Quality Control (QC) for WISPstation reflectance data

This function performs the Quality Control (QC) process and applies different algorithms to spectral signatures. The function applies a structured sequence of QC tests (QC1 - QC6), designed to identify and remove low-quality or physically implausible spectra. In addition, the function integrates independent quality assessment metrics derived from the literature (QA and QWIP), providing robust spectral validation through established optical criteria.

Usage

wisp_qc_reflectance_data(
  data,
  maxPeak = 0.05,
  maxPeak_blue = 0.02,
  qa_threshold = 0.5,
  qwip_threshold = 0.2,
  calc_scatt = TRUE,
  calc_SPM = TRUE,
  calc_TUR = TRUE,
  calc_TSS = TRUE,
  calc_gons = TRUE,
  calc_gons740 = TRUE,
  calc_NDCI = TRUE,
  calc_mishra = TRUE,
  calc_dom_wave = TRUE,
  calc_OWT = TRUE,
  save_csv = FALSE,
  out_dir = "outputs"
)

Arguments

data

A tibble. From wisp_get_reflectance_data() function.

maxPeak

A decimal. Maximum magnitude of the spectral signatures. We recommend setting this parameter to: 0.02 for clear and oligotrophic water, 0.05 for meso- to eutrophic water, and 0.08 for hypereutrophic and highly turbid water. Default is 0.05.

maxPeak_blue

A decimal. Maximum magnitude 350 nm values. We recommend setting this parameter to: 0.02 (default).

qa_threshold

A decimal. Minimum threshold for Quality Assurance (QA). We recommend setting this parameter to: 0.5 (default). To make QC more stringent, raise the threshold.

qwip_threshold

A decimal. Maximum threshold for Quality Water Index Polynomial (QWIP). We recommend setting this parameter to: 0.2 (default). To make QC more stringent, decrease the threshold.

calc_scatt

A logical. If TRUE, the function calculates the peak due to phytoplankton scattering (690-710 nm) and the ratio of the latter to the second chlorophyll absorption peak (670-680 nm). Default is TRUE.

calc_SPM

A logical. If TRUE, the function calculates the SPM concentrations in according to Novoa et al., (2017). Default is TRUE.

calc_TUR

A logical. If TRUE, the function calculates the turbidity (FNU) in according to Novoa et al., (2017). Default is TRUE.

calc_TSS

A logical. If TRUE, the function calculates the TSS concentrations in according to Jiang et al., (2021). Default is TRUE.

calc_gons

A logical. If TRUE, the function calculates chlorophyll using Gons et al. (2002) algorithm (NIR ~782 nm). Default is TRUE.

calc_gons740

A logical. If TRUE, the function calculates chlorophyll using Gons et al. (2002) algorithm (NIR ~740 nm). Default is TRUE.

calc_NDCI

A logical. If TRUE, the function calculates The Normalised Difference Chlorophyll Index algorithm by Mishra and Mishra (2012). Default is TRUE.

calc_mishra

A logical. If TRUE, the function calculates chlorophyll using Mishra and Mishra (2012) algorithm. Default is TRUE.

calc_dom_wave

A logical. If TRUE, the function calculates the hue angle and the dominant wavelength. Default is TRUE.

calc_OWT

A logical. If TRUE, the function calculates the Optical Water Type classification in according to Bi and Hieronymi (2024) (OWT_class), the membership probability (OWT_score), and the average Z-score (OWT_z_dist). In addition, it adds a column with the description of the corresponding OWT class. "OWT_class" represents the optical category to which the analyzed spectral signature belongs based on Gaussian Likelihood. "OWT_score" is a value between 0 and 1 representing the fuzzy membership grade; it indicates the probability of belonging to the selected class relative to the other available classes. "OWT_z_dist" indicates the statistical distance between the observed spectrum and the class mean, weighted by its standard deviation. 0-1.5 indicate an excellent fit with the OWT reference. Values above 3 suggest that the spectral signature is an outlier or deviates significantly from the typical range of that class. Default is TRUE.

save_csv

A logical. If TRUE, the function saves the reflectance data.

out_dir

A character. The directory where the CSV file will be saved. Default is "outputs" within the working directory.

Value

A tibble with the spectral signatures that have passed QC operation and all the extra parameters that were requested. In addition, a message containing the reason behind the elimination of each anomalous spectral signature. If parameter save_csv is TRUE, the function saves the reflectance data in a CSV file.

Author

Alessandro Oggioni, phD alessandro.oggioni@cnr.it

Nicola Ghirardi, phD nicola.ghirardi@cnr.it

Examples

# example code
if (FALSE) { # \dontrun{
## Not run:
reflect_data_qc <- wisp_qc_reflectance_data(
  data = reflect_data,
  maxPeak = 0.05,
  maxPeak_blue = 0.02,
  qa_threshold    = 0.5,
  qwip_threshold  = 0.2,
  calc_scatt = TRUE,
  calc_SPM = TRUE,
  calc_TUR = TRUE,
  calc_TSS = TRUE,
  calc_gons = TRUE,
  calc_gons740 = TRUE,
  calc_NDCI = TRUE,
  calc_mishra = TRUE,
  calc_dom_wave = TRUE,
  calc_OWT = TRUE,
  save_csv = FALSE,
  out_dir = "outputs"
)
} # }
## End (Not run)