## ----echo = TRUE, results = 'hide', warning=FALSE, eval=FALSE----------------- # userid <- Sys.getenv("WISP_IREA_USERID") # pwd <- Sys.getenv("WISP_IREA_PSW") ## ----echo = TRUE, results = 'hide', warning=FALSE, message=FALSE, eval=FALSE---- # 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() # ) ## ----echo = TRUE, results = 'hide', warning=FALSE, message=FALSE, eval=FALSE---- # 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 # # ---- # ## ----echo = TRUE, results = 'hide', warning=FALSE, eval=FALSE----------------- # 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() # ) ## ----warning=FALSE, out.width="100%", eval=FALSE------------------------------ # 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 ## ----warning=FALSE, message=TRUE, out.width="100%", eval=FALSE---------------- # 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 # ) # fig_trend