Package index • planktonr

Load Data

Functions to access data from the AODN.

pr_get_data(): Get plankton and biogeochemical data from IMOS surveys
pr_get_trips(): Get sampling trip metadata
pr_get_Indices(): Access derived ecological indices for timeseries and climatology plots
pr_get_EOVs(): Load Essential Ocean Variables (EOVs) for plankton biomass and diversity
pr_get_CTI(): Calculate Community Temperature Index (CTI) for plankton samples
pr_get_STI(): Get STI kernel density for each species
pr_get_STIdata(): Get data for STI plots of species abundance
pr_get_FuncGroups(): Aggregate plankton data by functional groups
pr_get_TaxaAccum(): Get taxa accumulation data for plotting
pr_get_FreqMap(): Prepare species occurrence data for frequency mapping
pr_get_LFData(): Get NRS larval fish abundance data
pr_get_LTnuts(): Get NRS long term nutrient timeseries data
pr_get_NRSEnvContour(): Prepare biogeochemical data for depth-time contour plots
pr_get_info(): Load plankton taxonomic or survey policy information
pr_get_ProgressMapData(): Prepare sampling coverage data for IMOS progress map visualisation
pr_get_DataLocs(): Extract sample locations and dates for satellite data matching
pr_get_Raw(): Download raw unprocessed data files directly from IMOS S3 storage
pr_get_s3(): Download raw data files from IMOS internal S3 storage (advanced users)
pr_get_DayNight(): Get data for plots of species abundance by day and night using CPR data
pr_get_SOTSMoorData(): Get data available from SOTS moorings (limited to use in BOO atm, other variables could be added, select from pr_get_SOTSvariables)
pr_get_SOTSvariables(): Get data files available from SOTS moorings
pr_get_PCIData(): Get Phytoplankton Colour Index (PCI) data from CPR samples
pr_get_SatData(): Load satellite-derived environmental data matched to plankton sampling locations

Plotting

Functions for plotting.

pr_plot_CPRmap(): Title Sidebar panel plot of selected CPR bioregions
pr_plot_Climatology(): Plot climatologies showing seasonal or interannual patterns
pr_plot_DayNight(): Visualise diel vertical migration patterns showing day vs night abundances
pr_plot_EOVs(): Essential Ocean Variables (EOV) plot for reporting
pr_plot_Enviro(): Plot environmental data with depth profiles
pr_plot_FreqMap(): Map seasonal occurrence frequency for individual plankton species
pr_plot_Gantt(): Plot Gantt Chart showing plankton sampling status
pr_plot_NRSEnvContour(): Plot environmental contours showing depth-time patterns
pr_plot_NRSmap(): Create map showing selected NRS station locations
pr_plot_PCImap(): Map Phytoplankton Colour Index (PCI) from CPR samples around Australia
pr_plot_PieFG(): Create pie charts showing functional group composition
pr_plot_ProgressMap(): Create interactive map showing IMOS plankton sampling coverage and progress
pr_plot_STI(): Plot Species Temperature Index (STI) kernel density distributions
pr_plot_TaxaAccum(): Plot taxonomic accumulation curves showing cumulative species discovery over time
pr_plot_TimeSeries(): Plot basic timeseries of plankton indices
pr_plot_Trends(): Plot temporal trends in plankton data with fitted lines
pr_plot_Voyagemap(): Create map showing CPR voyage tracks and sampling locations
pr_plot_box(): Simple boxplot function using common NRS colouring
pr_plot_latitude(): Create Hovmöller diagram showing latitudinal patterns over time
pr_plot_scatter(): Simple function to scatter 2 data columns using common NRS colouring
pr_plot_tsclimate(): Combined timeseries and climatology plots
pr_plot_tsfg(): Time series plot of functional group composition

Utilities

Helper functions for data manipulation and analysis.

pr_add_Bioregions(): Assign Australian Marine Bioregions to sample locations
pr_add_Carbon(): Add Carbon concentration to phytoplankton dataframe
pr_add_StationCode(): Add NRS station codes to data
pr_add_StationName(): Add NRS station full names to data
pr_apply_Flags(): Remove flagged data points based on IMOS quality control flags
pr_filter_data(): Filter data for plotting functions
pr_filter_NRSStations(): Filter dataframe on StationCode to return only NRS stations
pr_filter_Species(): Remove incorrect species names from dataframe
pr_harmonic(): Create harmonic functions for circular predictors
pr_make_climatology(): To produce the climatology for plotting
pr_model_data(): Fit linear models to plankton time series data
pr_remove_outliers(): Remove statistical outliers from plankton data
pr_get_coeffs(): Extract tidy model coefficients for trend analysis
theme_pr(): Define theme_pr() function

Satellite Matching

Functions for matching plankton samples to satellite data.

pr_match_Altimetry(): Match plankton samples to satellite altimetry data (sea level, currents)
pr_match_GHRSST(): Match plankton sample locations to GHRSST sea surface temperature data
pr_match_MODIS(): Match plankton samples to MODIS ocean colour data (chlorophyll, PAR, SST)

Data

Built-in datasets included with the package.

csDAT: Coastal microbial station locations
mbr: Marine bioregions (polygons and colours)

Deprecated

These functions are deprecated and will be removed in a future version. Please use [pr_get_data()], [pr_get_trips()], or [pr_get_info()] instead.

pr_get_NRSTrips() deprecated: Import NRS sampling trip metadata
pr_get_CPRTrips() deprecated: Get CPR sampling trip metadata
pr_get_NRSData() deprecated: Import NRS plankton data
pr_get_CPRData() deprecated: Import CPR plankton data
pr_get_NRSChemistry() deprecated: Load NRS chemistry data
pr_get_NRSPigments() deprecated: Load NRS pigments data
pr_get_NRSPico() deprecated: Load NRS picophytoplankton data
pr_get_NRSMicro() deprecated: Load microbial data
pr_get_NRSTSS() deprecated: Load NRS Total Suspended Solids data
pr_get_NRSCTD() deprecated: Load NRS CTD profile data
pr_get_CSChem() deprecated: Load Coastal Seas chemistry and nutrient data
pr_get_SpeciesInfo() deprecated: Get species information table for Phytoplankton and Zooplankton
pr_get_PlanktonInfo() deprecated: Load taxonomic information and trait data for plankton species
pr_get_PolicyInfo() deprecated: Load policy-relevant plankton indicators and Essential Ocean Variables
pr_get_Stations() deprecated: Import NRS Station information