02_plot.phenocam.R

## Define ciEnvelope function
ciEnvelope <- function(x,ylo,yhi,col="lightgrey",...){
  ## identify chunks of data with no missing values
  has.na = apply(is.na(cbind(x,ylo,yhi)),1,sum)
  block = cumsum(has.na);block[has.na>0] = NA
  blocks = na.omit(unique(block))
  
  for(i in blocks){
    sel = which(block==i)
    polygon(cbind(c(x[sel], rev(x[sel]), x[sel[1]]), c(ylo[sel], rev(yhi[sel]),
                                                       ylo[sel[1]])), col=col,border = NA,...) 
  }
}

##' Plot Phenocam data
##' 
##' @param dat  dataframe of date, gcc_mean, gcc_std
##' @param ...  additional graphing parameters
plot.phenocam <- function(dat,...){
  
  if(!is.null(dat)){
    
    ## QC flags
    gcc_mean = dat$gcc_mean
    gcc_mean[dat$outlierflag_gcc_mean>-9999] = NA
    
    ## base plot
    plot(dat$date,dat$gcc_mean,type='l',...)
    
    ## calculate CI
    ylo = dat$gcc_mean-1.96*dat$gcc_std
    yhi = dat$gcc_mean+1.96*dat$gcc_std
    
    ## add confidence envelope
    ciEnvelope(dat$date,ylo,yhi)
    
    ## replot mean line
    lines(dat$date,dat$gcc_mean,lwd=1.5)
    
  } else {
    print("plot.phenocam: input data not provided")
  }
  
}