data-raw/FMWT.R

In sbashevkin/discretewq: Integrated Dataset of Discrete Water Quality in the San Francisco Estuary

## code to prepare `FMWT` dataset goes here

library(readr)
library(dplyr)
library(lubridate)
require(tidyr)

FMWT_stations <-
  read_csv(
    file.path("data-raw", "FMWT", "StationsLookUp.csv"),
    col_types = cols_only(StationCode = "c", DD_Latitude = "d", DD_Longitude = "d")
  ) %>%
  rename(
    Station = StationCode,
    Latitude = DD_Latitude,
    Longitude = DD_Longitude
  ) %>%
  drop_na()

FMWT <-
  read_csv(
    file.path("data-raw", "FMWT", "Sample.csv"),
    col_types = cols_only(
      StationCode = "c",
      SampleDate = "c",
      SampleTimeStart = "c",
      WaterTemperature = "d",
      Turbidity = "d",
      Secchi = "d",
      SecchiEstimated = "l",
      ConductivityTop = "d",
      ConductivityBottom = "d",
      TideCode = "i",
      DepthBottom = "d",
      Microcystis = "d",
      BottomTemperature = "d"
    )
  ) %>%
  rename(
    Station = StationCode,
    Date = SampleDate,
    Tide = TideCode,
    Time = SampleTimeStart,
    Depth = DepthBottom,
    Conductivity = ConductivityTop,
    Conductivity_bottom = ConductivityBottom,
    Temperature = WaterTemperature,
    Secchi_estimated = SecchiEstimated,
    TurbidityNTU = Turbidity,
    Temperature_bottom = BottomTemperature
  ) %>%
  mutate(
    Date = parse_date_time(Date, "%m/%d/%Y %H:%M:%S", tz = "America/Los_Angeles"),
    Time = parse_date_time(Time, "%m/%d/%Y %H:%M:%S", tz = "America/Los_Angeles"),
    Time = if_else(hour(Time) == 0, parse_date_time(NA_character_, tz = "America/Los_Angeles"), Time),
    Tide = recode(Tide, `1` = "High Slack", `2` = "Ebb", `3` = "Low Slack", `4` = "Flood"),
    Datetime = parse_date_time(if_else(is.na(Time), NA_character_, paste0(Date, " ", hour(Time), ":", minute(Time))), "%Y-%m-%d %H:%M", tz = "America/Los_Angeles"),
    Microcystis = if_else(Microcystis == 6, 2, Microcystis),
    # Omit values equal to zero in Temperature_bottom and Conductivity_bottom
    across(c(Temperature_bottom, Conductivity_bottom), ~ na_if(.x, 0)),
    # Omit one Temperature_bottom value that was likely measured in degrees F
    Temperature_bottom = if_else(Temperature_bottom > 40, NA_real_, Temperature_bottom),
    Source = "FMWT",
    Secchi = Secchi * 100, # convert to cm
    Depth = Depth * 0.3048 # Convert to meters
  ) %>%
  left_join(FMWT_stations, by = "Station") %>%
  select(
    Source,
    Station,
    Latitude,
    Longitude,
    Date,
    Datetime,
    Depth,
    Tide,
    Microcystis,
    Secchi,
    Secchi_estimated,
    Temperature,
    Temperature_bottom,
    Conductivity,
    Conductivity_bottom,
    TurbidityNTU
  ) %>%
  # Remove rows where all WQ parameters have missing values
  filter(
    !if_all(
      c(
        Microcystis,
        Secchi,
        Temperature,
        Temperature_bottom,
        Conductivity,
        Conductivity_bottom,
        TurbidityNTU
      ),
      is.na
    )
  ) %>%
  distinct(Source, Station, Date, Datetime, .keep_all = T)

usethis::use_data(FMWT, overwrite = TRUE)