Last updated: 2020-03-18

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Knit directory: BloomSail/

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library(tidyverse)
library(lubridate)
library(zoo)
# library(dygraphs)
# library(xts)

CTD and pCO2 data

Merging summarized data sets

# Load Sensor and HydroC data ---------------------------------------------

CTD <- read_csv(here::here("Data/_summarized_data_files",
                              "Tina_V_Sensor_Profiles_Transects.csv"),
                   col_types = list("pCO2" = col_double())) %>% 
  rename(pCO2_analog = pCO2)

HC <- read_csv(here::here("Data/_summarized_data_files", "Tina_V_HydroC.csv"))
HC_full <- read_csv(here::here("Data/_summarized_data_files", "Tina_V_HydroC_full.csv"))

# Time offset correction ----------------------------------------------

# Time offset was determined by comparing zeroing reads from Sensor and HC
# in the plots produced in the section Time stamp synchronzity below
# before applying this correction

CTD <- CTD %>% 
  mutate(day = yday(date_time),
         date_time = if_else(day >= 206 & day <= 220,
                             date_time - 80, date_time - 10)) %>% 
  select(-day)

# Merge Sensor and HydroC data --------------------------------------------

df <- full_join(CTD, HC) %>% 
  arrange(date_time)

df_full <- full_join(CTD, HC_full) %>% 
  arrange(date_time)

rm(HC, HC_full, CTD)

Interpolation to common time stamp

CTD and auxillary recordings (15 sec measurment interval) are interpolated to HydroC time stamps (first 10 sec, than 1 sec measurement interval) when gaps between observations are not larger than 20. Thereafter, HydroC readings not falling in regular transects/profilings are removed, by removing rows with NA depth values. Furthermore, CTD readings without corresponding HydroC reading are removed, except during periods when HydroC was not operating.

# Interpolate Sensor data to HydroC timestamp

df <-
  df %>%
  mutate(dep = na.approx(dep, na.rm = FALSE, maxgap = 20),
         sal = na.approx(sal, na.rm = FALSE, maxgap = 20),
         tem = na.approx(tem, na.rm = FALSE, maxgap = 20),
         pCO2_analog = na.approx(pCO2_analog, na.rm = FALSE, maxgap = 20),
         pH = na.approx(pH, na.rm = FALSE, maxgap = 20),
         V_pH = na.approx(V_pH, na.rm = FALSE, maxgap = 20),
         O2 = na.approx(O2, na.rm = FALSE, maxgap = 20),
         Chl = na.approx(Chl, na.rm = FALSE, maxgap = 20)) %>% 
  filter(!is.na(dep)) %>% #remove HC readings not falling in regular transects/profilings
  fill(ID, type, station) %>% 
  filter(!is.na(deployment) | is.na(pCO2_analog)) # removes CTD readings without corresponding HydroC reading, except during periods when HydroC was not operating

df_full <-
  df_full %>%
  mutate(dep = na.approx(dep, na.rm = FALSE, maxgap = 20),
         sal = na.approx(sal, na.rm = FALSE, maxgap = 20),
         tem = na.approx(tem, na.rm = FALSE, maxgap = 20),
         pCO2_analog = na.approx(pCO2_analog, na.rm = FALSE, maxgap = 20),
         pH = na.approx(pH, na.rm = FALSE, maxgap = 20),
         V_pH = na.approx(V_pH, na.rm = FALSE, maxgap = 20),
         O2 = na.approx(O2, na.rm = FALSE, maxgap = 20),
         Chl = na.approx(Chl, na.rm = FALSE, maxgap = 20)) %>% 
  filter(!is.na(dep)) %>% #remove HC readings not falling in regular transects/profilings
  fill(ID, type, station) %>% 
  filter(!is.na(deployment) | is.na(pCO2_analog)) # removes CTD readings without corresponding HydroC reading, except during periods when HydroC was not operating

# Time stamp synchronzity -------------------------------------------------
# 
# df <- df %>% 
#   mutate(day = yday(date_time))
# 
# for (dayID in unique(df$day)) {
#   
#   df %>%
#     filter(day == dayID) %>% 
#       ggplot()+
#       geom_point(aes(date_time, pCO2, col="HC"))+
#       geom_point(aes(date_time, dep, col="dep"))+
#       geom_point(aes(date_time, pH, col="pH"))+
#       geom_point(aes(date_time, pCO2_analog, col="Sensor_int"))
#       
#     ggsave(here::here("/Plots/TinaV/Sensor/HydroC_diagnostics/Timing/day",
#                       paste(dayID,"_day_HydroC_merged.jpg", sep="")),
#            width = 10, height = 4)
# }
# 
# 
# for (depID in unique(df$deployment)) {
#   
#   df_dep <- df %>%
#     filter(deployment == depID, Zero == 1)
#   
#   for (zerID in unique(df_dep$Zero_ID)) {
#     
#     df_dep %>%
#       filter(Zero_ID == zerID) %>% 
#       ggplot()+
#       geom_point(aes(date_time, pCO2, col="HC"))+
#       geom_point(aes(date_time, pCO2_analog, col="Sensor_int"))
#     
#     ggsave(here::here("/Plots/TinaV/Sensor/HydroC_diagnostics/Timing/Zeroing",
#                       paste(depID,"_deployment_",zerID,"_Zero_ID_HydroC.jpg", sep="")),
#            width = 10, height = 4)
#     
#   }
# }
write_csv(df, here::here("Data/_merged_data_files", "BloomSail_CTD_HydroC.csv"))
write_csv(df_full, here::here("Data/_merged_data_files", "BloomSail_CTD_HydroC_full.csv"))

rm(df, df_full)
df <- read_csv(here::here("data/_merged_data_files",
                          "BloomSail_CTD_HydroC.csv"),
               col_types = cols(ID = col_character(),
                                pCO2_analog = col_double(),
                                pCO2 = col_double(),
                                Zero = col_factor(),
                                Flush = col_factor(),
                                Zero_ID = col_integer(),
                                deployment = col_integer(),
                                duration = col_double(),
                                mixing = col_character()))


df %>% 
  filter(!is.na(pCO2)) %>% 
  ggplot()+
  geom_path(aes(date_time, pCO2, col = "HydroC, drift corrected"))+
  geom_path(aes(date_time, pCO2_analog, col = "analog CTD"))+
  scale_color_brewer(palette = "Set1", name = "pCO2 record")+
  labs(y=expression(pCO[2]~(µatm)), x="")+
  facet_wrap(~ID, scales = "free_x", ncol = 1)
pCO~2~ record after interpolation to HydroC timestamp (analog output from HydroC and drift corrected data provided by Contos). ID refers to the starting date of each cruise. Please note that pCO~2~ measurement range is restricted to 100-500  µatm here due to the settings of the analog voltage output of the sensor. Zeroing periods are included.

pCO2 record after interpolation to HydroC timestamp (analog output from HydroC and drift corrected data provided by Contos). ID refers to the starting date of each cruise. Please note that pCO2 measurement range is restricted to 100-500 µatm here due to the settings of the analog voltage output of the sensor. Zeroing periods are included.

# ts <- xts(cbind(df$pCO2, df$dep), order.by = df$date_time)
# names(ts) <- c("pCO2", "Depth")
# 
# ts %>% 
#   dygraph() %>% 
#   dyRangeSelector() %>% #dateWindow = c("2012-01-01", "2016-12-31")
#   dySeries("pCO2", label = "pCO2") %>% 
#   dySeries("Depth", axis = 'y2', label = "Depth") %>% 
#   dyAxis("y", label = "pCO2 [µatm]") %>% 
#   dyAxis("y2", label = "Depth [m]") %>% 
#   dyOptions(drawPoints = TRUE, pointSize = 1)

Sensor and track data

Sensor <- read_csv(here::here("data/_merged_data_files",
                          "BloomSail_CTD_HydroC.csv"),
               col_types = cols(ID = col_character(),
                                pCO2_analog = col_double(),
                                pCO2 = col_double(),
                                Zero = col_factor(),
                                Flush = col_factor(),
                                Zero_ID = col_integer(),
                                deployment = col_integer(),
                                duration = col_double(),
                                mixing = col_character()))


track <- 
  read_csv(here::here("Data/_summarized_data_files",
                       "TinaV_Track.csv"))


df <- full_join(Sensor, track) %>% 
  arrange(date_time)

# interpolate track data and than remove columns that originate from track time stamp
df <-
  df %>%
  mutate(lat = na.approx(lat, na.rm = FALSE, maxgap = 20),
         lon = na.approx(lon, na.rm = FALSE, maxgap = 20)) %>% 
  filter(!is.na(dep))

df %>% 
  write_csv(here::here("Data/_merged_data_files", "BloomSail_CTD_HydroC_track.csv"))

rm(df)

```

Tasks / open questions

  • Check interpolation to CTD Sensor timestamp as alternative option

sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] zoo_1.8-6       lubridate_1.7.4 forcats_0.4.0   stringr_1.4.0  
 [5] dplyr_0.8.3     purrr_0.3.3     readr_1.3.1     tidyr_1.0.0    
 [9] tibble_2.1.3    ggplot2_3.3.0   tidyverse_1.3.0

loaded via a namespace (and not attached):
 [1] tidyselect_0.2.5   xfun_0.10          haven_2.2.0        lattice_0.20-35   
 [5] colorspace_1.4-1   vctrs_0.2.0        generics_0.0.2     htmltools_0.4.0   
 [9] yaml_2.2.0         rlang_0.4.5        later_1.0.0        pillar_1.4.2      
[13] withr_2.1.2        glue_1.3.1         DBI_1.0.0          RColorBrewer_1.1-2
[17] dbplyr_1.4.2       modelr_0.1.5       readxl_1.3.1       lifecycle_0.1.0   
[21] munsell_0.5.0      gtable_0.3.0       workflowr_1.6.0    cellranger_1.1.0  
[25] rvest_0.3.5        evaluate_0.14      labeling_0.3       knitr_1.26        
[29] httpuv_1.5.2       highr_0.8          broom_0.5.3        Rcpp_1.0.2        
[33] promises_1.1.0     backports_1.1.5    scales_1.0.0       jsonlite_1.6      
[37] fs_1.3.1           hms_0.5.2          digest_0.6.22      stringi_1.4.3     
[41] grid_3.5.0         rprojroot_1.3-2    here_0.1           cli_1.1.0         
[45] tools_3.5.0        magrittr_1.5       crayon_1.3.4       pkgconfig_2.0.3   
[49] zeallot_0.1.0      xml2_1.2.2         reprex_0.3.0       rstudioapi_0.10   
[53] assertthat_0.2.1   rmarkdown_2.0      httr_1.4.1         R6_2.4.0          
[57] nlme_3.1-137       git2r_0.26.1       compiler_3.5.0