WS23011_WS23011_WS23011_65

---

if (!nzchar(system.file(package = "librarian"))) {
  install.packages("librarian")
}

librarian::shelf(
  quiet = TRUE,
  readr, here, fs, ggplot2, glue, "jiho/castr", dplyr, oce, patchwork, purrr, tidyr
)

source(here("R/get_metadata_from_cast_id.R"))
metadata <- get_metadata_from_cast_id(params$cast_id)
station_id <- metadata$station_id
cruise_id <- metadata$cruise_id
dataFile <- here::here(glue::glue(
  "data/01_raw/{params$cast_id}.csv"
))

source(here::here("R/ctd_load_from_csv.R"))
cast <- ctd_load_from_csv(dataFile)

WS23011_WS23011_WS23011_65.csv 
Added 62 additional parameters to CTD object

# TODO: Include param here that specifies to handle QC flags. This should be done before converting to a OCE object. QC flag columns are listed in [this spreadsheet](https://docs.google.com/spreadsheets/d/1uCxEmJRqErU-HCQiRQ1FpyiIqtNaGgMSBI0WvrtwBRU/edit?gid=137286311#gid=137286311) and are not supposed to be included in the oce object. QC param values are : 
#   1 good
#   2 +/- 3*std_dev
#   4 +/- 5*std_dev
#   9 missing
# Data column should be set to NA if corresponding QC column has value greater than threshold (recommended threshold is 5*std_dev).
# Will need to loop through *_qc columns.

# TODO: drop spikes (how? low-pass?).

# TODO: combine replicate sensors (eg temp1 temp2).

Before Cleaning

print(glue("=== station: {cast@metadata$station[1]}"))

=== station: 65

print(glue("# scans: {length(cast@data$scan)}"))

# scans: 52

plot(cast)

after cleaning

tryCatch({
  
  trimmed_cast <- ctdTrim(cast)
  decimated_cast <- ctdDecimate(trimmed_cast, p = 0.1)

  # plotting can cause the xlim failure
  plot(decimated_cast)

  # === export ===
  # Get the scan numbers that remain after cleaning
  cleaned_scans <- decimated_cast@data$scan
  
  # Load original raw data to keep all columns
  ctd_raw <- readr::read_csv(dataFile, show_col_types = FALSE)
  
  # Filter raw data to only include the cleaned scans
  cast_df <- ctd_raw %>%
    filter(!is.na(sea_water_pressure)) %>%  # Remove rows without pressure data
    mutate(row_num = row_number()) %>%
    filter(row_num %in% cleaned_scans) %>%
    select(-row_num)
  
  # Add metadata
  cast_df <- mutate(
    cast_df,
    station = station_id,
    cruise_id = cruise_id
  )

  # Check if there are any rows in the cleaned data
  if (nrow(cast_df) == 0) {
    cat("\n=== WARNING: NO DATA AFTER CLEANING ===\n")
    cat("Cast ID:", params$cast_id, "\n")
    cat("Station:", station_id, "\n")
    cat("Cruise:", cruise_id, "\n\n")
    
    cat("Raw data rows (with pressure):", sum(!is.na(ctd_raw$sea_water_pressure)), "\n")
    cat("Cleaned scans to keep:", length(cleaned_scans), "\n")
    cat("Resulting rows:", nrow(cast_df), "\n\n")
    
    cat("Raw data summary:\n")
    print(summary(ctd_raw[c("sea_water_pressure", "sea_water_temperature", "sea_water_salinity")]))
    
    cat("\nCleaned scans (first 20):\n")
    print(head(cleaned_scans, 20))
    
    cat("\n=== CSV FILE NOT CREATED (no data) ===\n\n")
  } else {
    # create folder if doesn't exist
    clean_data_loc <- here::here("data/02_clean")
    try(fs::dir_create(clean_data_loc))

    # save ctd to .csv (without row names/indices)
    write.csv(cast_df, glue("{clean_data_loc}/{params$cast_id}.csv"), row.names = FALSE)
    
    cat("Successfully saved", nrow(cast_df), "rows to", glue("{params$cast_id}.csv"), "\n")
  }

}, error = function(e) {

  cat("\n=== CTD PROCESSING ERROR ===\n")
  cat("Cast ID:", params$cast_id, "\n")
  cat("Error message:\n", conditionMessage(e), "\n\n")

  # Safely inspect objects that might or might not exist when the error happened
  if (exists("decimated_cast")) {
    df <- try(as.data.frame(decimated_cast@data), silent = TRUE)
    if (!inherits(df, "try-error")) {

      cat("Dataframe columns:\n")
      print(names(df))

      cat("\nSummary of key columns (scan, pressure, temperature, salinity if present):\n")
      known_cols <- intersect(c("scan", "pressure", "temp", "temperature", "salinity", "conductivity"), names(df))
      print(summary(df[known_cols], digits = 3))

      cat("\nHead of dataframe:\n")
      print(head(df))
    } else {
      cat("Could not extract dataframe from decimated_cast.\n")
    }
  } else {
    cat("decimated_cast was never created before the error.\n")
  }

  cat("\n=== END ERROR DEBUG INFO ===\n\n")
})

=== WARNING: NO DATA AFTER CLEANING ===
Cast ID: WS23011_WS23011_WS23011_65 
Station: 65 
Cruise: WS23011 

Raw data rows (with pressure): 52 
Cleaned scans to keep: 0 
Resulting rows: 0 

Raw data summary:
 sea_water_pressure sea_water_temperature sea_water_salinity
 Min.   :2.846      Min.   :18.10         Min.   :32.05     
 1st Qu.:2.851      1st Qu.:18.10         1st Qu.:32.06     
 Median :2.854      Median :18.10         Median :32.06     
 Mean   :2.857      Mean   :18.10         Mean   :32.06     
 3rd Qu.:2.863      3rd Qu.:18.10         3rd Qu.:32.07     
 Max.   :2.879      Max.   :18.11         Max.   :32.07     

Cleaned scans (first 20):
integer(0)

=== CSV FILE NOT CREATED (no data) ===

---

NOTE: The following plots have been disabled.

To avoid an oversized website, the following plots have been disabled using eval:false. GitHub pages’ free hosting limits websites to 2GB in size; including these plots pushes this website over that limit. To view the outputs you can run the following code locally.

tryCatch({
  source(here::here("R/ctd_plot_available_params.R"))

  # Plotting function with specific parameters
  ctd_plot_available_params(
    decimated_cast,
    c(
      "sea_water_electrical_conductivity",
      "descent_rate", "sound_velocity",
      "sea_water_sigma_t","altimeter"
    )
  )
}, error = function(e) {
  cat("\n=== ERROR: Physical Parameters Plot ===\n")
  cat("Cast ID:", params$cast_id, "\n")
  cat("Error:", conditionMessage(e), "\n")
  if (exists("decimated_cast")) {
    cat("Available parameters:", paste(names(decimated_cast@data), collapse=", "), "\n")
  }
  cat("========================================\n\n")
})

tryCatch({
  source(here::here("R/ctd_plot_available_params.R"))

  ctd_plot_available_params(
    decimated_cast,
     c(
      "CDOM", "dissolved_oxygen",
      "oxygen_saturation",
      "chlorophyll_concentration", "chlorophyll_fluorescence"
    )
  )
}, error = function(e) {
  cat("\n=== ERROR: Nutrient Parameters Plot ===\n")
  cat("Cast ID:", params$cast_id, "\n")
  cat("Error:", conditionMessage(e), "\n")
  if (exists("decimated_cast")) {
    cat("Available parameters:", paste(names(decimated_cast@data), collapse=", "), "\n")
  }
  cat("========================================\n\n")
})

tryCatch({
  source(here::here("R/ctd_plot_available_params.R"))

  ctd_plot_available_params(
      decimated_cast,
      c(
        "photosynthetically_available_radiation",
        "beam_attenuation","beam_transmission"
      )
    )
}, error = function(e) {
  cat("\n=== ERROR: Optical Parameters Plot ===\n")
  cat("Cast ID:", params$cast_id, "\n")
  cat("Error:", conditionMessage(e), "\n")
  if (exists("decimated_cast")) {
    cat("Available parameters:", paste(names(decimated_cast@data), collapse=", "), "\n")
  }
  cat("========================================\n\n")
})