Merging and interpolation of observations
Jens Daniel Müller
28 April, 2020
Last updated: 2020-04-28
Checks: 7 0
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$Zero_ID)) {
#
# df_dep %>%
# filter(Zero_ID == zerID) %>%
# ggplot()+
# geom_point(aes(date_time, pCO2, col="HC"))+
# geom_point(aes(date_time, pCO2_analog, col="Sensor_int"))
#
# ggsave(here::here("/Plots/TinaV/Sensor/HydroC_diagnostics/Timing/Zeroing",
# paste(depID,"_deployment_",zerID,"_Zero_ID_HydroC.jpg", sep="")),
# width = 10, height = 4)
#
# }
# }write_csv(df, here::here("Data/_merged_data_files", "BloomSail_CTD_HydroC.csv"))
write_csv(df_full, here::here("Data/_merged_data_files", "BloomSail_CTD_HydroC_full.csv"))
rm(df, df_full)df <- read_csv(here::here("data/_merged_data_files",
"BloomSail_CTD_HydroC.csv"),
col_types = cols(ID = col_character(),
pCO2_analog = col_double(),
pCO2 = col_double(),
Zero = col_factor(),
Flush = col_factor(),
Zero_ID = col_integer(),
deployment = col_integer(),
duration = col_double(),
mixing = col_character()))
df %>%
filter(!is.na(pCO2)) %>%
ggplot()+
geom_path(aes(date_time, pCO2, col = "HydroC, drift corrected"))+
geom_path(aes(date_time, pCO2_analog, col = "analog CTD"))+
scale_color_brewer(palette = "Set1", name = "pCO2 record")+
labs(y=expression(pCO[2]~(µatm)), x="")+
facet_wrap(~ID, scales = "free_x", ncol = 1)
pCO2 record after interpolation to HydroC timestamp (analog output from HydroC and drift corrected data provided by Contos). ID refers to the starting date of each cruise. Please note that pCO2 measurement range is restricted to 100-500 µatm here due to the settings of the analog voltage output of the sensor. Zeroing periods are included.
# ts <- xts(cbind(df$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
<br>
<p>
<button type="button" class="btn btn-default btn-workflowr btn-workflowr-sessioninfo"
data-toggle="collapse" data-target="#workflowr-sessioninfo"
style = "display: block;">
<span class="glyphicon glyphicon-wrench" aria-hidden="true"></span>
Session information
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</p>
<div id="workflowr-sessioninfo" class="collapse">
```r
sessionInfo()R version 3.6.3 (2020-02-29)
Platform: i386-w64-mingw32/i386 (32-bit)
Running under: Windows 10 x64 (build 18363)
Matrix products: default
locale:
[1] LC_COLLATE=English_Germany.1252 LC_CTYPE=English_Germany.1252
[3] LC_MONETARY=English_Germany.1252 LC_NUMERIC=C
[5] LC_TIME=English_Germany.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] zoo_1.8-7 lubridate_1.7.4 forcats_0.5.0 stringr_1.4.0
[5] dplyr_0.8.5 purrr_0.3.3 readr_1.3.1 tidyr_1.0.2
[9] tibble_3.0.0 ggplot2_3.3.0 tidyverse_1.3.0 workflowr_1.6.1
loaded via a namespace (and not attached):
[1] RColorBrewer_1.1-2 jsonlite_1.6.1 rstudioapi_0.11 generics_0.0.2
[5] magrittr_1.5 farver_2.0.3 gtable_0.3.0 rmarkdown_2.1
[9] vctrs_0.2.4 fs_1.4.0 hms_0.5.3 xml2_1.3.0
[13] pillar_1.4.3 htmltools_0.4.0 haven_2.2.0 later_1.0.0
[17] broom_0.5.5 cellranger_1.1.0 lattice_0.20-41 tidyselect_1.0.0
[21] knitr_1.28 git2r_0.26.1 whisker_0.4 lifecycle_0.2.0
[25] pkgconfig_2.0.3 R6_2.4.1 digest_0.6.25 xfun_0.12
[29] colorspace_1.4-1 rprojroot_1.3-2 stringi_1.4.6 yaml_2.2.1
[33] evaluate_0.14 labeling_0.3 fansi_0.4.1 httr_1.4.1
[37] compiler_3.6.3 here_0.1 cli_2.0.2 withr_2.1.2
[41] backports_1.1.5 munsell_0.5.0 DBI_1.1.0 modelr_0.1.6
[45] Rcpp_1.0.4 readxl_1.3.1 highr_0.8 dbplyr_1.4.2
[49] ellipsis_0.3.0 assertthat_0.2.1 tools_3.6.3 reprex_0.3.0
[53] httpuv_1.5.2 scales_1.1.0 crayon_1.3.4 glue_1.3.2
[57] rlang_0.4.5 nlme_3.1-145 rvest_0.3.5 promises_1.1.0
[61] grid_3.6.3