOFI Grid Centroids for Extracting Effort
cc_grid_zones: CalCOFI Grid Zones
cc_places: CalCOFI Places
stations: Oceanographic stations

functions specific to database (Admin only)

cc_db_catalog(): Show CalCOFI database catalog as interactive table
cc_db_connect(): Connect to the CalCOFI PostgreSQL database (Admin only) - DEPRECATED
cc_db_info(): Get CalCOFI database information
cc_erd(): Generate Mermaid ERD from DuckDB Connection
cc_erd_color_map(): Build an ERD color map from table → dataset metadata
cc_get_db(): Connect to CalCOFI Database
cc_get_dm(): Get CalCOFI Database as dm Object with Relationships
cc_list_versions(): List available CalCOFI database versions
cc_list_view_templates(): List Available View Templates
cc_make_view(): Create a Derived VIEW in the Database
cc_read_sf(): Read Spatial Table from DuckDB as sf Object
cc_release_notes(): View CalCOFI database release notes
cc_tbl(): Access a CalCOFI Database Table
create_index(): Create index in database

check for other functions or datasets not captured by above categories

cc_match_bio_env(): Match biological to environmental observations
cc_match_ichthyo_by_name(): Match ichthyoplankton to environmental data by scientific name
cc_match_ichthyo_by_taxon(): Match ichthyoplankton to environmental data by WoRMS taxon subtree
cc_match_zooplankton_biomass(): Match zooplankton biomass to environmental data
get_taxon_children(): Retrieve Taxon Children from Database
plot(<cc_erd>): Plot a cc_erd object as an interactive diagram
updateMermaid(): Update the mermaid library in the package