runall_csls_inputs: Run all functions needed to summarise water budget inputs for...
In cvoter/isoH2Obudget: Lake Water Budget Using Stable Isotopes

Description Usage Arguments Details Value

Runs all major functions in the CSLSiso package to transform raw data into the final inputs data frame for one of the CSLS lakes. Can be calculated on a monthly basis (annual = FALSE) or based on all available data (annual = TRUE).

runall_csls_inputs(
  lake,
  threshold = 0.01,
  start_date = NULL,
  end_date = NULL,
  annual = FALSE
)

`lake`	name of lake (e.g., Pleasant, Long, or Plainfield)
`threshold`	minimum median difference between lake levels and groundwater levels during the month of measurement in order to classify groundwater measurement.
`start_date`	optional start date to use for analysis (first day of the month) in POSIXct. If not provided, defaults to NULL and timeseries is based on months with isotope samples.
`end_date`	optional end date to use for analysis (last day of the month) in POSIXct. If not provided, defaults to NULL and timeseries is based on months with isotope samples.
`annual`	defaults to FALSE to calculate water balance on a monthly basis. If TRUE, calculates the annual balance instead.

Loaded data includes the following data in a list format, where each lake has its own data frame. For example, to access groundwater levels for Pleasant Lake, the command would be gw_levels <- CSLSdata::gw_levels[["Pleasant"]].

weather, hourly weather data including date (POSIXct), atmp (air temperature, deg C), P (precipitation, mm), RH (relative humidity, percent), Rs (solar radiation, MJ), and wind (wind speed, m/s)
lst_HOBO, hourly lake surface temperature from HOBO loggers, including date (POSIXct), ltmp (lake surface temperature, deg C), and elev_m (elevation of the sensor, meters above mean sea level)
isotopes, stable isotope measurements including date (POSIXct), lake, site_id, d18O measurement, and d2H measurement
lake_levels, daily lake levels (meters above mean sea level) including date (POSIXct), site_no (USGS), obs_type ("LK"), and level_m (level in meters above mean sea level)
gw_levels, daily groundwater levels including date, site_no, obs_type ("GW"), level_m (level in meters above mean sea level), and site_id (CSLS site id)
dictionary, links site ids and characteristics together with columns for lake, obs_type ("LK", "GW", "P"), site_id (e.g., "LL-01"), SWIMS_station_id, USGS_id, WBIC, static_iso_class (e.g., "upgradient", "lake", "precipitation"), lat_deg, long_deg, elev_m, and bouy_bottom_elev_m

monthly_inputs, a data frame with the following columns:

`date`	date of month
`ltmp_degC`	average lake surface temperature, degrees C
`ltmp_K`	average lake surface temperature, Kelvin
`atmp_degC`	average air temperature, degrees C
`atmp_K`	average air temperature, Kelvin
`RH_pct`	average relative humidity, percent
`P_mm`	precipitaiton for month or year, mm
`E_mm`	lake evaporation for month or year, mm
`dV_mm`	change in lake volume for month or year, mm
`P_m3`	precipitation for month or year, m3
`E_m3`	lake evaporation for month or year, m3
`dV_m3`	change in lake volume for month or year, m3
`mean_vol_m3`	mean lake volume during the month or year (m3)
`mean_area_m2`	mean lake area during the month or year (m2)
`d18O_lake`	mean stable isotope measurement for d18O, lake (per mil)
`d18O_pcpn`	mean stable isotope measurement for d18O, precipitation (per mil)
`d18O_GWin`	mean stable isotope measurement for d18O, GWin (per mil)
`d18O_GWout`	mean stable isotope measurement for d18O, GWout (per mil)
`d18O_evap`	mean stable isotope measurement for d18O, evaporation (per mil)
`d2H_lake`	mean stable isotope measurement for d2H, lake (per mil)
`d2H_pcpn`	mean stable isotope measurement for d2H, precipitation (per mil)
`d2H_GWin`	mean stable isotope measurement for d2H, GWin (per mil)
`d2H_GWout`	mean stable isotope measurement for d2H, GWout (per mil)
`d2H_evap`	mean stable isotope measurement for d2H, evaporation (per mil)
`GWin_sites`	name of monitoring wells use for GWin isotopes
`GWout_sites`	name of monitoring wells use for GWout isotopes