Get plankton and biogeochemical data from IMOS surveys

A unified interface for retrieving plankton abundance, biovolume, and biogeochemical data from IMOS marine monitoring programs. This function consolidates multiple survey-specific functions into a single entry point.

Usage

pr_get_data(
  Survey = "NRS",
  Type = "Phytoplankton",
  Variable = NULL,
  Subset = NULL,
  Format = "all"
)

Arguments

Survey

Survey program to retrieve data from:

• "NRS" - National Reference Stations (default). Coastal monitoring stations around Australia with monthly sampling.

• "CPR" - Continuous Plankton Recorder. Ship-towed sampler providing broad-scale spatial coverage along shipping routes.

• "SOTS" - Southern Ocean Time Series. Deep-water mooring site south of Tasmania for monitoring Southern Ocean ecosystems.

• "Coastal" - Coastal Seas microbial monitoring sites.

• "GO-SHIP" - Global Ocean Ship-based Hydrographic Investigations Program.

• "HAB" - Phytoplankton monitoring data from state based and seafood industry monitoring programs

Type

Data type to retrieve (case-insensitive for Phytoplankton/Zooplankton):

• "Phytoplankton" - Phytoplankton abundance or biovolume (NRS, CPR, SOTS)

• "Zooplankton" - Zooplankton abundance (NRS, CPR, SOTS)

• "Chemistry" - Water chemistry including nutrients (NRS, Coastal)

• "Pigments" - HPLC photosynthetic pigments (NRS only)

• "Pico" - Picophytoplankton from flow cytometry (NRS only)

• "Micro" - Microbial community data (NRS, Coastal, GO-SHIP)

• "TSS" - Total Suspended Solids (NRS only)

• "CTD" - CTD profiles: temperature, salinity, fluorescence (NRS only)

Variable

Variable to retrieve (required for Phytoplankton/Zooplankton):

• "abundance" - Cell or individual counts

• "biovolume" - Cell biovolume in cubic micrometres (Phytoplankton only)

Subset

Data aggregation level (required for Phytoplankton/Zooplankton):

• "raw" - Raw taxonomic data as identified by analysts

• "htg" - Higher taxonomic groups (e.g., diatoms, dinoflagellates)

• "genus" - Aggregated to genus level

• "species" - Aggregated to species level

• "copepods" - Copepod data only (Zooplankton only)

Format

Output format for Pigments data:

• "all" - All individual pigment concentrations (default)

• "binned" - Pigments grouped into functional classes

Value

A dataframe containing the requested data. Structure varies by data type (see Details).

Details

Available Data by Survey

Survey	Available Types
NRS	Phytoplankton, Zooplankton, Chemistry, Pigments, Pico, Micro, TSS, CTD
CPR	Phytoplankton, Zooplankton
SOTS	Phytoplankton, Zooplankton
HAB	Phytoplankton
Coastal	Micro, Chemistry
GO-SHIP	Micro

Return Format

The structure of the returned dataframe varies by data type:

Wide format (taxa/variables as columns):

• Phytoplankton, Zooplankton: Taxa names as columns, samples as rows

• CTD: Measurement variables as columns, depth bins as rows

Long format (Parameters and Values columns):

• Chemistry, Pigments, Pico, Micro, TSS: Standardised long format with Parameters column containing variable names and Values column containing measurements

Parameter Requirements

• Variable and Subset are required for Phytoplankton and Zooplankton

• Format is only used for Pigments (defaults to "all")

• Unused parameters will generate a warning

See also

pr_get_trips() for sampling trip metadata, pr_get_Indices() for derived ecological indices, pr_get_info() for station and taxonomic information

Examples

# Get NRS phytoplankton abundance data at genus level
dat <- pr_get_data(Survey = "NRS", Type = "Phytoplankton",
                   Variable = "abundance", Subset = "genus")

# Get CPR zooplankton data
dat <- pr_get_data(Survey = "CPR", Type = "Zooplankton",
                   Variable = "abundance", Subset = "htg")

# Get NRS water chemistry
dat <- pr_get_data(Survey = "NRS", Type = "Chemistry")

# Get NRS pigments in binned format
dat <- pr_get_data(Survey = "NRS", Type = "Pigments", Format = "binned")

# Get NRS CTD profiles
dat <- pr_get_data(Survey = "NRS", Type = "CTD")

# Get GO-SHIP microbial data
dat <- pr_get_data(Survey = "GO-SHIP", Type = "Micro")

# Get Coastal Seas chemistry data
dat <- pr_get_data(Survey = "Coastal", Type = "Chemistry")

# Get HAB phytoplankton data
dat <- pr_get_data(Survey = "HAB", Type = "Phytoplankton",
                   Variable = "abundance", Subset = "genus")