Diagonal Recurrence Profile

Usage

rp_diagProfile(
  RM,
  diagWin = NULL,
  xname = "X-axis",
  yname = "Y-axis",
  theiler = 0,
  DLmin = 2,
  VLmin = 2,
  HLmin = 2,
  DLmax = length(Matrix::diag(RM)),
  VLmax = length(Matrix::diag(RM)),
  HLmax = length(Matrix::diag(RM)),
  doShuffle = FALSE,
  y1 = NULL,
  y2 = NULL,
  shuffleWhich = "y1",
  Nshuffle = 19,
  doEmbed = TRUE,
  AUTO = NULL,
  chromatic = FALSE,
  matrices = FALSE,
  doPlot = TRUE,
  minY = 0.5,
  returnOnlyPlot = FALSE
)

Arguments

RM

A binary recurrence matrix

diagWin

Window around the line of synchrony

xname

Label for x-axis

yname

Label for y-axis

theiler

Use a theiler window around the main diagonal (Line of Identity/Synchronisation) to remove auto-correlations at short time-lags:

0 will include the main diagonal in all RQA measure calculations.
1 will remove the main diagonal from all RQA measure calculations.
NA (default), will check if the matrix is symmetrical , if so, it will remove the diagonal by setting theiler = 1 (Line of Identity, Auto-RQA), if it is not symmetrical (Line of Synchronisation, Cross-RQA) it will set theiler = 0.
A value greater than 1 will remove that many diagonals around and including the diagonal from all RQA measure calculations. So theiler = 2 means exclude 2 diagonals around the main diagonal, including the main diagonal itself: [-1,0,1]. If theiler is a numeric vector of length(theiler) == 2 it is possible to exclude an asymmetrical window. The values are interpreted as end points in a sequence of diagonal ID's, e.g. theiler = c(-1,5) will exclude [-1,0,1,2,3,4,5]. If length(theiler) > 2, the values will be considered individual diagonal ID's, e.g. theiler = c(-3,-1,0,2,5), will exclude only those specific ID's. Also see the note.

DLmin

Minimal diagonal line length (default = 2)

VLmin

Minimal vertical line length (default = 2)

HLmin

Minimal horizontal line length (default = 2)

DLmax

Maximal diagonal line length (default = length of diagonal -1)

VLmax

Maximal vertical line length (default = length of diagonal -1)

HLmax

Maximal horizontal line length (default = length of diagonal -1)

doShuffle

Should a shuffled baseline be calculated (default = FALSE)

y1

The original y1 time series

y2

The original y2 time series

shuffleWhich

Which of the time series should be shuffled: 'y1' or 'y2'? (default = 'y2')

Nshuffle

How many shuffled versions to make up the baseline? The default is 19, which is the minimum for a one-sided surrogate test.

doEmbed

If doShuffle = TRUE, should the data in y1 and y2 be considered embedded time series? The temporal order of all columns in y2 will be randomly shuffled in the same way, keeping coordinates together (default = FALSE)

AUTO

Auto-recurrence? (default = FALSE)

chromatic

Force chromatic RQA? (default = FALSE)

matrices

Return matrices? (default = FALSE)

doPlot

Plot (default = TRUE)

minY

The minimum value of the Y-axis. The upper Y limit is determined by max(minY,max(RR)). Set to 1 to always show the theoretical maximum (default = 0.5)

returnOnlyPlot

Don't plot to graphics device, but do return the plot (default = FALSE)

Value

A plot and/or the data for the plot