WS19322

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: 1405 scans
12: 3553 scans
16: 1311 scans
18: 2238 scans
2:  3900 scans
21/LK:  3791 scans
30: 2927 scans
31: 2638 scans
33: 2155 scans
41: 1665 scans
45: 2277 scans
51: 1948 scans
54: 1712 scans
55: 239 scans
56: 1787 scans
57: 1502 scans
57.1:   2037 scans
57.2:   2156 scans
57.3:   2833 scans
58: 1933 scans
60: 2207 scans
64: 133 scans
65: 12 scans
68: 1143 scans
7:  2791 scans
9:  3952 scans
9.5:    8943 scans
BG2:    2437 scans
BG3:    2595 scans
BG4:    2171 scans
CAL1:   17 scans
CAL2:   2569 scans
CAL3:   2641 scans
CAL4:   3370 scans
CAL5:   3236 scans
CAL6:   3869 scans
CAL7:   3120 scans
CAL8:   2292 scans
CW1:    1854 scans
CW2:    2128 scans
CW3:    2503 scans
CW4:    2590 scans
CW5:    3368 scans
CW6:    3585 scans
GP5:    7967 scans
KW1:    2572 scans
KW2:    3013 scans
KW4:    2907 scans
MR: 3729 scans
RP1:    2345 scans
RP2:    2029 scans
RP3:    2557 scans
RP4:    2934 scans
TB1:    2458 scans
TB10:   3341 scans
TB2:    2213 scans
TB3:    3032 scans
TB4:    5107 scans
TB5:    3508 scans
TB6:    1406 scans
TB7:    1637 scans
TB8:    2054 scans
TB9:    2165 scans
V1: 2365 scans
V2: 2600 scans
V3: 3419 scans
V4: 3011 scans
V5: 3719 scans
V6: 3405 scans
V7: 3203 scans
V8: 4298 scans
V9: 4854 scans
WS: 4654 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: 1405

=== station: 12
# scans: 3553

=== station: 16
# scans: 1311

=== station: 18
# scans: 2238

=== station: 2
# scans: 3900

=== station: 21/LK
# scans: 3791

=== station: 30
# scans: 2927

=== station: 31
# scans: 2638

=== station: 33
# scans: 2155

=== station: 41
# scans: 1665

=== station: 45
# scans: 2277

=== station: 51
# scans: 1948

=== station: 54
# scans: 1712

=== station: 55
# scans: 239

=== station: 56
# scans: 1787

=== station: 57
# scans: 1502

=== station: 57.1
# scans: 2037

=== station: 57.2
# scans: 2156

=== station: 57.3
# scans: 2833

=== station: 58
# scans: 1933

=== station: 60
# scans: 2207

=== station: 64
# scans: 133

=== station: 65
# scans: 12

=== station: 68
# scans: 1143

=== station: 7
# scans: 2791

=== station: 9
# scans: 3952

=== station: 9.5
# scans: 8943

=== station: BG2
# scans: 2437

=== station: BG3
# scans: 2595

=== station: BG4
# scans: 2171

=== station: CAL1
# scans: 17

=== station: CAL2
# scans: 2569

=== station: CAL3
# scans: 2641

=== station: CAL4
# scans: 3370

=== station: CAL5
# scans: 3236

=== station: CAL6
# scans: 3869

=== station: CAL7
# scans: 3120

=== station: CAL8
# scans: 2292

=== station: CW1
# scans: 1854

=== station: CW2
# scans: 2128

=== station: CW3
# scans: 2503

=== station: CW4
# scans: 2590

=== station: CW5
# scans: 3368

=== station: CW6
# scans: 3585

=== station: GP5
# scans: 7967

=== station: KW1
# scans: 2572

=== station: KW2
# scans: 3013

=== station: KW4
# scans: 2907

=== station: MR
# scans: 3729

=== station: RP1
# scans: 2345

=== station: RP2
# scans: 2029

=== station: RP3
# scans: 2557

=== station: RP4
# scans: 2934

=== station: TB1
# scans: 2458

=== station: TB10
# scans: 3341

=== station: TB2
# scans: 2213

=== station: TB3
# scans: 3032

=== station: TB4
# scans: 5107

=== station: TB5
# scans: 3508

=== station: TB6
# scans: 1406

=== station: TB7
# scans: 1637

=== station: TB8
# scans: 2054

=== station: TB9
# scans: 2165

=== station: V1
# scans: 2365

=== station: V2
# scans: 2600

=== station: V3
# scans: 3419

=== station: V4
# scans: 3011

=== station: V5
# scans: 3719

=== station: V6
# scans: 3405

=== station: V7
# scans: 3203

=== station: V8
# scans: 4298

=== station: V9
# scans: 4854

=== station: WS
# scans: 4654

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 = 1405' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3553' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1311' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2238' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3900' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3791' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2927' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2638' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2155' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1665' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2277' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1948' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1712' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1787' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1502' 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 = 2156' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2833' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1933' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2207' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1143' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2791' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3952' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 8943' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2437' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2595' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2171' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2569' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2641' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3370' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3236' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3869' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3120' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2292' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1854' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2128' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2503' 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 = 3368' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3585' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 7967' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2572' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3013' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2907' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3729' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2345' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2029' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2557' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2934' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2458' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3341' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2213' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3032' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 5107' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3508' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1406' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1637' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2054' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2165' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2365' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2600' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3419' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3011' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3719' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3405' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3203' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 4298' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 4854' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 4654' 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] "need finite 'xlim' values"

[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] "need finite 'xlim' values"

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

[1] "need finite 'xlim' values"

[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] "need finite 'xlim' values"

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

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

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

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

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

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

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

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

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

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

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

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

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

[1] "need finite 'xlim' values"

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

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

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

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

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

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

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

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

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

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

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

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

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

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

[1] "need finite 'xlim' values"

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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)