Get photosynthetic pigments data from NRS stations

Source: R/utils_bgc.R

Load High-Performance Liquid Chromatography (HPLC) pigment data from NRS stations. Pigments can be retrieved as individual compounds or grouped into functional classes.

pr_get_NRSPigments(Format = "all")

Arguments

Format

Output format:

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

  • "binned" - Pigments grouped into functional classes (e.g., total chlorophyll, photoprotective carotenoids)

Value

A dataframe in long format with pigment data including:

  • StationCode, StationName - Station identifiers

  • SampleTime_Local - Local sampling date and time

  • SampleDepth_m - Sampling depth (numeric)

  • Parameters - Pigment name or pigment class

  • Values - Concentration (mg/m³)

Details

Individual Pigments (Format = "all")

Returns concentrations (mg/m³) of individual pigments including:

  • Chlorophylls: Cphl A, B, C1, C2, C3, chlorophyllide A

  • Carotenoids: fucoxanthin, peridinin, alloxanthin, zeaxanthin, etc.

  • Degradation products: phaeophytin A & B, phaeophorbide A, pyrophaeophorbide A

Binned Pigments (Format = "binned")

Returns pigments grouped into functional classes:

  • TotalChla - Total chlorophyll a (including degradation products)

  • TotalChl - All chlorophyll pigments combined

  • PPC - Photoprotective carotenoids (protect from high light)

  • PSC - Photosynthetic carotenoids (harvest light energy)

  • PSP - Total photosynthetic pigments (PSC + Total Chl)

  • TCaro - Total carotenoids

  • TAcc - Total accessory pigments (everything except Chl a)

  • TPig - Total pigments

  • TDP - Total diagnostic pigments (used for phytoplankton community analysis)

Quality control flags are applied and samples with zero total chlorophyll a are removed. Water column (WC) samples are excluded as they represent integrated samples rather than discrete depths.

See also

pr_get_NRSChemistry() for nutrient data, pr_plot_Enviro() for visualising pigment depth profiles, pr_remove_outliers() for outlier removal

Examples

# Get all individual pigments
df <- pr_get_NRSPigments()

# Get binned pigment classes
df <- pr_get_NRSPigments(Format = "binned")

# Filter for total chlorophyll a at Maria Island
df_chla <- df %>%
  dplyr::filter(Parameters == "TotalChla", StationCode == "MAI")