WS21093

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)
});

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)

.002:   3445 scans
.007:   29 scans
.010:   1661 scans
.016:   2491 scans
.058:   2018 scans
.060:   3042 scans
.064:   10 scans
.065:   1739 scans
.068:   2500 scans
.12:    3949 scans
.18:    3949 scans
.21LK:  5134 scans
.30:    4839 scans
.31:    5993 scans
.33:    3568 scans
.41:    2548 scans
.45:    2187 scans
.47:    2427 scans
.51:    1988 scans
.53:    807 scans
.54:    450 scans
.55:    41 scans
.56:    268 scans
.57:    2376 scans
.57_1:  1599 scans
.57_2:  2843 scans
.57_3:  3016 scans
.9: 3649 scans
.AM18:  5253 scans
.AM19:  4195 scans
.AMI1:  4246 scans
.AMI2:  2703 scans
.AMI3:  3356 scans
.AMI4:  3814 scans
.AMI5:  3561 scans
.AMI6:  3070 scans
.AMI7:  3785 scans
.BG1:   1671 scans
.BG2:   1900 scans
.BG3:   2097 scans
.BG4:   2657 scans
.CAL1:  3254 scans
.CAL2:  2145 scans
.CAL3:  2877 scans
.CAL4:  5100 scans
.CAL5:  3076 scans
.CAL6:  3921 scans
.GP5:   2940 scans
.KW1:   1649 scans
.KW2:   2213 scans
.KW4:   3918 scans
.MR:    3828 scans
.RP1:   2363 scans
.RP2:   2051 scans
.RP3:   2100 scans
.RP4:   2015 scans
.TB1:   2796 scans
.TB1_RECAST:    2138 scans
.TB10:  5217 scans
.TB2:   1714 scans
.TB3:   3703 scans
.TB4:   4615 scans
.TB5:   5415 scans
.V1:    3324 scans
.V2:    2616 scans
.V3:    4225 scans
.V4:    4691 scans
.V5:    4533 scans
.V6:    4683 scans
.V7:    3244 scans
.V8:    3959 scans
.V9:    4042 scans
.WS:    3743 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: .002
# scans: 3445

=== station: .007
# scans: 29

=== station: .010
# scans: 1661

=== station: .016
# scans: 2491

=== station: .058
# scans: 2018

=== station: .060
# scans: 3042

=== station: .064
# scans: 10

=== station: .065
# scans: 1739

=== station: .068
# scans: 2500

=== station: .12
# scans: 3949

=== station: .18
# scans: 3949

=== station: .21LK
# scans: 5134

=== station: .30
# scans: 4839

=== station: .31
# scans: 5993

=== station: .33
# scans: 3568

=== station: .41
# scans: 2548

=== station: .45
# scans: 2187

=== station: .47
# scans: 2427

=== station: .51
# scans: 1988

=== station: .53
# scans: 807

=== station: .54
# scans: 450

=== station: .55
# scans: 41

=== station: .56
# scans: 268

=== station: .57
# scans: 2376

=== station: .57_1
# scans: 1599

=== station: .57_2
# scans: 2843

=== station: .57_3
# scans: 3016

=== station: .9
# scans: 3649

=== station: .AM18
# scans: 5253

=== station: .AM19
# scans: 4195

=== station: .AMI1
# scans: 4246

=== station: .AMI2
# scans: 2703

=== station: .AMI3
# scans: 3356

=== station: .AMI4
# scans: 3814

=== station: .AMI5
# scans: 3561

=== station: .AMI6
# scans: 3070

=== station: .AMI7
# scans: 3785

=== station: .BG1
# scans: 1671

=== station: .BG2
# scans: 1900

=== station: .BG3
# scans: 2097

=== station: .BG4
# scans: 2657

=== station: .CAL1
# scans: 3254

=== station: .CAL2
# scans: 2145

=== station: .CAL3
# scans: 2877

=== station: .CAL4
# scans: 5100

=== station: .CAL5
# scans: 3076

=== station: .CAL6
# scans: 3921

=== station: .GP5
# scans: 2940

=== station: .KW1
# scans: 1649

=== station: .KW2
# scans: 2213

=== station: .KW4
# scans: 3918

=== station: .MR
# scans: 3828

=== station: .RP1
# scans: 2363

=== station: .RP2
# scans: 2051

=== station: .RP3
# scans: 2100

=== station: .RP4
# scans: 2015

=== station: .TB1
# scans: 2796

=== station: .TB1_RECAST
# scans: 2138

=== station: .TB10
# scans: 5217

=== station: .TB2
# scans: 1714

=== station: .TB3
# scans: 3703

=== station: .TB4
# scans: 4615

=== station: .TB5
# scans: 5415

=== station: .V1
# scans: 3324

=== station: .V2
# scans: 2616

=== station: .V3
# scans: 4225

=== station: .V4
# scans: 4691

=== station: .V5
# scans: 4533

=== station: .V6
# scans: 4683

=== station: .V7
# scans: 3244

=== station: .V8
# scans: 3959

=== station: .V9
# scans: 4042

=== station: .WS
# scans: 3743

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 = 3445' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 29' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1661' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2491' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2018' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3042' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2500' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3949' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3949' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 5134' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 4839' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 5993' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3568' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2548' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2187' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2427' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1988' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 807' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2376' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1599' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2843' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3016' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3649' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 5253' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 4195' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 4246' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2703' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3356' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3814' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3561' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3070' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3785' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1671' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1900' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2097' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2657' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3254' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2145' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2877' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 5100' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3076' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3921' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2940' 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 = 2213' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3918' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3828' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2363' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2051' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2100' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2015' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2796' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2138' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 5217' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1714' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3703' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 4615' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 5415' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3324' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2616' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 4225' 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 = 4533' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 4683' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3244' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3959' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 4042' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3743' 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"

[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"

# 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] "need finite 'xlim' values"

[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] "need finite 'xlim' values"

[1] "need finite 'xlim' values"

[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"

[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)