WS22215

if (!nzchar(system.file(package = "librarian"))) {
  install.packages("librarian")
}

librarian::shelf(
  quiet = TRUE,
  readr, here, fs, ggplot2, glue, "jiho/castr", dplyr, oce, patchwork, purrr, tidyr
)

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

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

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

Warning: Removed 2 rows containing missing values or values outside the scale range
(`geom_point()`).

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

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

Warning: Removed 4 rows containing missing values or values outside the scale range
(`geom_col()`).

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


  return(test_ctd)
}

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

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

WB22215.009:    903 scans
WB22215.009_5:  2023 scans
WB22215.012:    1642 scans
WB22215.030:    1354 scans
WB22215.031:    1270 scans
WB22215.033:    1558 scans
WB22215.041:    871 scans
WB22215.045:    712 scans
WB22215.047:    603 scans
WB22215.051:    722 scans
WB22215.056:    608 scans
WB22215.057:    781 scans
WB22215.057_1:  1130 scans
WB22215.057_2:  845 scans
WB22215.057_3:  1098 scans
WB22215.058:    1227 scans
WB22215.060:    945 scans
WB22215.068:    327 scans
WB22215.18: 1358 scans
WB22215.2:  620 scans
WB22215.21LK:   1203 scans
WB22215.AMI1:   303 scans
WB22215.AMI2:   782 scans
WB22215.AMI3:   633 scans
WB22215.AMI4:   645 scans
WB22215.AMI5:   575 scans
WB22215.AMI6:   1260 scans
WB22215.AMI7:   646 scans
WB22215.AMI8:   640 scans
WB22215.AMI9:   1381 scans
WB22215.BG1:    995 scans
WB22215.BG2:    1176 scans
WB22215.BG3:    1345 scans
WB22215.BG4:    2203 scans
WB22215.CAL1:   596 scans
WB22215.CAL2:   760 scans
WB22215.CAL3:   902 scans
WB22215.CAL4:   932 scans
WB22215.CAL5:   1281 scans
WB22215.CAL6:   1460 scans
WB22215.GP5:    2303 scans
WB22215.KW1:    1022 scans
WB22215.KW2:    897 scans
WB22215.KW4:    885 scans
WB22215.MR: 843 scans
WB22215.RP1:    753 scans
WB22215.RP2:    1140 scans
WB22215.RP3:    1296 scans
WB22215.RP4:    797 scans
WB22215.TB10:   1015 scans
WB22215.TB4:    483 scans
WB22215.TB5:    905 scans
WB22215.TEST2:  11 scans
WB22215.V1: 846 scans
WB22215.V2: 576 scans
WB22215.V3: 975 scans
WB22215.V4: 412 scans
WB22215.V5: 368 scans
WB22215.V6: 629 scans
WB22215.V7: 532 scans
WB22215.V8: 750 scans
WB22215.V9: 750 scans
WB22215.WS: 1119 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: WB22215.009
# scans: 903

=== station: WB22215.009_5
# scans: 2023

=== station: WB22215.012
# scans: 1642

=== station: WB22215.030
# scans: 1354

=== station: WB22215.031
# scans: 1270

=== station: WB22215.033
# scans: 1558

=== station: WB22215.041
# scans: 871

=== station: WB22215.045
# scans: 712

=== station: WB22215.047
# scans: 603

=== station: WB22215.051
# scans: 722

=== station: WB22215.056
# scans: 608

=== station: WB22215.057
# scans: 781

=== station: WB22215.057_1
# scans: 1130

=== station: WB22215.057_2
# scans: 845

=== station: WB22215.057_3
# scans: 1098

=== station: WB22215.058
# scans: 1227

=== station: WB22215.060
# scans: 945

=== station: WB22215.068
# scans: 327

=== station: WB22215.18
# scans: 1358

=== station: WB22215.2
# scans: 620

=== station: WB22215.21LK
# scans: 1203

=== station: WB22215.AMI1
# scans: 303

=== station: WB22215.AMI2
# scans: 782

=== station: WB22215.AMI3
# scans: 633

=== station: WB22215.AMI4
# scans: 645

=== station: WB22215.AMI5
# scans: 575

=== station: WB22215.AMI6
# scans: 1260

=== station: WB22215.AMI7
# scans: 646

=== station: WB22215.AMI8
# scans: 640

=== station: WB22215.AMI9
# scans: 1381

=== station: WB22215.BG1
# scans: 995

=== station: WB22215.BG2
# scans: 1176

=== station: WB22215.BG3
# scans: 1345

=== station: WB22215.BG4
# scans: 2203

=== station: WB22215.CAL1
# scans: 596

=== station: WB22215.CAL2
# scans: 760

=== station: WB22215.CAL3
# scans: 902

=== station: WB22215.CAL4
# scans: 932

=== station: WB22215.CAL5
# scans: 1281

=== station: WB22215.CAL6
# scans: 1460

=== station: WB22215.GP5
# scans: 2303

=== station: WB22215.KW1
# scans: 1022

=== station: WB22215.KW2
# scans: 897

=== station: WB22215.KW4
# scans: 885

=== station: WB22215.MR
# scans: 843

=== station: WB22215.RP1
# scans: 753

=== station: WB22215.RP2
# scans: 1140

=== station: WB22215.RP3
# scans: 1296

=== station: WB22215.RP4
# scans: 797

=== station: WB22215.TB10
# scans: 1015

=== station: WB22215.TB4
# scans: 483

=== station: WB22215.TB5
# scans: 905

=== station: WB22215.TEST2
# scans: 11

=== station: WB22215.V1
# scans: 846

=== station: WB22215.V2
# scans: 576

=== station: WB22215.V3
# scans: 975

=== station: WB22215.V4
# scans: 412

=== station: WB22215.V5
# scans: 368

=== station: WB22215.V6
# scans: 629

=== station: WB22215.V7
# scans: 532

=== station: WB22215.V8
# scans: 750

=== station: WB22215.V9
# scans: 750

=== station: WB22215.WS
# scans: 1119

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 = 903' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2023' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1642' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1354' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1270' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1558' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 871' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 712' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 603' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 722' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 608' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 781' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1130' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 845' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1098' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1227' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 945' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 327' in coercion to 'logical(1)'>

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

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 620' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1203' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 303' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 782' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 633' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 645' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 575' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1260' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 646' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 640' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1381' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 995' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1176' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1345' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2203' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 596' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 760' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 902' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 932' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1281' in coercion to 'logical(1)'>

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

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2303' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1022' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 897' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 885' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 843' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 753' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1140' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1296' in coercion to 'logical(1)'>

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

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1015' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 483' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 905' in coercion to 'logical(1)'>
<simpleError in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'plot': wrong sign in 'by' argument>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 846' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 576' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 975' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 412' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 368' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 629' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 532' in coercion to 'logical(1)'>

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

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

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1119' 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] "error in evaluating the argument 'x' in selecting a method for function 'plot': wrong sign in 'by' argument"

# 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] "error in evaluating the argument 'x' in selecting a method for function 'plot': wrong sign in 'by' argument"

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

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

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

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

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

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

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

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

[1] "In plot,ctd-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] "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] "error in evaluating the argument 'x' in selecting a method for function 'plot': wrong sign in 'by' argument"
[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)
  })
}

error in cast WB22215.TEST2
<simpleError in seq.default(0, p * floor(max(x[["pressure"]], na.rm = TRUE)/p),     p): wrong sign in 'by' argument>

# Save to CSV
file_path <- here(glue("data/cleaned/{cruise_id}.csv"))
write.csv(combined_df, file_path, row.names = FALSE)