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Aggregate plankton data by functional groups

Source: R/utils_plankton.R
pr_get_FuncGroups.Rd

Aggregate plankton data into major functional groups for community structure analysis. Functional groups represent taxa with similar ecological roles or morphological characteristics (e.g., diatoms, dinoflagellates, copepods).

Usage

pr_get_FuncGroups(Survey = "NRS", Type = "Zooplankton", ...)

Arguments

Survey

Survey type:

  • "NRS" - National Reference Stations

  • "CPR" - Continuous Plankton Recorder

  • "SOTS" - Southern Ocean Time Series

Type

Plankton type:

  • "Phytoplankton" - Includes centric diatoms, pennate diatoms, dinoflagellates, cyanobacteria, and other groups

  • "Zooplankton" - Includes copepods, appendicularians, molluscs, cladocerans, chaetognaths, thaliaceans, and other groups

...

Additional variables passed to pr_add_Bioregions(). For CPR data, you can use:

  • near_dist_km - Distance in kilometres to pad bioregion boundaries

Value

A dataframe in long format with columns for location/station, date, functional group (Parameters), and abundance (Values). Suitable for use with pr_plot_tsfg() and other functional group visualisation functions.

Details

Phytoplankton Functional Groups

The function aggregates phytoplankton into five major groups:

  • Centric diatoms - Radially symmetrical diatoms, typically bloom-forming

  • Pennate diatoms - Bilaterally symmetrical diatoms

  • Dinoflagellates - Flagellated protists, some toxic

  • Cyanobacteria - Photosynthetic bacteria (e.g., Synechococcus, Trichodesmium)

  • Other - All remaining groups (flagellates, ciliates, etc.)

Zooplankton Functional Groups

The function aggregates zooplankton into seven major groups:

  • Copepods - Dominant group of marine zooplankton

  • Appendicularians - Gelatinous filter feeders (larvaceans)

  • Molluscs - Primarily pteropods (sea butterflies, sea angels)

  • Cladocerans - Water fleas (e.g., Penilia, Evadne)

  • Chaetognaths - Arrow worms (predatory)

  • Thaliaceans - Gelatinous filter feeders (salps, doliolids, pyrosomes)

  • Other - All remaining groups

Data are based on higher taxonomic group (htg) abundance and aggregated by sample. Port Hacking 4 samples are excluded from NRS data.

See also

pr_plot_tsfg() for plotting functional group time series, pr_get_Indices() for community-level indices

Examples

# Get NRS zooplankton functional groups
NRSfgz <- pr_get_FuncGroups(Survey = "NRS", Type = "Zooplankton")

# Get NRS phytoplankton functional groups
NRSfgp <- pr_get_FuncGroups(Survey = "NRS", Type = "Phytoplankton")

# Get CPR functional groups with expanded bioregion boundaries
CPRfgz <- pr_get_FuncGroups(Survey = "CPR", Type = "Zooplankton", near_dist_km = 250)
CPRfgp <- pr_get_FuncGroups(Survey = "CPR", Type = "Phytoplankton")

# Examine the functional groups present
unique(NRSfgp$Parameters)
#> [1] Centric diatom Pennate diatom Dinoflagellate Cyanobacteria  Other         
#> Levels: Centric diatom Pennate diatom Dinoflagellate Cyanobacteria Other