R/center.buoyancy.R

In GLEON/rLakeAnalyzer: Lake Physics Tools

#' @title Calculates the center of buoyancy.
#' 
#' @description Calculate the center of buoyancy using buoyancy frequency with a center of
#' mass analysis. Brunt-Vaisala frequency is used for a temperature profile.
#' Negative values for N2 are set to 0 (as they represent transient
#' instabilities or sensor calibration issues) for this calculation.
#' 
#' 
#' @param wtr a numeric vector of water temperature in degrees C
#' @param depths a numeric vector corresponding to the depths (in m) of the wtr
#' measurements
#' @return Returns a value for the center of buoyancy.
#' @seealso \code{buoyancy.freq}, \code{ts.buoyancy.freq},
#' \code{center.buoyancy}
#' @keywords arith
#' @examples
#' 
#' 
#' 	# A vector of water temperatures
#' 	wtr = c(22.51, 22.42, 22.4, 22.4, 22.4, 22.36, 22.3, 22.21, 22.11, 21.23, 16.42, 
#' 		15.15, 14.24, 13.35, 10.94, 10.43, 10.36, 9.94, 9.45, 9.1, 8.91, 8.58, 8.43)
#' 
#' 	#A vector defining the depths
#' 	depths = c(0, 0.5, 1, 1.5, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 
#' 		17, 18, 19, 20)
#' 	
#' 	c.b = center.buoyancy(wtr, depths)
#' 
#' @export
center.buoyancy <- function(wtr, depths){
  
  if (depths[2] - depths[1] < 0 ){stop('depths must be in descending order')}
  N2 <- buoyancy.freq(wtr, depths)
  num.slices <- length(N2)
  areas <- vector('numeric',length = num.slices)
  cent.depths <- vector('numeric',length = num.slices)
  
  for (i in 1:num.slices){
    dz <- depths[i+1] - depths[i]
    areas[i] <- dz * N2[i] # assumes depths are in descending order
    cent.depths[i] <- mean(depths[i:(i+1)])
  }
  
  areas[areas < 0] <- 0
  cent.buoyancy <- sum(cent.depths*areas)/sum(areas)
  cent.buoyancy[cent.buoyancy == Inf] <- NA # division by zero
  return(cent.buoyancy)
}




#' @title Calculates the center of buoyancy for multiple temperature profiles.
#' 
#' @description Function for simplifying the calculation of the center of buoyancy. Can
#' usually be called directly on data loaded directly using
#' \code{\link{load.ts}} and \code{\link{load.bathy}}.
#' 
#' 
#' @param wtr A data frame of water temperatures (in Celsius). Loaded using
#' \code{\link{load.ts}}
#' @param na.rm Boolean indicated if step-by-step removal of NA's should be
#' tried. If false, a timestep with any NA values will return an NA value. If
#' true, best effort will be made to calculate indices despite NA values.
#' @return Returns a data frame with the timeseries of the center of buoyancy
#' frequency. Includes a \sQuote{datetime} column.
#' @seealso \code{center.buoyancy}, \code{load.bathy}, \code{load.ts}
#' @references Imberger, J., Patterson, J.C., 1990. \emph{Physical limnology}.
#' Advances in Applied Mechanics 27, 353-370.
#' @keywords arith
#' @examples
#' 
#' 
#'   #Get the path for the package example file included
#'   wtr.path <- system.file('extdata', 'Sparkling.daily.wtr', package="rLakeAnalyzer")
#' 	
#'   #Load data for example lake, Sparkilng Lake, Wisconsin.
#'   sp.wtr = load.ts(wtr.path)
#' 	 
#'   #calculate and plot the thermocline depth
#'   t.d = ts.thermo.depth(sp.wtr)
#'   
#'   center.N2 = ts.center.buoyancy(sp.wtr)
#' 	
#'   plot(center.N2, type='l', ylab='Depth (m)', xlab='Date', ylim=c(19,0), lwd = 1.5)
#'   lines(t.d, type='l', col='red', lwd = 1.5)
#'   legend(x = t.d[3,1], y = .25,
#'      c('center of buoyancy','thermocline depth'),
#'      lty=c(1,1),
#'      lwd=c(1.5,1.5),col=c("black","red"), bty = "n")
#' 	
#' @export
ts.center.buoyancy <- function(wtr, na.rm=FALSE){
  
  depths = get.offsets(wtr)
  
  n = nrow(wtr)
  
  wtr.mat = as.matrix(wtr[,-1])
  cent.n2 = rep(NA, n)
    
  for(i in 1:n){
    if(na.rm){
      temps = wtr.mat[i,]
      notNA = !is.na(temps)
      cent.n2[i] <- center.buoyancy(temps[notNA], depths[notNA])
    }else{
      cent.n2[i] <- center.buoyancy(wtr.mat[i, ], depths)
    }
  }
  
  cent.buoyancy = data.frame(wtr[,'datetime', drop=FALSE], cent.n2)
  
  return(cent.buoyancy)
}