QPotential: Computes the quasi-potential for a system of stochastic...
In bmarkslash7/QPot: Quasi-Potential Analysis for Stochastic Differential Equations

Description Usage Arguments Value Examples

Computes the quasi-potential for a system of stochastic differential equations using the ordered upwind method.

QPotential(
  x.rhs = NULL,
  x.start = NULL,
  x.bound = NULL,
  x.num.steps = NULL,
  y.rhs = NULL,
  y.start = NULL,
  y.bound = NULL,
  y.num.steps = NULL,
  filename = NULL,
  save.to.R = TRUE,
  save.to.HD = FALSE,
  bounce = "d",
  bounce.edge = 0.01,
  verboseR = FALSE,
  verboseC = TRUE,
  debugC = FALSE,
  k.x = 20,
  k.y = 20,
  INFINITY = 1e+06
)

`x.rhs`	a string containing the right hand side of the equation for x.
`x.start`	the starting value of x, usually the x value of the current equilibrium.
`x.bound`	the x boundaries denoted as c(minimum, maximum).
`x.num.steps`	the number of steps between the minimum and maximum x value defined in x range.
`y.rhs`	a string containing the right hand side of the equation for y.
`y.start`	the starting value of y, usually the y value of the current equilibrium.
`y.bound`	the y boundaries denoted as c(minimum, maximum).
`y.num.steps`	the number of steps between the minimum and maximum y value defined in y range.
`filename`	string for the name of the file saved to the hard drive. If save.to.HD=TRUE and filename is left blank, output file saved as defaultname-xX.STARTyY.START.txt, where X.START and Y.START are values in x.start and y.start, respectively. Matrix stored as a tab-delimited file.
`save.to.R`	boolean to output the matrix of results for the ordered upwind method to the current R session. The default is to write the matrix to the R session. save.to.R=FALSE prevents the output from being written to the R session.
`save.to.HD`	boolean to write the matrix of results for the ordered upwind method to the hard drive in a file named filename. Default is FALSE.
`bounce`	by default, the ordered upwind method stops when the boundaries are reached (x.bound and y.bound). The bounce parameter allows the default action (bounce = 'd'), only positive values to be tested (bounce = 'p'), or reflection near the boundaries (bounce = 'b').
`bounce.edge`	if bounce = 'b', then to prevent the ordered upwind method from reaching the boundaries, temporary boundaries are created inside the boundaries defined by x.bound and y.bound. The boundary edge is bounce.edge of the total range. Default is 0.01
`verboseR`	NOT IMPLEMENTED: Flag (default = FALSE) for printing out information in QPotential R wrapper.
`verboseC`	flag (default = TRUE) for printing out useful-for-everyone information from C code implementing the upwind-ordered method (quasipotential.C).
`debugC`	NOT IMPLEMENTED: Flag (default = FALSE) for printing out debugging C code
`k.x`	integer anisotropic factor for x. See journal article. Default is 20.
`k.y`	integer anisotropic factor for y. See journal article. Default is 20.
`INFINITY`	largest possible quasi-potential value. If computed quasi-potential is ever greater than this number, program will stop. Especially useful when bounce = 'b'. Default is 1,000,000 with a tolerance of 1e-12

filetoHD if save.to.HD enabled, then saves a file in the current directory as either filename or as defaultname-xXSTARTyYSTART.txt

filetoR if save.to.R enabled, then the function QPotential returns a matrix containing the upwind-ordered results to be used for plotting. Requires a variable to catch the returned matrix, i.e. storage <- QPotential(parameters...)

# First, System of equations
	equationx <- "1.54*x*(1.0-(x/10.14)) - (y*x*x)/(1.0+x*x)"
	equationy <- "((0.476*x*x*y)/(1+x*x)) - 0.112590*y*y"

# Second, shared parameters for each quasi-potential run
	xbounds <- c(-0.5, 8.0)
	ybounds <- c(-0.5, 8.0)
	xstepnumber <- 200
	ystepnumber <- 200

# Third, a local quasi-potential run
	xinit1 <- 1.40491
	yinit1 <- 2.80808
	storage.eq1 <- QPotential(x.rhs = equationx, x.start = xinit1, 
	x.bound = xbounds, x.num.steps = xstepnumber, y.rhs = equationy, 
	y.start = yinit1, y.bound = ybounds, y.num.steps = ystepnumber)
# Visualize the quasi-potential
QPContour(storage.eq1, dens = c(xstepnumber, ystepnumber), 
	x.bound = xbounds, y.bound = ybounds, c.parm = 5)