tryCatch({ plots <-list()for (station_name inunique(cruise_df$station)) { subset_df <-filter(cruise_df, station == station_name) plots[[station_name]] <-ggplot(subset_df, aes(x = time_elapsed)) +geom_point(aes(y = depth), color ="blue") +# Plot depth in bluegeom_line(aes(y = sea_water_pressure), color ="red") +# Plot sea water pressure in redggtitle(glue("{station_name}")) +theme(axis.title.x =element_blank(),axis.title.y =element_blank(),axis.text.x =element_blank(),axis.text.y =element_blank(),axis.ticks.x =element_blank(),axis.ticks.y =element_blank() ) # Remove individual axis titles and text }# drop nulls plots <- purrr::compact(plots)# Combine all plots into a grid combined_plot <-wrap_plots(plots) +plot_layout(ncol =4) +# Adjust ncol to set number of columns in the gridplot_annotation(title ="Depth (blue) and Pressure (red)",subtitle ="Each panel represents a different station",caption ="Time Elapsed (x-axis) vs Depth & Pressure (y-axis)" ) +theme(plot.tag =element_text(size =12, face ="bold"),plot.tag.position ="topleft",axis.title.x =element_text(margin =margin(t =10)),axis.title.y =element_text(margin =margin(r =10)) )print(combined_plot)}, error =function(er){print(er)});
p <-ggplot(cruise_df, aes(x = time, y = depth, fill = station)) +geom_col() +# This creates the bars# geom_text(aes(label = station), vjust = -0.3) + # This adds labels to each bar, adjust vjust for positionlabs(x ="Time", y ="Depth", title ="Depth over Time by Station") +# Set labels and titletheme_minimal() # Use a minimal themeprint(p)
create oce.ctd objects from dataframes
ctd_load <-function(data, other_params =NULL) {# create csv into ctd object test_ctd <-as.ctd(salinity = data$sea_water_salinity,temperature = data$sea_water_temperature,pressure = data$sea_water_pressure,station = data$station )# add additional columns to ctd objectif (!is.null(other_params)) {for (param_name in other_params) { test_ctd <-oceSetData(object = test_ctd,name = param_name,value = data[[param_name]] ) } }print(glue("{data$station[1]}:\t{length(test_ctd@data$scan)} scans"))return(test_ctd)}# Define other parameters to addother_params <-c("cruise_id", "station", "time", "time_elapsed", "latitude", "longitude", "sea_water_electrical_conductivity", "CDOM", "dissolved_oxygen","oxygen_saturation", "chlorophyll_concentration", "chlorophyll_fluorescence", "photosynthetically_available_radiation", "beam_attenuation","beam_transmission", "depth", "sea_water_sigma_t","descent_rate", "sound_velocity")# Split data by station and create data listctd_FK <- cruise_df %>%split(.$station) %>%map(~ctd_load(.x, other_params = other_params)) # ~ is a lambda(x)
for (i inseq(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: 1783
=== station: 12
# scans: 2403
=== station: 15
# scans: 4028
=== station: 15.5
# scans: 13409
=== station: 16
# scans: 825
=== station: 18
# scans: 3829
=== station: 2
# scans: 3895
=== station: 21.5
# scans: 8472
=== station: 21/LK
# scans: 2914
=== station: 22
# scans: 3826
=== station: 6
# scans: 2434
=== station: 7
# scans: 1389
=== station: 9
# scans: 4182
=== station: 9.5
# scans: 8605
=== station: 9.6
# scans: 9783
=== station: 9.7
# scans: 8709
=== station: 9.8
# scans: 12744
=== station: MR
# scans: 2230
=== station: WS
# scans: 4073
plotting each cast in the first list
for (i inseq(ctd_FK)){ cast <- ctd_FK[[i]] # 1 is selecting only the first sublisttryCatch({plot(ctdDecimate(ctdTrim(cast))) }, error =function(e){print(e) })}
plotting other physical parameters for each cast
# Loop through each CTD castfor (i inseq(ctd_FK)){ cast <- ctd_FK[[i]] # Assuming each sublist contains only one relevant CTD objecttryCatch({# 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 titlepar(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" ),main =""# No main title for individual subplots )# Place a single overall title at the top of the plot framemtext(overall_title, side =3, line =1, outer =TRUE, cex =1.5)# Reset outer margins to defaultpar(oma =c(0, 0, 0, 0)) }, error =function(e) {print(e$message) # Print any errors that occur during plotting })}
[1] "need finite 'xlim' values"
plotting other nutrient parameters for each cast
# Loop through each CTD castfor (i inseq(ctd_FK)){ cast <- ctd_FK[[i]] # Assuming each sublist contains only one relevant CTD objecttryCatch({# Extract metadata for station name and cruise ID station_name <- cast@metadata$station[1] cruise_id <- cast@data$cruise_id[1]# Generate a title with station name and cruise ID overall_title <- glue::glue("Station: {station_name}, Cruise ID: {cruise_id}")# Set margins: increase the outer margin for the titlepar(oma =c(0, 0, 3, 0)) # Top outer margin increased for title# Plotting function with specific parameters oce::plot(x =ctdDecimate(ctdTrim(cast)),which =c("CDOM", "dissolved_oxygen","oxygen_saturation","chlorophyll_concentration", "chlorophyll_fluorescence" ),main =""# No main title for individual subplots )# Place a single overall title at the top of the plot framemtext(overall_title, side =3, line =1, outer =TRUE, cex =1.5)# Reset outer margins to defaultpar(oma =c(0, 0, 0, 0)) }, error =function(e) {print(e$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"
plotting other optical parameters for each cast
# Loop through each CTD castfor (i inseq(ctd_FK)){ cast <- ctd_FK[[i]] # Assuming each sublist contains only one relevant CTD objecttryCatch({# 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 titlepar(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 framemtext(overall_title, side =3, line =1, outer =TRUE, cex =1.5)# Reset outer margins to defaultpar(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"
loop through every cast, clean, & save
combined_df <-data.frame()for (i inseq(ctd_FK)){ 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)}# Save to CSVfile_path <-here(glue("data/cleaned/{cruise_id}.csv"))write.csv(combined_df, file_path, row.names =FALSE)