phasePortrait: Phase Portrait

In cboettig/bs-tipping: Bifurcation or State Tipping in a Trophic Cascade Experiment

Description

Plot a phase portrait of a dynamical system that includes the vector field, nullclines, example trajectories, and the identification and classification of equilibria.

Usage

phasePortrait(qE, pars, func = fs2D, x.lim = c(0, 2000), y.lim = c(0,
  100), add = FALSE, nFlow = 20, nNull = 300, t.end = 50,
  inits = matrix(c(1, 90, 200, 20, 800, 20, 500, 50, 1000, 80), byrow = TRUE,
  ncol = 2), addLeg = FALSE, legPos = "topright")

Arguments

qE	numeric scalar for harvest
pars	optional named numeric vector for additional parameters to be passed to func
func,	function that returns local derivatives, defaults to fs2D, which is just a formatting wrapper for fishStep2D; currently only works for default due to use of getRoot2D_df in stabClass
x.lim, y.lim	minimum and maximum values for each of the two states variables to be used when plotting and searching for equilibria
add	local, if FALSE (default) makes a new plot
nFlow	square root of the number of arrows to draw in the vector field
nNull	numeric scalar, number of points used in drawing the nullclines
t.end	number of time steps (in model time units) to use when simulating the trajectories
inits	matrix of initial values to use for trajectories
addLeg	if TRUE, adds a legend
legPos	character position of legend; see graphics::legend

Details

This function is largely a wrapper for phaseR::flowField, phaseR::trajectory, phaseR::nullclines, and phaseR::stability. This function does not call phaseR::stability directly, and instead uses stabClass.

Value

a data.frame with stability information; see stabClass

Examples

# shortInits <- eval(formals(phasePortrait)$inits)[1:3,]
# pars <- c(q=8,s=0.7,h=0.15, b=0.001)
qEvals <- c(0.2, 0.5, 1, 1.25)
par(mfrow=c(2,2), mar=c(2,2,1,0.5), mgp=c(1,0.25,0), tcl=-0.15, cex=1, ps=9, cex.axis=0.85)
for(j in 1:4){
	(phasePortrait(
		qE=qEvals[j], pars=NULL,
		nFlow=5, nNull=5,t.end=5,
		addLeg=TRUE
	))
}

cboettig/bs-tipping documentation built on May 5, 2019, 7:08 a.m.