Package index • planktonr

Load Data Functions to access data from the AODN.
`pr_get_CPRData()`	Import CPR Data
`pr_get_CPRTrips()`	Get CPR sampling trip metadata
`pr_get_CSChem()`	Load Coastal Seas chemistry and nutrient data
`pr_get_CTI()`	Calculate Community Temperature Index (CTI) for plankton samples
`pr_get_DataLocs()`	Extract sample locations and dates for satellite data matching
`pr_get_DayNight()`	Get data for plots of species abundance by day and night using CPR data
`pr_get_EOVs()`	Load Essential Ocean Variables (EOVs) for plankton biomass and diversity
`pr_get_FreqMap()`	Prepare species occurrence data for frequency mapping
`pr_get_FuncGroups()`	Aggregate plankton data by functional groups
`pr_get_Indices()`	Access derived ecological indices for timeseries and climatology plots
`pr_get_LFData()`	Get NRS larval fish abundance data
`pr_get_LTnuts()`	Get NRS long term nutrient timeseries data
`pr_get_NRSCTD()`	Load NRS CTD profile data (temperature, salinity, fluorescence)
`pr_get_NRSChemistry()`	Load National Reference Station chemistry data
`pr_get_NRSData()`	Import NRS Data
`pr_get_NRSEnvContour()`	Prepare biogeochemical data for depth-time contour plots
`pr_get_NRSMicro()`	Load microbial abundance data from flow cytometry
`pr_get_NRSPico()`	Load picophytoplankton data from NRS stations
`pr_get_NRSPigments()`	Get photosynthetic pigments data from NRS stations
`pr_get_NRSTSS()`	Load Total Suspended Solids (TSS) data
`pr_get_NRSTrips()`	Import NRS sampling trip metadata
`pr_get_NonTaxaColumns()`	Return columns that are not taxonomic
`pr_get_PCIData()`	Generate Phytoplankton Colour Index (PCI) data from CPR samples
`pr_get_PlanktonInfo()`	Load taxonomic information and trait data for plankton species
`pr_get_PolicyInfo()`	Load policy-relevant plankton indicators and Essential Ocean Variables
`pr_get_ProgressMapData()`	Prepare sampling coverage data for IMOS progress map visualisation
`pr_get_Raw()`	Download raw unprocessed data files directly from IMOS S3 storage
`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_STI()`	Get STI kernel density for each species
`pr_get_STIdata()`	Get data for STI plots of species abundance
`pr_get_SatData()`	Load satellite-derived environmental data matched to plankton sampling locations
`pr_get_Site()`	Get URL template for AODN GeoServer WFS plankton data access
`pr_get_SpeciesInfo()`	Get species information table for Phytoplankton and Zooplankton
`pr_get_Stations()`	Import NRS Station information
`pr_get_TaxaAccum()`	Get taxa accumulation data for plotting
`pr_get_coeffs()`	Extract tidy model coefficients for trend analysis
`pr_get_s3()`	Download raw data files from IMOS internal S3 storage (advanced users)
`pr_get_s3site()`	Get IMOS S3 bucket URL for internal plankton data storage
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_apply_Time()`	Add Month & year columns to df
`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()`	For use in models to create a circular predictor
`pr_make_climatology()`	To produce the climatology for plotting
`pr_model_data()`	Fit linear models to plankton time series data
`pr_relabel()`	Format a parameter string for plotting
`pr_remove_outliers()`	Remove statistical outliers from plankton data
`pr_rename()`	Standardise column names in IMOS plankton dataframes
`pr_reorder()`	Order the Station or region in the df by latitude for consistent plotting
`pr_title()`	Helper function to reformat Titles
`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)

Reference

Load Data

Plotting

Utilities

Satellite Matching

Data