IPMpack (version 1.6)

contourPlot: Produces a graph with the smooth kernel and associated value label.

Description

Outputs a graph with a smoothed surface of the IPM kernel or other chosen matrix. This graph also contains a label for values of changes on stage conditional on survival and per-capita sexual/clonal contributions. This function is applicable to the different components of the IPM separately (i.e. Pmatrix, Fmatrix, C matrix) or to the kernel of the sensitivity and elasticity IPM. This function can also be applied with lifecycles with discrete stages (e.g. seedbank in "hyperDataCovSubset") but the user must be careful with the interpretation of perturbation analyses between discrete and continuous stages since they are logically on a different scale.

Usage

contourPlot(M, meshpts, upper, lower, color)

Arguments

M

a matrix of the type P matrix, F matrix, C matrix, the full IPM (= P + F + C), its sensitivity or elasticity. The function transposes the matrix internally so the user does not have to worry about having size in time t as the x axis and size in time t+1 a

meshpts

meshpoints of the kernel to be plotted.

upper

the highest value to be displayed in the "z" axis. If plotting the full IPM, it is recommended to set this value carefully so that the P matrix (which is constrained between 0 and 1) is not visually "lost" due to potentially high value of the F/C matrices

lower

the lowest value to be displayed in the "z" axis. If plotting P, F, IPM, mesh-level sensitivity/elasticity values, it is recommended to set this value to 0 since those kernels are always non-negative. If using this function to display mesh-level LTRE diff

color

color scheme with which to display the z values of the kernel. Options are extracted directly from the palette options available via the library "graphics", in function "filled.contour" and library "grDevices", in "palette". Options are: rainbow, heat.col

Value

• a graph.

References

For more details on plotting contour surfaces: the Graphics R package. http://stat.ethz.ch/R-manual/R-patched/library/graphics/html/00Index.html

Further literature for LTREs: Caswell, 2001, Matrix Population Models: construction, analysis, interpretation. 2nd ed. Sinauer. p206-256.

de Kroon, Plaisier, van Groenendael and Caswell. 1986. Elasticity: the relative contribution of demographic parameters to population growth rate. Ecology 67, p1427-1431.

de Kroon, van Groenendael and Ehrlen. 2000. Elasticities: a review of methods and model limitations. Ecology 81, p607-618.

See Also

sens, elas

Examples

dff <- generateData()
Pmatrix <- createIPMPmatrix(minSize = min(dff$size, na.rm=TRUE),
maxSize = max(dff$size, na.rm = TRUE), growObj = makeGrowthObj(dff),
survObj = makeSurvObj(dff))

Fmatrix <- createIPMFmatrix(minSize = min(dff$size, na.rm = TRUE),
maxSize = max(dff$size, na.rm = TRUE), fecObj = makeFecObj(dff))

IPM <- Pmatrix + Fmatrix

#Plot P matrix contour plot
minSize <- 0
maxSize <- max(Pmatrix)
contourPlot(Pmatrix, Pmatrix@meshpoints, minSize, maxSize, heat.colors)

#Plot F matrix contour plot
minSize <- 0
maxSize <- max(Fmatrix)
contourPlot(Fmatrix, Fmatrix@meshpoints, minSize, maxSize, heat.colors)

#Plot IPM contour plot
contourPlot(IPM, Pmatrix@meshpoints, minSize, maxSize, heat.colors)
 
#Plot IPM sensitivity contour plot
senIPM <- sens(IPM)
minSize <- 0
maxSize <- max(senIPM)
contourPlot(senIPM, Pmatrix@meshpoints, minSize, maxSize, heat.colors)

#Plot IPM elasticity contour plot
elaIPM <- elas(IPM)
minSize <- 0
maxSize <- max(elaIPM)
contourPlot(senIPM, Pmatrix@meshpoints, minSize, maxSize, heat.colors)