WS20006

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)
});

<error/rlang_error>
Error in `geom_point()`:
! Problem while computing aesthetics.
ℹ Error occurred in the 1st layer.
Caused by error:
! object 'time_elapsed' not found
---
Backtrace:
     ▆
  1. ├─base::tryCatch(...)
  2. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  3. │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
  4. │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
  5. ├─base::print(combined_plot)
  6. └─patchwork:::print.patchwork(combined_plot)
  7.   └─patchwork:::build_patchwork(plot, plot$layout$guides %||% "auto")
  8.     └─base::lapply(x$plots, plot_table, guides = guides)
  9.       ├─patchwork (local) FUN(X[[i]], ...)
 10.       └─patchwork:::plot_table.ggplot(X[[i]], ...)
 11.         └─ggplot2::ggplotGrob(x)
 12.           ├─ggplot2::ggplot_gtable(ggplot_build(x))
 13.           │ └─ggplot2:::attach_plot_env(data$plot$plot_env)
 14.           │   └─base::options(ggplot2_plot_env = env)
 15.           ├─ggplot2::ggplot_build(x)
 16.           └─ggplot2:::ggplot_build.ggplot(x)
 17.             └─ggplot2:::by_layer(...)
 18.               ├─rlang::try_fetch(...)
 19.               │ ├─base::tryCatch(...)
 20.               │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 21.               │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 22.               │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 23.               │ └─base::withCallingHandlers(...)
 24.               └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
 25.                 └─l$compute_aesthetics(d, plot)
 26.                   └─ggplot2 (local) compute_aesthetics(..., self = self)
 27.                     └─base::lapply(aesthetics, eval_tidy, data = data, env = env)
 28.                       └─rlang (local) FUN(X[[i]], ...)

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)

10: 1353 scans
12: 6615 scans
16: 1697 scans
18: 4576 scans
2:  1879 scans
21.5:   11304 scans
21.5B:  10569 scans
21/LK:  3971 scans
30: 3364 scans
31: 2038 scans
33: 3272 scans
41: 2161 scans
45: 1891 scans
51: 1649 scans
54: 2209 scans
55: 73 scans
56: 2041 scans
57: 3287 scans
57.1:   2417 scans
57.2:   2558 scans
57.3:   2454 scans
58: 3393 scans
60: 3105 scans
64: 1913 scans
65: 2042 scans
68: 174 scans
7:  2 scans
9:  5276 scans
9.5:    9876 scans
BG2:    2510 scans
BG5:    3110 scans
CAL1:   2309 scans
CAL2:   2037 scans
CAL3:   2182 scans
CAL4:   2878 scans
CAL5:   4305 scans
CAL6:   4691 scans
GP5:    4902 scans
KW1:    3494 scans
KW2:    3259 scans
KW4:    3209 scans
MR: 5898 scans
RP1:    1718 scans
RP2:    2127 scans
RP3:    2598 scans
RP4:    3435 scans
V1: 1499 scans
V2: 3541 scans
V3: 2784 scans
V4: 3221 scans
V5: 3528 scans
V6: 3498 scans
V7: 3801 scans
V8: 5586 scans
V9: 4433 scans
WS: 3919 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: 10
# scans: 1353

=== station: 12
# scans: 6615

=== station: 16
# scans: 1697

=== station: 18
# scans: 4576

=== station: 2
# scans: 1879

=== station: 21.5
# scans: 11304

=== station: 21.5B
# scans: 10569

=== station: 21/LK
# scans: 3971

=== station: 30
# scans: 3364

=== station: 31
# scans: 2038

=== station: 33
# scans: 3272

=== station: 41
# scans: 2161

=== station: 45
# scans: 1891

=== station: 51
# scans: 1649

=== station: 54
# scans: 2209

=== station: 55
# scans: 73

=== station: 56
# scans: 2041

=== station: 57
# scans: 3287

=== station: 57.1
# scans: 2417

=== station: 57.2
# scans: 2558

=== station: 57.3
# scans: 2454

=== station: 58
# scans: 3393

=== station: 60
# scans: 3105

=== station: 64
# scans: 1913

=== station: 65
# scans: 2042

=== station: 68
# scans: 174

=== station: 7
# scans: 2

=== station: 9
# scans: 5276

=== station: 9.5
# scans: 9876

=== station: BG2
# scans: 2510

=== station: BG5
# scans: 3110

=== station: CAL1
# scans: 2309

=== station: CAL2
# scans: 2037

=== station: CAL3
# scans: 2182

=== station: CAL4
# scans: 2878

=== station: CAL5
# scans: 4305

=== station: CAL6
# scans: 4691

=== station: GP5
# scans: 4902

=== station: KW1
# scans: 3494

=== station: KW2
# scans: 3259

=== station: KW4
# scans: 3209

=== station: MR
# scans: 5898

=== station: RP1
# scans: 1718

=== station: RP2
# scans: 2127

=== station: RP3
# scans: 2598

=== station: RP4
# scans: 3435

=== station: V1
# scans: 1499

=== station: V2
# scans: 3541

=== station: V3
# scans: 2784

=== station: V4
# scans: 3221

=== station: V5
# scans: 3528

=== station: V6
# scans: 3498

=== station: V7
# scans: 3801

=== station: V8
# scans: 5586

=== station: V9
# scans: 4433

=== station: WS
# scans: 3919

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 = 1353' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 6615' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1697' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 4576' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1879' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 11304' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 10569' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3971' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3364' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2038' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3272' 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 = 1891' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1649' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2209' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3287' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2417' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2558' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2454' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3393' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3105' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1913' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2042' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 174' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 5276' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 9876' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2510' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3110' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2309' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2037' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2182' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2878' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 4305' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 4691' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 4902' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3494' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3259' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3209' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 5898' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1718' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2127' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2598' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3435' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1499' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3541' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2784' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3221' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3528' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3498' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3801' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 5586' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 4433' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3919' 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"

# 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"

# 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)