Example of WISP.data functions

Provide the account of your station

userid <- Sys.getenv("WISP_IREA_USERID")
pwd <- Sys.getenv("WISP_IREA_PSW")

Get data from the WISP station server for a single or multiple dates.

In this function if the save_csv parameter is set to TRUE, the function will save the reflectance data as a .csv file in the ‘output’ folder within the working directory.

reflect_data <- WISP.data::wisp_get_reflectance_multi_data(
  time_from = "2024-09-11T09:00",
  time_to   = "2024-09-17T14:00",
  station   = "WISPstation012",
  userid    = userid,
  pwd       = pwd,
  save_csv  = FALSE,
  out_dir   = tempdir()
)

Quality Check (QC) of the reflectance data

In this function if the save_csv parameter is set to TRUE, the function will save the quality checked reflectance data as a .csv file in the ‘output’ folder within the working directory.

User-configurable Parameters:

maxPeak (numeric): maximum allowed reflectance peak threshold. Default: 0.05
maxPeak_blue (numeric): maximum allowed threshold for the blue region. Default: 0.02
qa_threshold (numeric): maximum threshold for the QA index. Default: 0.5
qwip_threshold (numeric): minimum threshold for the QWIP index. Default: 0.2
calc_scatt (logical): if TRUE, computes scattering parameters and band ratios
calc_SPM (logical): if TRUE, computes SPM concentration according to Novoa et al. (2017)
calc_TUR (logical): if TRUE, computes TUR concentration according to Novoa et al. (2017)
calc_TSS (logical): if TRUE, computes SPM concentration according to Jiang et al. (2021)
calc_gons (logical): if TRUE, computes CHL concentration according to Gons et al. (2002)
calc_gons740 (logical): if TRUE, computes CHL concentration according to Gons et al. (2002)
calc_NDCI (logical): if TRUE, computes NDCI index according to Mishra et al. (2012)
calc_mishra (logical): if TRUE, computes CHL concentration according to Mishra et al. (2012)
calc_dom_wave (logical): if TRUE, computes dominant wavelength and Hue Angle
calc_OWT (logical): if TRUE, computes Optical Water Type classification

reflect_data_qc <- WISP.data::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        = tempdir()
)

# ----
# 106 spectral signatures were removed during QC:
# 
# - 16 spectral signatures were removed thanks to QA+QWIP
# - 2 spectral signatures were removed thanks to QC1+QA+QWIP
# - 4 spectral signatures were removed thanks to QC2+QA+QWIP
# - 1 spectral signatures were removed thanks to QC3+QC4+QA+QWIP
# - 4 spectral signatures were removed thanks to QC4+QA+QWIP
# - 79 spectral signatures were removed thanks to QC6+QA+QWIP
# 
# The spectral signature of 2024-09-11 09:00:05 has been removed thanks to: QC6 QA QWIP
# The spectral signature of 2024-09-11 09:15:05 has been removed thanks to: QC6 QA QWIP
# The spectral signature of 2024-09-11 09:30:05 has been removed thanks to: QC6 QA QWIP
# The spectral signature of 2024-09-11 09:45:05 has been removed thanks to: QC6 QA QWIP
# The spectral signature of 2024-09-11 10:00:05 has been removed thanks to: QC6 QA QWIP
# The spectral signature of 2024-09-11 10:15:05 has been removed thanks to: QA QWIP
# The spectral signature of 2024-09-11 10:30:05 has been removed thanks to: QC6 QA QWIP
# The spectral signature of 2024-09-11 10:45:05 has been removed thanks to: QC6 QA QWIP
# The spectral signature of 2024-09-11 11:00:05 has been removed thanks to: QC6 QA QWIP
# The spectral signature of 2024-09-11 11:15:05 has been removed thanks to: QC2 QA QWIP
# The spectral signature of 2024-09-11 11:30:05 has been removed thanks to: QC6 QA QWIP
# The spectral signature of 2024-09-11 11:45:05 has been removed thanks to: QC6 QA QWIP
# The spectral signature of 2024-09-11 12:00:05 has been removed thanks to: QC6 QA QWIP
# The spectral signature of 2024-09-11 12:15:05 has been removed thanks to: QC6 QA QWIP
# The spectral signature of 2024-09-11 12:30:06 has been removed thanks to: QC6 QA QWIP
# The spectral signature of 2024-09-11 12:45:05 has been removed thanks to: QC6 QA QWIP
# The spectral signature of 2024-09-11 13:00:05 has been removed thanks to: QC6 QA QWIP
# The spectral signature of 2024-09-11 13:15:05 has been removed thanks to: QC6 QA QWIP
# The spectral signature of 2024-09-11 13:30:05 has been removed thanks to: QC6 QA QWIP
# ...
# The spectral signature of 2024-09-17 09:00:05 has been removed thanks to: QC3 QC4 QA QWIP
# The spectral signature of 2024-09-17 09:15:05 has been removed thanks to: QC4 QA QWIP
# The spectral signature of 2024-09-17 09:30:05 has been removed thanks to: QA QWIP
# The spectral signature of 2024-09-17 09:45:05 has been removed thanks to: QA QWIP
# The spectral signature of 2024-09-17 10:00:05 has been removed thanks to: QA QWIP
# The spectral signature of 2024-09-17 10:15:05 has been removed thanks to: QC6 QA QWIP
# The spectral signature of 2024-09-17 10:30:05 has been removed thanks to: QC6 QA QWIP
# The spectral signature of 2024-09-17 10:45:05 has been removed thanks to: QC6 QA QWIP
# The spectral signature of 2024-09-17 11:00:05 has been removed thanks to: QC6 QA QWIP
# The spectral signature of 2024-09-17 11:15:05 has been removed thanks to: QC6 QA QWIP
# The spectral signature of 2024-09-17 11:30:05 has been removed thanks to: QC6 QA QWIP
# The spectral signature of 2024-09-17 11:45:05 has been removed thanks to: QC6 QA QWIP
# The spectral signature of 2024-09-17 12:00:05 has been removed thanks to: QC6 QA QWIP
# The spectral signature of 2024-09-17 12:15:05 has been removed thanks to: QC6 QA QWIP
# The spectral signature of 2024-09-17 12:30:05 has been removed thanks to: QC6 QA QWIP
# The spectral signature of 2024-09-17 12:45:05 has been removed thanks to: QC6 QA QWIP
# The spectral signature of 2024-09-17 13:00:05 has been removed thanks to: QC6 QA QWIP
# The spectral signature of 2024-09-17 13:15:05 has been removed thanks to: QC6 QA QWIP
# The spectral signature of 2024-09-17 13:30:05 has been removed thanks to: QC4 QA QWIP
# The spectral signature of 2024-09-17 13:45:05 has been removed thanks to: QC6 QA QWIP
# 
# QA remove spectral signatures with low quality based on Wei et al. (2016)
# QC1 remove spectral signatures with negative values below 845 nm
# QC2 remove spectral signatures with outliers in the NIR (840 nm > 700 nm)
# QC3 remove spectral signatures with maximum peak greater than maxPeak
# QC4 remove spectral signatures with outliers in the Blue domain
# QC6 remove 'invalid' and 'None' spectral signatures according to level2.quality
# QWIP remove spectral signatures with low quality based on Dierssen et al., 2022
# ----

Skyglint Removal (SR) of the reflectance data

In this function if the save_csv parameter is set to TRUE, the function will save the reflectance data with the sunglint removed as a .csv file in the ‘output’ folder within the working directory.

User-configurable Parameters:

calc_scatt (logical): if TRUE, computes scattering parameters and band ratios
calc_SPM (logical): if TRUE, computes SPM concentration according to Novoa et al. (2017)
calc_TUR (logical): if TRUE, computes TUR concentration according to Novoa et al. (2017)
calc_TSS (logical): if TRUE, computes SPM concentration according to Jiang et al. (2021)
calc_gons (logical): if TRUE, computes CHL concentration according to Gons et al. (2002)
calc_gons740 (logical): if TRUE, computes CHL concentration according to Gons et al. (2002)
calc_NDCI (logical): if TRUE, computes NDCI index according to Mishra et al. (2012)
calc_mishra (logical): if TRUE, computes CHL concentration according to Mishra et al. (2012)
calc_dom_wave (logical): if TRUE, computes dominant wavelength and Hue Angle
calc_OWT (logical): if TRUE, computes Optical Water Type classification

reflect_data_sr <- WISP.data::wisp_sr_reflectance_data(
  qc_data       = reflect_data_qc,
  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       = tempdir()
)

Plot the reflectance data

In this function, you can set to TRUE for the parameters you want to display in the legend for each of the three plots (raw, QC, SR).

custom_raw <- list(
  legend_TSM  = TRUE, 
  legend_Chla = TRUE, 
  legend_Kd   = TRUE, 
  legend_cpc  = TRUE
)

custom_qc <- list(
  legend_TSM            = TRUE, 
  legend_Chla           = TRUE, 
  legend_Kd             = TRUE, 
  legend_cpc            = TRUE, 
  legend_scatt          = TRUE,
  legend_ratio          = TRUE,
  legend_novoa_SPM      = TRUE,
  legend_novoa_TUR      = TRUE,
  legend_jiang_TSS      = TRUE,
  legend_gons_CHL       = TRUE,
  legend_gons740_CHL    = TRUE,
  legend_NDCI           = TRUE,
  legend_mishra_CHL     = TRUE,
  legend_hue_angle      = TRUE, 
  legend_dom_wavelength = TRUE,
  legend_OWT_class      = TRUE,
  legend_OWT_score      = TRUE,
  legend_OWT_z_dist     = TRUE
)

custom_sr <- list(
  legend_TSM            = TRUE, 
  legend_Chla           = TRUE, 
  legend_Kd             = TRUE, 
  legend_cpc            = TRUE, 
  legend_scatt          = TRUE,
  legend_ratio          = TRUE,
  legend_novoa_SPM      = TRUE,
  legend_novoa_TUR      = TRUE,
  legend_jiang_TSS      = TRUE,
  legend_gons_CHL       = TRUE,
  legend_gons740_CHL    = TRUE,
  legend_NDCI           = TRUE,
  legend_mishra_CHL     = TRUE,
  legend_hue_angle      = TRUE, 
  legend_dom_wavelength = TRUE,
  legend_OWT_class      = TRUE,
  legend_OWT_score      = TRUE,
  legend_OWT_z_dist     = TRUE
)

fig_comparison <- WISP.data::wisp_plot_comparison(
  raw_data = reflect_data, 
  qc_data  = reflect_data_qc, 
  sr_data  = reflect_data_sr,
  raw_args = custom_raw,
  qc_args  = custom_qc,
  sr_args  = custom_sr
)
fig_comparison

Plot the temporal trend

In this function, you can modify the following variables:

params (character vector): list of parameters to visualize
aggregate (character): defines how temporal aggregation is applied:
- none: displays all individual measurements (ideal for single-day analysis)
- daily_mean: calculates the daily mean and adds a ribbon (standard deviation)
- daily_median: calculates the daily median
merge_plot (logical): if TRUE, parameters sharing the same unit are overlaid in a single plot

fig_trend <- WISP.data::wisp_trend_plot(
  data       = reflect_data_sr,
  params     = c("TSM", "Chla", "Novoa_SPM", "Mishra_CHL"),
  aggregate  = "daily_mean",
  merge_plot = TRUE
)

## 
## ----------------------------------------------------------------------
## Parameters available (`params`): TSM, Chla, Kd, cpc, scatt, ratio, Novoa_SPM, Novoa_TUR, Jiang_TSS, Gons_CHL, Gons740_CHL, NDCI, Mishra_CHL, Hue_Angle, Dom_Wave

## 
## Aggregation methods (`aggregate`):
##  - 'none': Plot all available values (requires only one day in `wisp_get_reflectance_data()`).
##  - 'daily_mean': Plot the daily average and standard deviation (requires multiple days in `wisp_get_reflectance_data()`).
##  - 'daily_median': Plot the daily median (requires multiple days in `wisp_get_reflectance_data()`)
## ----------------------------------------------------------------------