envelope.plot: Plot the plateau envelopes produced by 'fit.glm.env' and...

In MarkJBrewer/plateau: Fit plateau climate envelopes in species distribution models for presence/absence data

Description

envelope.plot plots the plateau envelopes produced by the functions fit.glm.env and fit.bugs.env.

Usage

envelope.plot(envelope.fit, type = "persp", x.plot.lims = c(0, 1),
  len = 100, plot.vars, x.labels, fix.values, close.points = "",
  contour.levels)

Arguments

envelope.fit	The fitted object from either fit.glm.env or fit.bugs.env.
type	String taking values "persp" or "contour" to specify which type of plot is required; ignored if fitted object has only one climate variable (when a univariate plot with rug is plotted).
x.plot.lims	Vector of two numerics containing the endpoints for the plotting regions in the (scaled) climate variables.
len	The number of points to use for plotting in each dimension.
plot.vars	If p>2 (currentl implying p==3), need to know which two variables to plot; this vector of two climate column names makes the selection.
x.labels	Labels to plot on the x-axes, notionally the variable names; if omitted, the code will use "Variable 1" etc.
fix.values	Vector of numeric length p with named elements corresponding to the values (and names) of the non-plotted variables; ignored if p<3.
close.points	String indicating how to plot points in contour or perspective plots: the value "shade" plots filled circles for points which are "close" to the chosen values of the held out variables, and empty circles otherwise; the value "plot" is as for shade but without the empty circles; and for any other value of close.points, the full data set will be plotted as filled circles.
contour.levels	If specified, the probability values to be plotted in the contour plots; this is especially important when using plot.envelope to make a "video".

Value

For the case of a single climate variable, the plot produced is a line graph, possibly with rugplot and points. For two climate covariates, either a contour plot or a perspective plot is produced. For three climate covariates, the same choice of contour or perspective plot is made for two of the variables for a fixed value of the third covariate.

See Also

link{map.plot}, link{fit.bugs.env}

MarkJBrewer/plateau documentation built on May 7, 2019, 3:35 p.m.