R/schmidt.plot.R

In GLEON/rLakeAnalyzer: Lake Physics Tools

#' @title Creates a time series plot of Schmidt's stability
#' 
#' @description Generates a time series of Schmidt's stability where each value represents
#' water column stability for each time step of data. See
#' \code{\link{schmidt.stability}} for more details and reference.
#' 
#' 
#' @param wtr Data frame of water temperature loaded with \code{\link{load.ts}}
#' @param bth A data frame containing hypsometric data. Loaded using
#' \code{\link{load.bathy}}
#' @seealso \code{\link{schmidt.stability}}
#' @references See \code{\link{schmidt.stability}}
#' @keywords hplot
#' @examples
#' 
#' 	# Get system data file paths 
#'   wtr.path <- system.file('extdata', 'Sparkling.wtr', package="rLakeAnalyzer")
#' 	bth.path <- system.file('extdata', 'Sparkling.bth', package="rLakeAnalyzer")
#' 
#' 	# Load data for example lake, Sparkilng Lake, Wisconsin.
#' 	wtr = load.ts(wtr.path)
#' 	bth = load.bathy(bth.path)
#' 	
#' 	\dontrun{
#'   # Generate default plot
#'   schmidt.plot(wtr,bth)
#'   }
#' @export
schmidt.plot = function(wtr,bth){

  ss = ts.schmidt.stability(wtr,bth)
  
  starttime = min(ss[,1]) #earliest date
  endtime = max(ss[,1]) #latest date
  
  # defining units and labels for x axis
  ss.dates = ss$datetime # turn datetime into vector
  datestoshow = pretty(ss.dates) # pretty vector to specify tick mark location 
  sec.endtime = as.numeric(endtime) # show time as seconds
  sec.starttime = as.numeric(starttime) # show time as seconds
  tt = sec.endtime - sec.starttime # time range of data frame; used to specify time axis
  
  # specify x axis format based upon time range of data 
  ttformat = c()
  if(tt < 1.1*60) { # if time is less than 1 hr units are seconds
    ttformat <- "%S"
  } else if (tt < 1.1*60*60) { # if time is less than 1.1 hours units are min:sec
    ttformat <- "%M:%S"
  } else if (tt < 60*60*24*2) {# if time is less than 2 days units are hour:min
    ttformat <- "%H:%M"
  } else if (tt < 60*60*24*7) { # if time is less than 7 days units are Jul 25 10:15
    ttformat <- "%d %b %H"
  } else if (tt < 60*60*24*7*8.9) {# if time is less than 2 months units are ex. Jul 25 10:15
    ttformat <- "%d %b %H:%M"
  } else if (tt < 60*60*24*7*4.4*12) { # if time is less than 12 months units are Jun, Jul, Aug  
    ttformat <- "%b"
  } else if (tt < 60*60*24*7*4.4*12*1.1){ # if time is more than 12.1 years units are Jul 2013
    ttformat <- "%b %Y"
  }
  
  # specify x axis labels based upon time range of data 
  xxlab = c()
  if(tt < 1.1*60) { # if time is less than 1 minutes units are seconds
    xxlab  <- "Seconds"
  } else if (tt < 1.1*60*60) { # if time is less than 1.1 hours units are min:sec
    xxlab <- "Minutes"
  } else if (tt < 60*60*24*2) {# if time is less than 2 days units are hour:min
    xxlab <- "Hours"
  } else if (tt < 60*60*24*7) { # if time is less than 7 days units are Jul 25 10:15
    xxlab <- " "
  } else if (tt < 60*60*24*7*8.9) {# if time is less than 2 months units are ex. Jul 25 
    xxlab <- " "
  } else if (tt < 60*60*24*7*4.4*12) { # if time is less than 12 months units are Jun, Jul, Aug  
    xxlab <- " "
  } else if (tt < 60*60*24*7*4.4*12*1.1){ # if time is more than 12.1 years units are Jul 2013
    xxlab <- " "
  }
  
  graphics::plot(ss[,2]~ss[,1],
       type='l',
       lwd = 2,
       col="black",
       ylab=expression("Schmidt's Stability"~(J~m^-2)),
       xlab=xxlab,
       bty="n",
       xlim=c(starttime,endtime),
       axes=F
  )
  
  # x axis
  graphics::axis(side = 1, labels=format(datestoshow, ttformat), at = datestoshow, pos = c(min(ss[,2],na.rm=TRUE)), tck = -0.03)
  graphics::segments(c(starttime),c(min(ss[,2],na.rm=TRUE)),c(endtime),c(min(ss[,2],na.rm=TRUE)), col = "black", lty = 1)
  
  # y axis
  graphics::axis (side  = 2, pos = c(starttime), at = NULL, las = 1)
  graphics::segments(c(starttime),c(min(ss[,2],na.rm=TRUE)),c(starttime),c(max(ss[,2],na.rm=TRUE)), col = "black")
  
}