Last updated: 2019-11-08

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Knit directory: BloomSail/

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html 33e3659 jens-daniel-mueller 2019-10-22 Build site.
Rmd efcafd1 jens-daniel-mueller 2019-10-22 Added data base, merging, and RT determination
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Rmd 4131b9c jens-daniel-mueller 2019-10-21 finisehd read CTD and HydroC, created merging Rmd

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"))

# 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)

rm(HC, 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, cast) %>% 
  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)
#     
#   }
# }
# add counter for date_time observations

df <- df %>% 
  add_count(date_time)

# find triplicated time stamp and select only first observation, and merge

df_no_triple <- df %>% 
  filter(n <= 2)

df_triple_clean <- df %>% 
  filter(n > 2) %>% 
  slice(1)

df <- full_join(df_no_triple, df_triple_clean)

rm(list=setdiff(ls(), "df"))


# find duplicated time stamps and shift first by one second, and merge

df %>% 
  distinct(date_time)
# A tibble: 603,770 x 1
   date_time          
   <dttm>             
 1 2018-06-16 03:58:45
 2 2018-06-16 03:59:00
 3 2018-06-16 03:59:15
 4 2018-06-16 03:59:30
 5 2018-06-16 03:59:45
 6 2018-06-16 04:00:00
 7 2018-06-16 04:00:15
 8 2018-06-16 04:00:30
 9 2018-06-16 04:00:45
10 2018-06-16 04:01:00
# ... with 603,760 more rows
df_no_duplicated <- df %>%
  filter(n == 1)

df_duplicated <- df %>% 
  filter(n == 2)

df_duplicated_first <- df_duplicated %>% 
  group_by(date_time) %>% 
  slice(1) %>% 
  ungroup() %>% 
  mutate(date_time = date_time - 1)

df_duplicated_second <- df_duplicated %>% 
  group_by(date_time) %>% 
  slice(2) %>% 
  ungroup()

df_duplicated_clean <- full_join(df_duplicated_first, df_duplicated_second) %>% 
  arrange(date_time)

df <- full_join(df_no_duplicated, df_duplicated_clean)

df %>% 
  distinct(date_time)
# A tibble: 607,747 x 1
   date_time          
   <dttm>             
 1 2018-06-16 03:58:45
 2 2018-06-16 03:59:00
 3 2018-06-16 03:59:15
 4 2018-06-16 03:59:30
 5 2018-06-16 03:59:45
 6 2018-06-16 04:00:00
 7 2018-06-16 04:00:15
 8 2018-06-16 04:00:30
 9 2018-06-16 04:00:45
10 2018-06-16 04:01:00
# ... with 607,737 more rows
rm(list=setdiff(ls(), "df"))

# remaining duplicates are observations where other observations with a +/- 1 sec timestamp exist
# for those cases, only the first duplicated observation is selected (similar to triplicate treatment)

df_still_no_duplicated <- df %>% 
  select(-n) %>% 
  add_count(date_time) %>% 
  filter(n == 1)

df_still_duplicated_first <- df %>% 
  select(-n) %>% 
  add_count(date_time) %>% 
  filter(n == 2) %>% 
  group_by(date_time) %>% 
  slice(1)

df <- full_join(df_still_no_duplicated, df_still_duplicated_first)

df %>% 
  distinct(date_time)
# A tibble: 607,747 x 1
   date_time          
   <dttm>             
 1 2018-06-16 03:58:45
 2 2018-06-16 03:59:00
 3 2018-06-16 03:59:15
 4 2018-06-16 03:59:30
 5 2018-06-16 03:59:45
 6 2018-06-16 04:00:00
 7 2018-06-16 04:00:15
 8 2018-06-16 04:00:30
 9 2018-06-16 04:00:45
10 2018-06-16 04:01:00
# ... with 607,737 more rows
rm(list=setdiff(ls(), "df"))

df <- df %>% 
  select(-n)
write_csv(df, here::here("Data/_merged_data_files", "BloomSail_CTD_HydroC.csv"))
HC <-
  read_csv2(here::here("Data/TinaV/Sensor/HydroC-pCO2/corrected_Contros",
                       "parameter&pCO2s(method 43).txt"),
            col_names = c("date_time", "Zero", "Flush", "p_NDIR",
                          "p_in", "T_control", "T_gas", "%rH_gas",
                          "Signal_raw", "Signal_ref", "T_sensor",
                          "pCO2", "Runtime", "nr.ave")) %>% 
  mutate(Flush = as.factor(as.character(Flush)),
         Zero = as.factor(as.character(Zero)))
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.

Version Author Date
33e3659 jens-daniel-mueller 2019-10-22
# 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)

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 17763)

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_3.2.1   tidyverse_1.2.1

loaded via a namespace (and not attached):
 [1] tidyselect_0.2.5   xfun_0.10          haven_2.1.1       
 [4] lattice_0.20-35    colorspace_1.4-1   vctrs_0.2.0       
 [7] generics_0.0.2     htmltools_0.4.0    yaml_2.2.0        
[10] utf8_1.1.4         rlang_0.4.1        pillar_1.4.2      
[13] glue_1.3.1         withr_2.1.2        RColorBrewer_1.1-2
[16] modelr_0.1.5       readxl_1.3.1       lifecycle_0.1.0   
[19] munsell_0.5.0      gtable_0.3.0       workflowr_1.4.0   
[22] cellranger_1.1.0   rvest_0.3.4        evaluate_0.14     
[25] labeling_0.3       knitr_1.25         fansi_0.4.0       
[28] highr_0.8          broom_0.5.2        Rcpp_1.0.2        
[31] scales_1.0.0       backports_1.1.5    jsonlite_1.6      
[34] fs_1.3.1           hms_0.5.1          digest_0.6.22     
[37] stringi_1.4.3      grid_3.5.0         rprojroot_1.3-2   
[40] here_0.1           cli_1.1.0          tools_3.5.0       
[43] magrittr_1.5       lazyeval_0.2.2     crayon_1.3.4      
[46] whisker_0.4        pkgconfig_2.0.3    zeallot_0.1.0     
[49] ellipsis_0.3.0     xml2_1.2.2         assertthat_0.2.1  
[52] rmarkdown_1.16     httr_1.4.1         rstudioapi_0.10   
[55] R6_2.4.0           nlme_3.1-137       git2r_0.26.1      
[58] compiler_3.5.0