inst/old_files/FindBioDensityOutliers.R

In bmcnellis/SDEF.analysis: Data Analysis for 2016 San Dimas Experimental Forest Project

#####
FindBioDensityOutliers <- function(data, frame.depth=0.78, outlier.cutoff = 0.1,
                                   save=FALSE) {
  stopifnot(
    is.data.frame(data),
    date %in% colnames(data)
  )
  # Fix the date
  data$date <- as.character(data$date)
  data$date <- as.Date(data$date, format="%m/%d/%Y")
  outlier.data <- CalculateBioDensity(data=data, frame.depth=frame.depth)
  message("Generating plot of outlier location, by date:")
  print(plot(
    x=outlier.data$date[which(outlier.data$biodensity > outlier.cutoff)],
    y=outlier.data$biodensity[which(outlier.data$biodensity > outlier.cutoff)]
  ))
  message("Proportion of data above cutoff:")
  print(
    length(test.data$biodensity[which(test.data$biodensity > 0.1)]) / nrow(test.data) * 100
  )
  if (save == TRUE) {
    write.csv(x=outlier.data, file=paste(deparse(substitute(outlier.data)),".csv",sep=""))
  }
}