WS1015

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/cruise_load.R"))
cruise_df <- cruise_load(params$cruise_id)

Warning: One or more parsing issues, call `problems()` on your data frame for details,
e.g.:
  dat <- vroom(...)
  problems(dat)

tryCatch({
  plots <- list()
  
  for (station_name in unique(cruise_df$station)) {
    subset_df <- filter(cruise_df, station == station_name)
    plots[[station_name]] <- ggplot(subset_df, aes(x = time_elapsed)) +
      geom_point(aes(y = depth), color = "blue") +  # Plot depth in blue
      geom_line(aes(y = sea_water_pressure), color = "red") +  # Plot sea water pressure in red
      ggtitle(glue("{station_name}")) +
      theme(
        axis.title.x = element_blank(),
        axis.title.y = element_blank(),
        axis.text.x = element_blank(),
        axis.text.y = element_blank(),
        axis.ticks.x = element_blank(),
        axis.ticks.y = element_blank()
      )  # Remove individual axis titles and text
  }
  
  # drop nulls
  plots <- purrr::compact(plots)
  
  # Combine all plots into a grid
  combined_plot <- wrap_plots(plots) + 
    plot_layout(ncol = 4) +  # Adjust ncol to set number of columns in the grid
    plot_annotation(
      title = "Depth (blue) and Pressure (red)",
      subtitle = "Each panel represents a different station",
      caption = "Time Elapsed (x-axis) vs Depth & Pressure (y-axis)"
    ) +
    theme(
      plot.tag = element_text(size = 12, face = "bold"),
      plot.tag.position = "topleft",
      axis.title.x = element_text(margin = margin(t = 10)),
      axis.title.y = element_text(margin = margin(r = 10))
    )
  
  print(combined_plot)
}, error = function(er){
  print(er)
});

p <- ggplot(cruise_df, aes(x = time, y = depth, fill = station)) +
  geom_col() +  # This creates the bars
  # geom_text(aes(label = station), vjust = -0.3) +  # This adds labels to each bar, adjust vjust for position
  labs(x = "Time", y = "Depth", title = "Depth over Time by Station") +  # Set labels and title
  theme_minimal()  # Use a minimal theme
print(p)

ctd_load <- function(data, other_params = NULL) {
  
  # create csv into ctd object
  test_ctd <-
    as.ctd(
      salinity    = data$sea_water_salinity,
      temperature = data$sea_water_temperature,
      pressure    = data$sea_water_pressure,
      station     = data$station
    )
  
  # add additional columns to ctd object
  if (!is.null(other_params)) {
    for (param_name in other_params) {
      test_ctd <-
        oceSetData(
          object = test_ctd,
          name   = param_name,
          value  = data[[param_name]]
        )
    }
  }
  print(glue("{data$station[1]}:\t{length(test_ctd@data$scan)} scans"))


  return(test_ctd)
}

# Define other parameters to add
other_params <- c(
  "cruise_id", "station", "time", "time_elapsed", 
  "latitude", "longitude", "sea_water_electrical_conductivity", 
  "CDOM", "dissolved_oxygen","oxygen_saturation", "chlorophyll_concentration", 
  "chlorophyll_fluorescence", "photosynthetically_available_radiation", 
  "beam_attenuation","beam_transmission", "depth", "sea_water_sigma_t",
  "descent_rate", "sound_velocity","altimeter"
)

# Split data by station and create data list
ctd_FK <- cruise_df %>%
  split(.$station) %>%
  map(~ ctd_load(.x, other_params = other_params)) # ~ is a lambda(x)

1:  5369 scans
10: 1998 scans
11: 1886 scans
12: 2960 scans
13: 1628 scans
15: 4617 scans
15.5:   7497 scans
16: 2304 scans
17: 2897 scans
18: 2380 scans
19: 31 scans
1B: 197 scans
20: 1116 scans
21: 3994 scans
21.5:   6540 scans
22: 1917 scans
22.5:   6711 scans
23: 797 scans
24: 706 scans
3:  6512 scans
31: 3241 scans
32: 2364 scans
34: 2374 scans
39: 2161 scans
4:  37 scans
41: 2731 scans
42: 2783 scans
45: 2915 scans
49: 2591 scans
5:  37 scans
50: 918 scans
53: 51 scans
54: 750 scans
56: 431 scans
58: 914 scans
59: 925 scans
6:  3301 scans
6.5:    6410 scans
60: 549 scans
68: 2590 scans
69: 2707 scans
7:  2499 scans
8:  2763 scans
9.5:    6010 scans
CAL1:   105 scans
CAL3:   1018 scans
CAL4:   2181 scans
CAL5:   1614 scans
CH2:    1358 scans
CH3:    1849 scans
CH4:    2109 scans
CH5:    4380 scans

for (i in seq(ctd_FK)){
  cast <- ctd_FK[[i]]  # 1 is selecting only the first sublist
  # print(i)
  print(glue("=== station: {cast@metadata$station[1]}"))
  print(glue("# scans: {length(cast@data$scan)}"))
  plotScan(cast)
}

=== station: 1
# scans: 5369

=== station: 10
# scans: 1998

=== station: 11
# scans: 1886

=== station: 12
# scans: 2960

=== station: 13
# scans: 1628

=== station: 15
# scans: 4617

=== station: 15.5
# scans: 7497

=== station: 16
# scans: 2304

=== station: 17
# scans: 2897

=== station: 18
# scans: 2380

=== station: 19
# scans: 31

=== station: 1B
# scans: 197

=== station: 20
# scans: 1116

=== station: 21
# scans: 3994

=== station: 21.5
# scans: 6540

=== station: 22
# scans: 1917

=== station: 22.5
# scans: 6711

=== station: 23
# scans: 797

=== station: 24
# scans: 706

=== station: 3
# scans: 6512

=== station: 31
# scans: 3241

=== station: 32
# scans: 2364

=== station: 34
# scans: 2374

=== station: 39
# scans: 2161

=== station: 4
# scans: 37

=== station: 41
# scans: 2731

=== station: 42
# scans: 2783

=== station: 45
# scans: 2915

=== station: 49
# scans: 2591

=== station: 5
# scans: 37

=== station: 50
# scans: 918

=== station: 53
# scans: 51

=== station: 54
# scans: 750

=== station: 56
# scans: 431

=== station: 58
# scans: 914

=== station: 59
# scans: 925

=== station: 6
# scans: 3301

=== station: 6.5
# scans: 6410

=== station: 60
# scans: 549

=== station: 68
# scans: 2590

=== station: 69
# scans: 2707

=== station: 7
# scans: 2499

=== station: 8
# scans: 2763

=== station: 9.5
# scans: 6010

=== station: CAL1
# scans: 105

=== station: CAL3
# scans: 1018

=== station: CAL4
# scans: 2181

=== station: CAL5
# scans: 1614

=== station: CH2
# scans: 1358

=== station: CH3
# scans: 1849

=== station: CH4
# scans: 2109

=== station: CH5
# scans: 4380

for (i in seq(ctd_FK)){
  cast <- ctd_FK[[i]]  # 1 is selecting only the first sublist
  tryCatch({
    plot(ctdDecimate(ctdTrim(cast)))
  }, error = function(e){
    print(e)
  })
}

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 5369' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1998' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1886' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2960' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1628' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 4617' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 7497' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2304' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2897' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2380' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 31' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 197' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1116' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3994' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 6540' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1917' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 6711' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 797' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 706' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 6512' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3241' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2364' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2374' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2161' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 37' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2731' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2783' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2915' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2591' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 918' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 51' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 750' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 431' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 914' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 925' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3301' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 6410' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 549' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2590' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2707' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2499' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2763' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 6010' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 105' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1018' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2181' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1614' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1358' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1849' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2109' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 4380' in coercion to 'logical(1)'>

# Loop through each CTD cast
for (i in seq(ctd_FK)){
  cast <- ctd_FK[[i]]  # Assuming each sublist contains only one relevant CTD object
  tryCatch({
    # Extract metadata for station name and cruise ID
    station_name <- cast@metadata$station[1]
    cruise_id <- cast@data$cruise_id[1]

    # Generate a title with station name and cruise ID
    overall_title <- glue::glue("Station: {station_name}, Cruise ID: {cruise_id}")

    # Set margins: increase the outer margin for the title
    par(oma = c(0, 0, 3, 0))  # Top outer margin increased for title

    # Plotting function with specific parameters
    oce::plot(
      x = ctdDecimate(ctdTrim(cast)),
      which = c(
        "sea_water_electrical_conductivity",
        "descent_rate", "sound_velocity",
        "sea_water_sigma_t","altimeter"
      ),
      main = ""  # No main title for individual subplots
    )

    # Place a single overall title at the top of the plot frame
    mtext(overall_title, side = 3, line = 1, outer = TRUE, cex = 1.5)

    # Reset outer margins to default
    par(oma = c(0, 0, 0, 0))

  }, error = function(e) {
    print(e$message)  # Print any errors that occur during plotting
  })
}

[1] "need finite 'xlim' values"

[1] "need finite 'xlim' values"

[1] "need finite 'xlim' values"

[1] "need finite 'xlim' values"

[1] "need finite 'xlim' values"

[1] "need finite 'xlim' values"

# Loop through each CTD cast
for (i in seq(ctd_FK)){
  cast <- ctd_FK[[i]]  # Assuming each sublist contains only one relevant CTD object
  tryCatch({
    # Extract metadata for station name and cruise ID
    station_name <- cast@metadata$station[1]
    cruise_id <- cast@data$cruise_id[1]

    # Generate a title with station name and cruise ID
    overall_title <- glue::glue("Station: {station_name}, Cruise ID: {cruise_id}")

    # Set margins: increase the outer margin for the title
    par(oma = c(0, 0, 3, 0))  # Top outer margin increased for title

    # Plotting function with specific parameters
    oce::plot(
      x = ctdDecimate(ctdTrim(cast)),
      which = c(
        "CDOM", "dissolved_oxygen",
        "oxygen_saturation",
        "chlorophyll_concentration", "chlorophyll_fluorescence"
      ),
      main = ""  # No main title for individual subplots
    )

    # Place a single overall title at the top of the plot frame
    mtext(overall_title, side = 3, line = 1, outer = TRUE, cex = 1.5)

    # Reset outer margins to default
    par(oma = c(0, 0, 0, 0))

  }, error = function(e) {
    print(e$message)  # Print any errors that occur during plotting
  })
}

[1] "In plot,ctd-method() : which=\"CDOMdissolved_oxygenoxygen_saturationchlorophyll_concentrationchlorophyll_fluorescence\" cannot be handled"
[1] "In plot,ctd-method() : which=\"CDOMdissolved_oxygenoxygen_saturationchlorophyll_concentrationchlorophyll_fluorescence\" cannot be handled"
[1] "In plot,ctd-method() : which=\"CDOMdissolved_oxygenoxygen_saturationchlorophyll_concentrationchlorophyll_fluorescence\" cannot be handled"
[1] "In plot,ctd-method() : which=\"CDOMdissolved_oxygenoxygen_saturationchlorophyll_concentrationchlorophyll_fluorescence\" cannot be handled"
[1] "In plot,ctd-method() : which=\"CDOMdissolved_oxygenoxygen_saturationchlorophyll_concentrationchlorophyll_fluorescence\" cannot be handled"
[1] "In plot,ctd-method() : which=\"CDOMdissolved_oxygenoxygen_saturationchlorophyll_concentrationchlorophyll_fluorescence\" cannot be handled"
[1] "In plot,ctd-method() : which=\"CDOMdissolved_oxygenoxygen_saturationchlorophyll_concentrationchlorophyll_fluorescence\" cannot be handled"
[1] "In plot,ctd-method() : which=\"CDOMdissolved_oxygenoxygen_saturationchlorophyll_concentrationchlorophyll_fluorescence\" cannot be handled"
[1] "In plot,ctd-method() : which=\"CDOMdissolved_oxygenoxygen_saturationchlorophyll_concentrationchlorophyll_fluorescence\" cannot be handled"
[1] "In plot,ctd-method() : which=\"CDOMdissolved_oxygenoxygen_saturationchlorophyll_concentrationchlorophyll_fluorescence\" cannot be handled"
[1] "In plot,ctd-method() : which=\"CDOMdissolved_oxygenoxygen_saturationchlorophyll_concentrationchlorophyll_fluorescence\" cannot be handled"
[1] "In plot,ctd-method() : which=\"CDOMdissolved_oxygenoxygen_saturationchlorophyll_concentrationchlorophyll_fluorescence\" cannot be handled"
[1] "In plot,ctd-method() : which=\"CDOMdissolved_oxygenoxygen_saturationchlorophyll_concentrationchlorophyll_fluorescence\" cannot be handled"
[1] "In plot,ctd-method() : which=\"CDOMdissolved_oxygenoxygen_saturationchlorophyll_concentrationchlorophyll_fluorescence\" cannot be handled"
[1] "In plot,ctd-method() : which=\"CDOMdissolved_oxygenoxygen_saturationchlorophyll_concentrationchlorophyll_fluorescence\" cannot be handled"
[1] "In plot,ctd-method() : which=\"CDOMdissolved_oxygenoxygen_saturationchlorophyll_concentrationchlorophyll_fluorescence\" cannot be handled"
[1] "In plot,ctd-method() : which=\"CDOMdissolved_oxygenoxygen_saturationchlorophyll_concentrationchlorophyll_fluorescence\" cannot be handled"
[1] "In plot,ctd-method() : which=\"CDOMdissolved_oxygenoxygen_saturationchlorophyll_concentrationchlorophyll_fluorescence\" cannot be handled"
[1] "In plot,ctd-method() : which=\"CDOMdissolved_oxygenoxygen_saturationchlorophyll_concentrationchlorophyll_fluorescence\" cannot be handled"
[1] "In plot,ctd-method() : which=\"CDOMdissolved_oxygenoxygen_saturationchlorophyll_concentrationchlorophyll_fluorescence\" cannot be handled"
[1] "In plot,ctd-method() : which=\"CDOMdissolved_oxygenoxygen_saturationchlorophyll_concentrationchlorophyll_fluorescence\" cannot be handled"
[1] "In plot,ctd-method() : which=\"CDOMdissolved_oxygenoxygen_saturationchlorophyll_concentrationchlorophyll_fluorescence\" cannot be handled"
[1] "In plot,ctd-method() : which=\"CDOMdissolved_oxygenoxygen_saturationchlorophyll_concentrationchlorophyll_fluorescence\" cannot be handled"
[1] "In plot,ctd-method() : which=\"CDOMdissolved_oxygenoxygen_saturationchlorophyll_concentrationchlorophyll_fluorescence\" cannot be handled"
[1] "In plot,ctd-method() : which=\"CDOMdissolved_oxygenoxygen_saturationchlorophyll_concentrationchlorophyll_fluorescence\" cannot be handled"
[1] "In plot,ctd-method() : which=\"CDOMdissolved_oxygenoxygen_saturationchlorophyll_concentrationchlorophyll_fluorescence\" cannot be handled"
[1] "In plot,ctd-method() : which=\"CDOMdissolved_oxygenoxygen_saturationchlorophyll_concentrationchlorophyll_fluorescence\" cannot be handled"
[1] "In plot,ctd-method() : which=\"CDOMdissolved_oxygenoxygen_saturationchlorophyll_concentrationchlorophyll_fluorescence\" cannot be handled"
[1] "In plot,ctd-method() : which=\"CDOMdissolved_oxygenoxygen_saturationchlorophyll_concentrationchlorophyll_fluorescence\" cannot be handled"
[1] "In plot,ctd-method() : which=\"CDOMdissolved_oxygenoxygen_saturationchlorophyll_concentrationchlorophyll_fluorescence\" cannot be handled"
[1] "In plot,ctd-method() : which=\"CDOMdissolved_oxygenoxygen_saturationchlorophyll_concentrationchlorophyll_fluorescence\" cannot be handled"
[1] "In plot,ctd-method() : which=\"CDOMdissolved_oxygenoxygen_saturationchlorophyll_concentrationchlorophyll_fluorescence\" cannot be handled"
[1] "In plot,ctd-method() : which=\"CDOMdissolved_oxygenoxygen_saturationchlorophyll_concentrationchlorophyll_fluorescence\" cannot be handled"
[1] "In plot,ctd-method() : which=\"CDOMdissolved_oxygenoxygen_saturationchlorophyll_concentrationchlorophyll_fluorescence\" cannot be handled"
[1] "In plot,ctd-method() : which=\"CDOMdissolved_oxygenoxygen_saturationchlorophyll_concentrationchlorophyll_fluorescence\" cannot be handled"
[1] "In plot,ctd-method() : which=\"CDOMdissolved_oxygenoxygen_saturationchlorophyll_concentrationchlorophyll_fluorescence\" cannot be handled"
[1] "In plot,ctd-method() : which=\"CDOMdissolved_oxygenoxygen_saturationchlorophyll_concentrationchlorophyll_fluorescence\" cannot be handled"
[1] "In plot,ctd-method() : which=\"CDOMdissolved_oxygenoxygen_saturationchlorophyll_concentrationchlorophyll_fluorescence\" cannot be handled"
[1] "In plot,ctd-method() : which=\"CDOMdissolved_oxygenoxygen_saturationchlorophyll_concentrationchlorophyll_fluorescence\" cannot be handled"
[1] "In plot,ctd-method() : which=\"CDOMdissolved_oxygenoxygen_saturationchlorophyll_concentrationchlorophyll_fluorescence\" cannot be handled"
[1] "In plot,ctd-method() : which=\"CDOMdissolved_oxygenoxygen_saturationchlorophyll_concentrationchlorophyll_fluorescence\" cannot be handled"
[1] "In plot,ctd-method() : which=\"CDOMdissolved_oxygenoxygen_saturationchlorophyll_concentrationchlorophyll_fluorescence\" cannot be handled"
[1] "In plot,ctd-method() : which=\"CDOMdissolved_oxygenoxygen_saturationchlorophyll_concentrationchlorophyll_fluorescence\" cannot be handled"
[1] "In plot,ctd-method() : which=\"CDOMdissolved_oxygenoxygen_saturationchlorophyll_concentrationchlorophyll_fluorescence\" cannot be handled"
[1] "In plot,ctd-method() : which=\"CDOMdissolved_oxygenoxygen_saturationchlorophyll_concentrationchlorophyll_fluorescence\" cannot be handled"
[1] "In plot,ctd-method() : which=\"CDOMdissolved_oxygenoxygen_saturationchlorophyll_concentrationchlorophyll_fluorescence\" cannot be handled"
[1] "In plot,ctd-method() : which=\"CDOMdissolved_oxygenoxygen_saturationchlorophyll_concentrationchlorophyll_fluorescence\" cannot be handled"
[1] "In plot,ctd-method() : which=\"CDOMdissolved_oxygenoxygen_saturationchlorophyll_concentrationchlorophyll_fluorescence\" cannot be handled"
[1] "In plot,ctd-method() : which=\"CDOMdissolved_oxygenoxygen_saturationchlorophyll_concentrationchlorophyll_fluorescence\" cannot be handled"
[1] "In plot,ctd-method() : which=\"CDOMdissolved_oxygenoxygen_saturationchlorophyll_concentrationchlorophyll_fluorescence\" cannot be handled"
[1] "In plot,ctd-method() : which=\"CDOMdissolved_oxygenoxygen_saturationchlorophyll_concentrationchlorophyll_fluorescence\" cannot be handled"
[1] "In plot,ctd-method() : which=\"CDOMdissolved_oxygenoxygen_saturationchlorophyll_concentrationchlorophyll_fluorescence\" cannot be handled"

# Loop through each CTD cast
for (i in seq(ctd_FK)){
  cast <- ctd_FK[[i]]  # Assuming each sublist contains only one relevant CTD object
  tryCatch({
    # Extract metadata for station name and cruise ID
    station_name <- cast@metadata$station[1]
    cruise_id <- cast@data$cruise_id[1]

    # Generate a title with station name and cruise ID
    overall_title <- glue::glue("Station: {station_name}, Cruise ID: {cruise_id}")

    # Set margins: increase the outer margin for the title
    par(oma = c(0, 0, 3, 0))  # Top outer margin increased for title

    # Plotting function with specific parameters
    oce::plot(
      x = ctdDecimate(ctdTrim(cast)),
      which = c(
        "photosynthetically_available_radiation",
        "beam_attenuation","beam_transmission"
      ),
      main = ""  # No main title for individual subplots
    )

    # Place a single overall title at the top of the plot frame
    mtext(overall_title, side = 3, line = 1, outer = TRUE, cex = 1.5)

    # Reset outer margins to default
    par(oma = c(0, 0, 0, 0))

  }, error = function(e) {
    print(e$message)  # Print any errors that occur during plotting
  })
}

[1] "need finite 'xlim' values"

combined_df <- data.frame()
for (i in seq(ctd_FK)){
  tryCatch({
    cast <- ctd_FK[[i]]  # 1 is selecting only the first sublist
    
    # print(class(cast))
    # clean cast 
    trimmed_cast <- ctdTrim(cast)
    decimated_cast <- ctdDecimate(trimmed_cast, p = 0.5)  # binned to 0.5 m
    
    # convert to df
    cast_df <- as.data.frame(decimated_cast@data)
    
    # Add metadata
    # assumes station ID and cruise ID the same for all & just uses 1st one
    cast_df <- mutate(
      cast_df,
      station = cast@data$station[1],
      cruise_id = cast@data$cruise_id[1]
    )
  
    # drop NA rows left by cleaning
    cast_df <- subset(cast_df, !is.na(scan))
    
    # Append the data to the combined dataframe
    combined_df <- rbind(combined_df, cast_df)
  }, error = function(e){
    print(glue("error in cast {cast@metadata$station[1]}"))
    print(e)
  })
}
# Save to CSV
file_path <- here(glue("data/cleaned/{cruise_id}.csv"))
write.csv(combined_df, file_path, row.names = FALSE)