R/get_temp.R

In USGS-R/glmtools: Tools for working with the General Lake Model (GLM)

#'@title get water temperatures from a GLM simulation
#'@description 
#'Creates a data.frame with DateTime and temperatures (in deg C).  \cr
#'Temperatures that are sampled out of the GLM output are taken relative 
#'to the surface (\code{reference = 'surface'}) or the bottom of the lake 
#'(\code{reference = 'bottom'}).
#'
#'@param file a string with the path to the netcdf output from GLM
#'@param reference a string which specifies the vertical reference ('surface' or 'bottom')
#'@param z_out an optional vector of depths for temperature output (in meters). 
#'If NULL, depths will be determined based on the depth of the lake
#'@param t_out a vector of POSIXct dates for temporal resampling (order is important)
#'@param ... additional arguments passed to \code{resample_sim()}
#'@return a data.frame with DateTime and temperature at depth 
#'@keywords methods
#'@seealso \link{resample_sim}
#'@author
#'Jordan S. Read, Luke A. Winslow
#'@examples 
#'sim_folder <- run_example_sim(verbose = FALSE)
#'nc_file <- file.path(sim_folder, 'output/output.nc')
#'temp_surf <- get_temp(nc_file, reference = 'surface', z_out = c(0,1,2))
#'temp_bot <- get_temp(nc_file, reference = 'bottom', z_out = c(0,1,2))
#'temp_bot <- get_temp(nc_file)
#'
#'#-- get temporal subset--
#'t_out <- seq(as.POSIXct("2015-04-15"), as.POSIXct("2015-06-01"), by = 86400)
#'temp_surf <- get_temp(nc_file, reference = 'surface', z_out = 0, t_out = t_out)
#'plot(temp_surf)
#'@export
get_temp <-  function(file='output.nc', reference = 'bottom', z_out = NULL, t_out = NULL, ...){
  glm_temp <- get_var(file, reference, z_out, t_out, var_name = 'temp')
  
  return(glm_temp)
}