R/Examples.R

In rEDM: Empirical Dynamic Modeling ('EDM')

#------------------------------------------------------------------------
# 
#------------------------------------------------------------------------
Examples = function() {

  library( rEDM )
  
  # make sure data is loaded
  tryCatch(
    expr = {
      data( TentMap,             envir = environment() )
      data( TentMapNoise,        envir = environment() )
      data( block_3sp,           envir = environment() )
      data( circle,              envir = environment() )
      data( sardine_anchovy_sst, envir = environment() )
    },
    error = function( err ) {
      print( err )
      stop("Examples(): Failed to load package data.")
    }
  )

  if ( is.null( dev.list() ) ) {
    newPlot( mfrow = c( 4, 2 ) )
  }
  else {
    par( mfrow = c( 4, 2 ) )
  }
  
  # EmbedDimension()
  cmd = paste0('EmbedDimension( dataFrame = TentMap,',
               ' lib = "1 100", pred = "201 500",',
               ' columns = "TentMap", target = "TentMap")' )
  df = eval( parse( text = cmd ) )
  
  # PredictInterval()
  cmd = paste0('PredictInterval( dataFrame = TentMap,',
               ' lib = "1 100", pred = "201 500", E = 2,',
               ' columns = "TentMap", target = "TentMap") ')
  df = eval( parse( text = cmd ) )
  
  # PredictNonlinear()
  cmd = paste0('PredictNonlinear( dataFrame = TentMapNoise,',
               ' E = 2,lib = "1 100", pred = "201 500", ',
               ' columns = "TentMap",target = "TentMap") ')
  df = eval( parse( text = cmd ) )

  # Simplex() 
  # Tent map : specify multivariable columns embedded = TRUE
  cmd = paste0('Simplex( dataFrame = block_3sp,',
               ' lib = "1 99", pred = "100 195", ',
               ' E = 3, embedded = TRUE, showPlot = TRUE,',
               ' columns = "x_t y_t z_t", target = "x_t") ')
  df = eval( parse( text = cmd ) )

  # Simplex() 
  # Tent map : Embed column x_t to E = 3, embedded  =  False
  cmd = paste0('Simplex( dataFrame = block_3sp,',
               ' lib = "1 99", pred = "105 190", ',
               ' E = 3, showPlot = TRUE,',
               ' columns = "x_t", target = "x_t") ')
  df = eval( parse( text = cmd ) )

  # Multiview()
  cmd = paste0('Multiview( dataFrame = block_3sp,',
               ' lib = "1 99", pred = "105 190", ',
               ' E = 3, columns = "x_t y_t z_t", target = "x_t",',
               ' showPlot = TRUE) ')
  df = eval( parse( text = cmd ) )

  # CCM demo
  cmd = paste0('CCM( dataFrame = sardine_anchovy_sst,',
               ' E = 3, Tp = 0, columns = "anchovy", target = "np_sst",',
               ' libSizes = "10 70 10", sample = 100, verbose = TRUE, ',
               ' showPlot = TRUE) ')
  df = eval( parse( text = cmd ) )

  par( ask = TRUE )
  # SMap circle : specify multivariable columns embedded = TRUE
  cmd = paste0('SMap( dataFrame = circle,',
               ' lib = "1 100", pred = "110 190", theta = 4, E = 2,',
               ' verbose = TRUE, showPlot = TRUE, embedded = TRUE,',
               ' columns = "x y", target = "x") ')
  df = eval( parse( text = cmd ) )
  par( ask = FALSE )
}

#------------------------------------------------------------------------
# 
#------------------------------------------------------------------------
newPlot = function(
  mar      = c( 4, 4, 1, 1 ),
  mgp      = c( 2.3, 0.8, 0 ),
  cex      = 1.5, 
  cex.axis = 1.3,
  cex.lab  = 1.3,
  mfrow    = c( 1, 1 )
) {
    dev.new()
    par( mar = mar )
    par( mgp = mgp )
    par( cex = cex )
    par( cex.axis = cex.axis )
    par( cex.lab = cex.lab )
    par( mfrow = mfrow )
    invisible( dev.cur() )
}