tests/testthat/test-utils-jitter.R

In NOAA-EDAB/Rpath: R implementation of Ecopath with Ecosim

source("test-constants.R")

#' Add Jitter (i.e., random noise)
#' 
#' Adds random noise to the specified matrix.
#'
#' @param matrix : data matrix to be jittered
#' @param factor : the R jitter factor (the larger the number the greater the jitter amount)
#' @param seedOffset : offset to the seed value, useful for getting "groups" of seed values
#' @param xlabel : x axis label for plot
#' @param ylabel : y axis label for plot 
#' @param title : main title for plot
#'
#' @return Returns the jittered matrix
#' 
addJitter <- function(matrix,seedOffset,xlabel,ylabel,title) {
  set.seed(seedOffset) # *SEED_VALUE)
  # From jitter() doc: If amount == 0, jitter returns factor * z/50, where
  # z = max(x0) - min(x), aka the range. So if factor=5 and amount=0, jitter()
  # returns a random value within a tenth of the range.
  
  jitteredMatrix <- jitter(matrix,factor=FACTOR_VALUE,amount=NULL)
  if (xlabel != '' && ylabel != '' & title != '') {
    # plot(jitteredMatrix,type='l',lwd=5,xlab=xlabel,ylab=ylabel,main=title)    
  } 
  return(jitteredMatrix)
}

#' Create a jittered vector
#' 
#' Used for jittering a matrix column. Can't use replicate because need to pass a different seed for every value for reproducibility.
#'
#' @param value : value to add jitter to
#' @param numElements : number of elements in vector
#' @param seedOffset : offset to the main seed value
#' @param xlabel : x axis label for plot
#' @param ylabel : y axis label for plot
#' @param title : main title for plot
#'
#' @return Returns the column-jittered matrix
#' 
createJitterVectorFromValue <- function(typeData,value,numElements,seedOffset,xlabel,ylabel,title,randomNumberType) {
  jitterVector <- c()
  migrationScaleFactor <- 1
  if (typeData == FORCED_MIGRATION) {
      migrationScaleFactor = FORCED_MIGRATION_SCALE_FACTOR_JITTER # = 1000
  }
  for (i in 1:numElements) {
    #   jitteredValue <- addJitter(value,seedOffset+i,'','','')
    randVal <- randomNumber(seedOffset+i,migrationScaleFactor*JITTER_AMOUNT_PCT,randomNumberType) # JITTER_AMOUNT_PCT = 0.01
    jitteredValue <- value * (1.0 + randVal)
    jitterVector <- append(jitterVector,jitteredValue)
  }
  # plot(jitterVector,type='l',lwd=5,xlab=xlabel,ylab=ylabel,main=title)
  return(jitterVector)
}