WS0612

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)

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)
});

Warning: Removed 1 row containing missing values or values outside the scale range
(`geom_point()`).

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)

Warning: Removed 1 row containing missing values or values outside the scale range
(`geom_col()`).

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:  2163 scans
10: 2343 scans
11: 2428 scans
12: 2949 scans
13: 2431 scans
14: 2227 scans
15: 3413 scans
15.5:   8025 scans
16: 1565 scans
17: 2178 scans
18: 2990 scans
19: 1720 scans
2:  1723 scans
20: 2174 scans
21: 2952 scans
21.5:   8665 scans
22: 3052 scans
22.5:   7534 scans
23: 1885 scans
24: 2222 scans
25: 4505 scans
25.5:   13944 scans
26: 1902 scans
27: 2479 scans
28: 2904 scans
28.5:   3383 scans
29: 3671 scans
29.5:   3787 scans
3:  4536 scans
30: 3288 scans
30.5:   2764 scans
31: 2428 scans
32: 1713 scans
33: 2750 scans
34: 1677 scans
39: 2079 scans
4:  1324 scans
40: 2081 scans
41: 2931 scans
42: 638 scans
45: 2443 scans
46: 2665 scans
47: 2516 scans
48: 1949 scans
49: 1632 scans
5:  1867 scans
5.5:    1860 scans
50: 2314 scans
51: 1563 scans
52: 2683 scans
53: 29 scans
54: 1257 scans
55: 1122 scans
56: 1906 scans
57: 2307 scans
6:  2189 scans
6.5:    7225 scans
60: 1629 scans
61: 1538 scans
62: 1782 scans
63: 1887 scans
64: 875 scans
65: 1460 scans
66: 1556 scans
67: 1801 scans
68: 1843 scans
69: 1675 scans
7:  1776 scans
70: 2274 scans
71: 2083 scans
8:  2272 scans
9:  3483 scans
9.5:    7644 scans
CAL1:   2611 scans
CAL2:   1364 scans
CAL3:   2714 scans
CAL4:   2748 scans
CAL5:   3267 scans
CH1:    2871 scans
CH2:    2856 scans
CH3:    2543 scans
CH4:    3251 scans
CH5:    4048 scans
DT01:   3024 scans
DT02:   2604 scans
DT03:   4488 scans
DT04:   5008 scans
DT05:   4623 scans
DT06:   8535 scans
DT07:   19828 scans
DT08:   9116 scans
DT09:   4978 scans
DT10:   2648 scans
DT11:   2443 scans
DTXX:   522 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: 2163

=== station: 10
# scans: 2343

=== station: 11
# scans: 2428

=== station: 12
# scans: 2949

=== station: 13
# scans: 2431

=== station: 14
# scans: 2227

=== station: 15
# scans: 3413

=== station: 15.5
# scans: 8025

=== station: 16
# scans: 1565

=== station: 17
# scans: 2178

=== station: 18
# scans: 2990

=== station: 19
# scans: 1720

=== station: 2
# scans: 1723

=== station: 20
# scans: 2174

=== station: 21
# scans: 2952

=== station: 21.5
# scans: 8665

=== station: 22
# scans: 3052

=== station: 22.5
# scans: 7534

=== station: 23
# scans: 1885

=== station: 24
# scans: 2222

=== station: 25
# scans: 4505

=== station: 25.5
# scans: 13944

=== station: 26
# scans: 1902

=== station: 27
# scans: 2479

=== station: 28
# scans: 2904

=== station: 28.5
# scans: 3383

=== station: 29
# scans: 3671

=== station: 29.5
# scans: 3787

=== station: 3
# scans: 4536

=== station: 30
# scans: 3288

=== station: 30.5
# scans: 2764

=== station: 31
# scans: 2428

=== station: 32
# scans: 1713

=== station: 33
# scans: 2750

=== station: 34
# scans: 1677

=== station: 39
# scans: 2079

=== station: 4
# scans: 1324

=== station: 40
# scans: 2081

=== station: 41
# scans: 2931

=== station: 42
# scans: 638

=== station: 45
# scans: 2443

=== station: 46
# scans: 2665

=== station: 47
# scans: 2516

=== station: 48
# scans: 1949

=== station: 49
# scans: 1632

=== station: 5
# scans: 1867

=== station: 5.5
# scans: 1860

=== station: 50
# scans: 2314

=== station: 51
# scans: 1563

=== station: 52
# scans: 2683

=== station: 53
# scans: 29

=== station: 54
# scans: 1257

=== station: 55
# scans: 1122

=== station: 56
# scans: 1906

=== station: 57
# scans: 2307

=== station: 6
# scans: 2189

=== station: 6.5
# scans: 7225

=== station: 60
# scans: 1629

=== station: 61
# scans: 1538

=== station: 62
# scans: 1782

=== station: 63
# scans: 1887

=== station: 64
# scans: 875

=== station: 65
# scans: 1460

=== station: 66
# scans: 1556

=== station: 67
# scans: 1801

=== station: 68
# scans: 1843

=== station: 69
# scans: 1675

=== station: 7
# scans: 1776

=== station: 70
# scans: 2274

=== station: 71
# scans: 2083

=== station: 8
# scans: 2272

=== station: 9
# scans: 3483

=== station: 9.5
# scans: 7644

=== station: CAL1
# scans: 2611

=== station: CAL2
# scans: 1364

=== station: CAL3
# scans: 2714

=== station: CAL4
# scans: 2748

=== station: CAL5
# scans: 3267

=== station: CH1
# scans: 2871

=== station: CH2
# scans: 2856

=== station: CH3
# scans: 2543

=== station: CH4
# scans: 3251

=== station: CH5
# scans: 4048

=== station: DT01
# scans: 3024

=== station: DT02
# scans: 2604

=== station: DT03
# scans: 4488

=== station: DT04
# scans: 5008

=== station: DT05
# scans: 4623

=== station: DT06
# scans: 8535

=== station: DT07
# scans: 19828

=== station: DT08
# scans: 9116

=== station: DT09
# scans: 4978

=== station: DT10
# scans: 2648

=== station: DT11
# scans: 2443

=== station: DTXX
# scans: 522

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 = 2163' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2343' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2428' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2949' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2431' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2227' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3413' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 8025' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1565' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2178' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2990' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1720' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1723' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2174' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2952' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 8665' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3052' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 7534' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1885' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2222' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 4505' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 13944' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1902' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2479' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2904' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3383' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3671' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3787' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 4536' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3288' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2764' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2428' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1713' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2750' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1677' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2079' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1324' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2081' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2931' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 638' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2443' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2665' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2516' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1949' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1632' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1867' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1860' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2314' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1563' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2683' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1257' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1122' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1906' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2307' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2189' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 7225' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1629' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1538' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1782' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1887' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1460' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1556' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1801' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1843' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1675' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1776' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2274' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2083' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2272' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3483' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 7644' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2611' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1364' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2714' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2748' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3267' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2871' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2856' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2543' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3251' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 4048' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3024' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2604' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 4488' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 5008' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 4623' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 8535' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 19828' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 9116' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 4978' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2648' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2443' 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"

[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"
[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"

[1] "need finite 'xlim' values"

[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)