Load National Reference Station chemistry data

Source: R/utils_bgc.R

Load water chemistry measurements from NRS stations, including nutrients (nitrogen, phosphorus, silicate), dissolved oxygen, carbon chemistry, and physical properties. Data are quality controlled using IMOS flags.

pr_get_NRSChemistry()

Value

A dataframe in long format with chemistry data including:

  • StationCode, StationName - Station identifiers

  • SampleTime_Local - Local sampling date and time

  • SampleDepth_m - Sampling depth

  • Parameters - Chemistry parameter name

  • Values - Measured or calculated value

Details

The function retrieves and processes the following parameters:

Nutrients:

  • Nitrate_umolL - Nitrate concentration (µmol/L)

  • Nitrite_umolL - Nitrite concentration (µmol/L)

  • Ammonium_umolL - Ammonium concentration (µmol/L)

  • Phosphate_umolL - Phosphate concentration (µmol/L)

  • Silicate_umolL - Silicate concentration (µmol/L)

  • NOx_umolL - Nitrogen oxides (nitrate + nitrite, µmol/L)

  • DIN_umolL - Dissolved inorganic nitrogen (NOx + ammonium, µmol/L)

Carbon Chemistry:

  • DIC_umolkg - Dissolved inorganic carbon (µmol/kg)

  • Alkalinity_umolkg - Total alkalinity (µmol/kg)

Other:

  • Oxygen_umolL - Dissolved oxygen (µmol/L)

  • Salinity - Salinity (unitless, PSU)

  • SecchiDepth_m - Secchi depth, measure of water clarity (m)

  • Redfield - N:P ratio (calculated as NOx/Phosphate)

Quality control flags are applied using pr_apply_Flags(). Samples are filtered to include only NRS stations.

NOx, DIN, and Redfield ratio are calculated from the measured nutrient values.

See also

pr_get_NRSPigments() for photosynthetic pigment data, pr_get_NRSCTD() for CTD profile data, pr_get_NRSEnvContour() to format data for contour plots

Examples

df <- pr_get_NRSChemistry()

# Examine available parameters
unique(df$Parameters)
#>  [1] "SecchiDepth_m"     "Silicate_umolL"    "Phosphate_umolL"  
#>  [4] "Ammonium_umolL"    "Nitrate_umolL"     "Nitrite_umolL"    
#>  [7] "Oxygen_umolL"      "DIC_umolkg"        "Alkalinity_umolkg"
#> [10] "Salinity"          "NOx_umolL"         "DIN_umolL"        
#> [13] "Redfield"         

# Filter for surface nitrate at specific stations
df_nitrate <- df %>%
  dplyr::filter(Parameters == "Nitrate_umolL", 
                SampleDepth_m == 0,
                StationCode %in% c("MAI", "PHB"))