WS22022

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)

.10:    1711 scans
.12:    3581 scans
.16:    2619 scans
.18:    3540 scans
.2: 2900 scans
.21LK:  4921 scans
.30:    3067 scans
.31:    3694 scans
.33:    2368 scans
.41:    2802 scans
.45:    2676 scans
.47:    2767 scans
.49:    2844 scans
.51:    2716 scans
.53:    22 scans
.54:    230 scans
.55:    247 scans
.56:    3211 scans
.57:    2482 scans
.57_1:  3095 scans
.57_2:  2981 scans
.57_3:  2843 scans
.58:    2797 scans
.60:    2635 scans
.64:    31 scans
.65:    103 scans
.68:    403 scans
.7: 1837 scans
.9: 4317 scans
.9_5:   10084 scans
.AMI1:  3028 scans
.AMI2:  2364 scans
.AMI3:  2669 scans
.AMI6:  4801 scans
.AMI7:  6116 scans
.AMI8:  5566 scans
.AMI9:  6105 scans
.BG1:   2456 scans
.BG2:   3995 scans
.BG3:   2699 scans
.BG4:   3908 scans
.CAL1:  2440 scans
.CAL2:  2555 scans
.CAL3:  2893 scans
.CAL4:  3641 scans
.CAL5:  2733 scans
.CAL6:  4857 scans
.GP5:   3012 scans
.KW1:   3045 scans
.KW2:   3528 scans
.KW4:   3215 scans
.MR:    2477 scans
.RP1:   3349 scans
.RP2:   2647 scans
.RP3:   2339 scans
.RP4:   3074 scans
.TB1:   2725 scans
.TB10:  4493 scans
.TB2:   2490 scans
.TB3:   3545 scans
.TB4:   4024 scans
.TB5:   4107 scans
.V1:    3102 scans
.V2:    3554 scans
.V3:    3336 scans
.V4:    3234 scans
.V5:    3898 scans
.V6:    4607 scans
.V7:    4384 scans
.V8:    4133 scans
.V9:    4376 scans
.WS:    4192 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: 1711

=== station: .12
# scans: 3581

=== station: .16
# scans: 2619

=== station: .18
# scans: 3540

=== station: .2
# scans: 2900

=== station: .21LK
# scans: 4921

=== station: .30
# scans: 3067

=== station: .31
# scans: 3694

=== station: .33
# scans: 2368

=== station: .41
# scans: 2802

=== station: .45
# scans: 2676

=== station: .47
# scans: 2767

=== station: .49
# scans: 2844

=== station: .51
# scans: 2716

=== station: .53
# scans: 22

=== station: .54
# scans: 230

=== station: .55
# scans: 247

=== station: .56
# scans: 3211

=== station: .57
# scans: 2482

=== station: .57_1
# scans: 3095

=== station: .57_2
# scans: 2981

=== station: .57_3
# scans: 2843

=== station: .58
# scans: 2797

=== station: .60
# scans: 2635

=== station: .64
# scans: 31

=== station: .65
# scans: 103

=== station: .68
# scans: 403

=== station: .7
# scans: 1837

=== station: .9
# scans: 4317

=== station: .9_5
# scans: 10084

=== station: .AMI1
# scans: 3028

=== station: .AMI2
# scans: 2364

=== station: .AMI3
# scans: 2669

=== station: .AMI6
# scans: 4801

=== station: .AMI7
# scans: 6116

=== station: .AMI8
# scans: 5566

=== station: .AMI9
# scans: 6105

=== station: .BG1
# scans: 2456

=== station: .BG2
# scans: 3995

=== station: .BG3
# scans: 2699

=== station: .BG4
# scans: 3908

=== station: .CAL1
# scans: 2440

=== station: .CAL2
# scans: 2555

=== station: .CAL3
# scans: 2893

=== station: .CAL4
# scans: 3641

=== station: .CAL5
# scans: 2733

=== station: .CAL6
# scans: 4857

=== station: .GP5
# scans: 3012

=== station: .KW1
# scans: 3045

=== station: .KW2
# scans: 3528

=== station: .KW4
# scans: 3215

=== station: .MR
# scans: 2477

=== station: .RP1
# scans: 3349

=== station: .RP2
# scans: 2647

=== station: .RP3
# scans: 2339

=== station: .RP4
# scans: 3074

=== station: .TB1
# scans: 2725

=== station: .TB10
# scans: 4493

=== station: .TB2
# scans: 2490

=== station: .TB3
# scans: 3545

=== station: .TB4
# scans: 4024

=== station: .TB5
# scans: 4107

=== station: .V1
# scans: 3102

=== station: .V2
# scans: 3554

=== station: .V3
# scans: 3336

=== station: .V4
# scans: 3234

=== station: .V5
# scans: 3898

=== station: .V6
# scans: 4607

=== station: .V7
# scans: 4384

=== station: .V8
# scans: 4133

=== station: .V9
# scans: 4376

=== station: .WS
# scans: 4192

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 = 3581' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2619' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3540' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2900' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 4921' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3067' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3694' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2368' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2802' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2676' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2767' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2844' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2716' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 230' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 247' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3211' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2482' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3095' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2981' 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 = 2797' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2635' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 31' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 403' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 1837' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 10084' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3028' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2364' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2669' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 4801' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 6116' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 5566' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 6105' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2440' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2555' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2893' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3641' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2733' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 4857' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3045' in coercion to 'logical(1)'>

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

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3215' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2477' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3349' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2647' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2339' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3074' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2725' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 4493' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 2490' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3545' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 4024' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 4107' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3554' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3336' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3234' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 3898' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 4607' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 4384' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 4133' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 4376' in coercion to 'logical(1)'>

<simpleError in !is.null(x@metadata$station) && !is.na(x@metadata$station): 'length = 4192' 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] "plot.new has not been called yet"

[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] "plot.new has not been called yet"

[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(
        "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] "plot.new has not been called yet"

[1] "need finite 'xlim' values"

combined_df <- data.frame()
for (i in seq(ctd_FK)){
  tryCatch({
    cast <- ctd_FK[[i]]  # 1 is selecting only the first sublist
    
    # print(class(cast))
    # clean cast 
    trimmed_cast <- ctdTrim(cast)
    decimated_cast <- ctdDecimate(trimmed_cast, p = 0.5)  # binned to 0.5 m
    
    # convert to df
    cast_df <- as.data.frame(decimated_cast@data)
    
    # Add metadata
    # assumes station ID and cruise ID the same for all & just uses 1st one
    cast_df <- mutate(
      cast_df,
      station = cast@data$station[1],
      cruise_id = cast@data$cruise_id[1]
    )
  
    # drop NA rows left by cleaning
    cast_df <- subset(cast_df, !is.na(scan))
    
    # Append the data to the combined dataframe
    combined_df <- rbind(combined_df, cast_df)
  }, error = function(e){
    print(glue("error in cast {cast@metadata$station[1]}"))
    print(e)
  })
}
# Save to CSV
file_path <- here(glue("data/cleaned/{cruise_id}.csv"))
write.csv(combined_df, file_path, row.names = FALSE)