loc-01-setup.Rmd

---
title: "loc-01-setup"
author: "Kate Morkeski"
date: "`r Sys.Date()`"
output: html_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

## load libraries

```{r}

library(here)
library(lubridate)
library(tidyverse)

```

## read in GPS and other underway data

```{r}

combined <- read_delim(here('LOC-01_Combined_Nav_TSG_Fluo_HydroFIA.txt')) 

combined$DateTime_UTC <- as.POSIXct(combined$DateTime_UTC, tz = "UTC", format="%d-%b-%Y %H:%M:%OS")

met <- read_delim(here('Metdat.dat'), skip = 1)

pressure <- met |> select(TIMESTAMP, BaroPress)  

pressure <- pressure |> rename(BaroPress_hPa = BaroPress) 
pressure <- pressure[-1,]
pressure <- pressure[-1,]

#format columns as date and time for later interpolation
pressure$TIMESTAMP <- as.POSIXct(pressure$TIMESTAMP, tz = "UTC", format="%Y-%m-%d %H:%M:%OS")
pressure$BaroPress_hPa <- as.double(pressure$BaroPress_hPa)

```

```{r}

ggplot(combined, aes(x = DateTime_UTC, y = Temp1_C)) +
  geom_point() +
  theme_minimal()

ggplot(combined, aes(x = DateTime_UTC, y = Temp2_C)) +
  geom_point() +
  theme_minimal()

ggplot(combined, aes(x = DateTime_UTC, y = Corrected_TA_umol_kg_)) +
  geom_point() +
  theme_minimal()

ggplot(pressure, aes(x = TIMESTAMP, y = BaroPress_hPa)) +
  geom_line() +
  theme_minimal()

```

```{r}

# read in GO data
GOfiles <- dir(here("LOC-01_GO-Data/"), "*.txt") # get file names

GO_LOC01 <- GOfiles %>% map_dfr(~ read_tsv(here("LOC-01_GO-Data/", .), show_col_types = FALSE, ))

```

```{r}

# handle date and time columns
# combine date and time
GO_LOC01$PcDate <- as.character(GO_LOC01$PcDate) 
GO_LOC01$PcTime <- as.character(GO_LOC01$PcTime) 
#GO_LOC01$PcTime <- as.character(GO_LOC01$PcTime) 
GO_LOC01$date_time <- paste(GO_LOC01$PcDate, GO_LOC01$PcTime)
GO_LOC01$date_time_utc <- as.POSIXct(GO_LOC01$date_time, tz = "UTC", format="%d/%m/%y %H:%M:%OS")


ggplot(GO_LOC01, aes(x = date_time_utc, y = EquPress)) +
  geom_point() +
  theme_minimal()

ggplot(GO_LOC01, aes(x = date_time_utc, y = CO2ppm)) +
  geom_point() +
  theme_minimal()

```

# Interpolate CTD data to GO timestamps

```{r}


Lat <- data.frame(approx(combined$DateTime_UTC, combined$Latitude, xout = GO_LOC01$date_time_utc, rule = 2, method = "linear"))
latitude <- Lat$y 

Lon <- data.frame(approx(combined$DateTime_UTC, combined$Longitude, xout = GO_LOC01$date_time_utc, rule = 2, method = "linear"))
longitude <- Lon$y 

dye <- data.frame(approx(combined$DateTime_UTC, combined$Dye_ppb, xout = GO_LOC01$date_time_utc, rule = 2, method = "linear"))
dye_ppb <- dye$y 

Temp1_C <- data.frame(approx(combined$DateTime_UTC, combined$Temp1_C, xout = GO_LOC01$date_time_utc, rule = 2, method = "linear"))
temp1_C <- Temp1_C$y 

Temp2_C <- data.frame(approx(combined$DateTime_UTC, combined$Temp2_C, xout = GO_LOC01$date_time_utc, rule = 2, method = "linear"))
temp2_C <- Temp2_C$y 

sal <- data.frame(approx(combined$DateTime_UTC, combined$Salinity_PSU, xout = GO_LOC01$date_time_utc, rule = 2, method = "linear"))
salinity_psu <- sal$y 

alk <- data.frame(approx(combined$DateTime_UTC, combined$Corrected_TA_umol_kg_, xout = GO_LOC01$date_time_utc, rule = 2, method = "linear"))
alkalinity_umolkg <- alk$y 

press <- data.frame(approx(pressure$TIMESTAMP, pressure$BaroPress_hPa, xout = GO_LOC01$date_time_utc, rule = 1, method = "linear"))
atm_pressure_hPa <- press$y 

GO_LOC01 <- cbind(GO_LOC01, latitude, longitude, atm_pressure_hPa, dye_ppb, temp1_C, temp2_C, salinity_psu, alkalinity_umolkg)


```
# Inspect interpolated ancillary data

```{r}

ggplot(GO_LOC01, aes(x = date_time_utc, y = temp1_C)) +
  geom_point() +
  theme_minimal()

ggplot(GO_LOC01, aes(x = date_time_utc, y = temp2_C)) +
  geom_point() +
  theme_minimal()

ggplot(GO_LOC01, aes(x = date_time_utc, y = salinity_psu)) +
  geom_point() +
  theme_minimal()

ggplot(GO_LOC01, aes(x = date_time_utc, y = alkalinity_umolkg)) +
  geom_point() +
  theme_minimal()

```
# Adjust columns and write csv

```{r}

GO_LOC01 <- GO_LOC01 |>
  select(-date_time, -'N/A') |>
  relocate(date_time_utc, .before = Type) |>
  relocate(latitude, .before = Type) |>
  relocate(longitude, .before = Type) 
  

write.csv(GO_LOC01, here('GO_LOC01.csv'), row.names = FALSE)

```

# Add bottle salinity to CTD data set

```{r}

ctd_bottles <- read_csv(here('CTD_Bottles_combined.csv')) 

#combined$DateTime_UTC <- as.POSIXct(combined$DateTime_UTC, tz = "UTC", format="%d-%b-%Y %H:%M:%OS")

sal <- read_delim(here('LOC-01_CTD_bottle_salinometer.txt'), col_names = FALSE)

# define headers for columns in desired order
sal <- sal |> 
  rename('Salinity bottle' = X1) |>
  select(-X2) |>
  rename(salinity_psu = X3) |>
  rename(flag = X4) 

ctd_bottles <- left_join(ctd_bottles, sal, by = 'Salinity bottle')

ggplot(ctd_bottles, aes(x = salinity_psu, y = Sal00)) +
  geom_point() +
  theme_minimal()
ggsave('ctd-vs-bottle-sal.png')

write.csv(ctd_bottles, here('CTD_Bottles_combined_bottlesal.csv'), row.names = FALSE)

```