plotRSA: Plots a response surface of a polynomial equation of second...

In RSA: Response Surface Analysis

Plots a response surface of a polynomial equation of second degree

Description

Plots an RSA object, or a response surface with specified parameters

Usage

plotRSA(
  x = 0,
  y = 0,
  x2 = 0,
  y2 = 0,
  xy = 0,
  w = 0,
  wx = 0,
  wy = 0,
  x3 = 0,
  xy2 = 0,
  x2y = 0,
  y3 = 0,
  b0 = 0,
  type = "3d",
  model = "full",
  xlim = NULL,
  ylim = NULL,
  zlim = NULL,
  xlab = NULL,
  ylab = NULL,
  zlab = NULL,
  main = "",
  surface = "predict",
  lambda = NULL,
  suppress.surface = FALSE,
  suppress.box = FALSE,
  suppress.grid = FALSE,
  suppress.ticklabels = FALSE,
  rotation = list(x = -63, y = 32, z = 15),
  label.rotation = list(x = 19, y = -40, z = 92),
  gridsize = 21,
  bw = FALSE,
  legend = TRUE,
  param = TRUE,
  coefs = FALSE,
  axes = c("LOC", "LOIC", "PA1", "PA2"),
  axesStyles = list(LOC = list(lty = "solid", lwd = 2, col = ifelse(bw == TRUE, "black",
    "blue")), LOIC = list(lty = "solid", lwd = 2, col = ifelse(bw == TRUE, "black",
    "blue")), PA1 = list(lty = "dotted", lwd = 2, col = ifelse(bw == TRUE, "black",
    "gray30")), PA2 = list(lty = "dotted", lwd = 2, col = ifelse(bw == TRUE, "black",
    "gray30"))),
  project = c("contour"),
  maxlines = FALSE,
  cex.tickLabel = 1,
  cex.axesLabel = 1,
  cex.main = 1,
  points = list(data = NULL, show = NA, value = "raw", jitter = 0, color = "black", cex =
    0.5, stilt = NULL, out.mark = FALSE, fill = NULL),
  fit = NULL,
  link = "identity",
  tck = c(1.5, 1.5, 1.5),
  distance = c(1.3, 1.3, 1.4),
  border = FALSE,
  contour = list(show = FALSE, color = "grey40", highlight = c()),
  hull = NA,
  showSP = FALSE,
  showSP.CI = FALSE,
  pal = NULL,
  pal.range = "box",
  pad = 0,
  claxes.alpha = 0.05,
  demo = FALSE,
  ...
)

Arguments

x	Either an RSA object (returned by the RSA function), or the coefficient for the X predictor
y	Y coefficient
x2	X^2 coefficient
y2	Y^2 coefficient
xy	XY interaction coefficient
w	W coefficient (for (un)constrained absolute difference model)
wx	WX coefficient (for (un)constrained absolute difference model)
wy	WY coefficient (for (un)constrained absolute difference model)
x3	X^3 coefficient
xy2	XY^2 coefficient
x2y	X^2Y coefficient
y3	Y^3 coefficient
b0	Intercept
type	3d for 3d surface plot, contour for 2d contour plot, "interactive" for interactive rotatable plot. Shortcuts (i.e., first letter of string) are sufficient
model	If x is an RSA object: from which model should the response surface be computed?
xlim	Limits of the x axis
ylim	Limits of the y axis
zlim	Limits of the z axis
xlab	Label for x axis
ylab	Label for y axis
zlab	Label for z axis
main	the main title of the plot
surface	Method for the calculation of the surface z values. "predict" takes the predicted values from the model, "smooth" uses a thin plate smoother (function Tps from the fields package) of the raw data
lambda	lambda parameter for the smoother. Default (NULL) means that it is estimated by the smoother function. Small lambdas around 1 lead to rugged surfaces, big lambdas to very smooth surfaces.
suppress.surface	Should the surface be suppressed (only for type="3d")? Useful for only showing the data points, or for didactic purposes (e.g., first show the cube, then fade in the surface).
suppress.box	Should the surrounding box be suppressed (only for type="3d")?
suppress.grid	Should the grid lines be suppressed (only for type="3d")?
suppress.ticklabels	Should the numbers on the axes be suppressed (only for type="3d")?
rotation	Rotation of the 3d surface plot (when type == "3d")
label.rotation	Rotation of the axis labls (when type == "3d")
gridsize	Number of grid nodes in each dimension
bw	Print surface in black and white instead of colors?
legend	Print color legend for z values?
param	Should the surface parameters a1 to a5 be shown on the plot? In case of a 3d plot a1 to a5 are printed on top of the plot; in case of a contour plot the principal axes are plotted. Surface parameters are not printed for cubic surfaces.
coefs	Should the regression coefficients b1 to b5 (b1 to b9 for cubic models) be shown on the plot? (Only for 3d plot)
axes	A vector of strings specifying the axes that should be plotted. Can be any combination of c("LOC", "LOIC", "PA1", "PA2", "E2", "K1", "K2"). LOC = line of congruence, LOIC = line of incongruence, PA1 = first principal axis, PA2 = second principal axis, E2 = second extremum line in the CA or RRCA model, K1, K2 = boundary lines of the regions of significance in the CL or RRCL model.
axesStyles	Define the visual styles of the axes LOC, LOIC, PA1, PA2, E2, K1, and K2. Provide a named list: axesStyles=list(LOC = list(lty="solid", lwd=2, col=ifelse(bw==TRUE, "black", "blue")). It recognizes three parameters: lty, lwd, and col. If you define a style for an axis, you have to provide all three parameters, otherwise a warning will be shown.
project	A vector of graphic elements that should be projected on the floor of the cube. Can include any combination of c("LOC", "LOIC", "PA1", "PA2", "contour", "points", "E2", "K1", "K2"). Note that projected elements are plotted in the order given in the vector (first elements are plotted first and overplotted by later elements).
maxlines	Should the maximum lines be plotted? (red: maximum X for a given Y, blue: maximum Y for a given X). Works only in type="3d"
cex.tickLabel	Font size factor for tick labels
cex.axesLabel	Font size factor for axes labels
cex.main	Factor for main title size
points	A list of parameters which define the appearance of the raw scatter points: data: Data frame which contains the coordinates of the raw data points. First column = x, second = y, third = z. This data frame is automatically generated when the plot is based on a fitted RSA-object show = TRUE: Should the original data points be overplotted? color = "black": Color of the points. Either a single value for all points, or a vector with the same size as data points provided. If parameter fill is also defined, color refers to the border of the points. fill = NULL: Fill of the points. Either a single value for all points, or a vector with the same size as data points provided. As a default, this is set to NULL, which means that all points simply have the color color. value="raw": Plot the original z value, "predicted": plot the predicted z value jitter = 0: Amount of jitter for the raw data points. For z values, a value of 0.005 is reasonable cex = .5: multiplication factor for point size. Either a single value for all points, or a vector with the same size as data points provided. stilt: Should stilts be drawn for selected data points (i.e., lines from raw data points to the floor)? A logical vector with the same size as data points provided, indicating which points should get a stilt. out.mark = FALSE: If set to TRUE, outliers according to Bollen & Jackman (1980) are printed as red X symbols, but only when they have been removed in the RSA function: RSA(..., out.rm=TRUE). If out.rm == TRUE (in RSA()) and out.mark == FALSE (in plotRSA()), the outlier is removed from the model and *not plotted* in plotRSA. If out.rm == TRUE (in RSA()) and out.mark == TRUE (in plotRSA()), the outlier is removed from the model but plotted and marked in plotRSA. If out.rm == FALSE (in RSA()): Outliers are not removed and cannot be plotted. Example syntax: plotRSA(r1, points=list(show=TRUE, out.mark=TRUE)) As a shortcut, you can also set points=TRUE to set the defaults.
fit	Do not change that parameter (internal use only)
link	Link function to transform the z axes. Implemented are "identity" (no transformation; default), "probit", and "logit"
tck	A vector of three values defining the position of labels to the axes (see ?wireframe)
distance	A vector of three values defining the distance of labels to the axes
border	Should a thicker border around the surface be plotted? Sometimes this border leaves the surrounding box, which does not look good. In this case the border can be suppressed by setting border=FALSE.
contour	A list defining the appearance of contour lines (aka. height lines). show=TRUE: Should the contour lines be plotted on the 3d wireframe plot? (Parameter only relevant for type="3d"). color = "grey40": Color of the contour lines. highlight = c(): A vector of heights which should be highlighted (i.e., printed in bold). Be careful: the highlighted line is not necessarily exactly at the specified height; instead the nearest height line is selected.
hull	Plot a bag plot on the surface (This is a bivariate extension of the boxplot. 50% of points are in the inner bag, 50% in the outer region). See Rousseeuw, Ruts, & Tukey (1999).
showSP	Plot the stationary point? (only relevant for type="contour")
showSP.CI	Plot the CI of the stationary point? (only relevant for type="contour")
pal	A palette for shading. You can use colorRampPalette to construct a color ramp, e.g. plot(r.m, pal=colorRampPalette(c("darkgreen", "yellow", "darkred"))(20)). If pal="flip", the default palette is used, but reversed (so that red is on top and green on the bottom).
pal.range	Should the color range be scaled to the box (pal.range = "box", default), or to the min and max of the surface (pal.range = "surface")? If set to "box", different surface plots can be compared along their color, as long as the zlim is the same for both.
pad	Pad controls the margin around the figure (positive numbers: larger margin, negative numbers: smaller margin)
claxes.alpha	Alpha level that is used to determine the axes K1 and K2 that demarcate the regions of significance for the cubic models "CL" and "RRCL"
demo	Do not change that parameter (internal use only)
...	Additional parameters passed to the plotting function (e.g., sub="Title"). A useful title might be the R squared of the plotted model: sub = as.expression(bquote(R^2==.(round(getPar(x, "r2", model="full"), 3))))

Details

Each plot type has its distinctive advantages. The two-dimensional contour plot gives a clear view of the position of the principal axes and the stationary point. The 3d plot gives a three dimensional impression of the surface, allows overplotting of the original data points (in case an RSA object is provided), and allows the interactive adjustment of regression weights in the RSA function. The interactive plot allows rotating and exploring a three-dimensional surface with the mouse (nice for demonstration purposes). If you want to export publication-ready plots, it is recommended to export it with following commands: p1 <- plot(r1, bw=TRUE) trellis.device(device="cairo_pdf", filename="RSA_plot.pdf") print(p1) dev.off()

References

Rousseeuw, P. J., Ruts, I., & Tukey, J. W. (1999). The Bagplot: A Bivariate Boxplot. The American Statistician, 53(4), 382-387. doi:10.1080/00031305.1999.10474494

See Also

demoRSA, RSA

Examples

# Plot response surfaces from known parameters
# example of Edwards (2002), Figure 3
## Not run: 
# Default: 3d plot:
plotRSA(x=.314, y=-.118, x2=-.145, y2=-.102, xy=.299, b0=5.628)
# Contour plot:
plotRSA(x=.314, y=-.118, x2=-.145, y2=-.102, xy=.299, b0=5.628, type="c")
# Interactive plot (try the mouse!):
plotRSA(x=.314, y=-.118, x2=-.145, y2=-.102, xy=.299, b0=5.628, type="i")

# Plot response surface from an RSA object
set.seed(0xBEEF)
n <- 300
err <- 2
x <- rnorm(n, 0, 5)
y <- rnorm(n, 0, 5)
df <- data.frame(x, y)
df <- within(df, {
	diff <- x-y
	absdiff <- abs(x-y)
	SD <- (x-y)^2
	z.diff <- diff + rnorm(n, 0, err)
	z.abs <- absdiff + rnorm(n, 0, err)
	z.sq <- SD + rnorm(n, 0, err)
	z.add <- diff + 0.4*x + rnorm(n, 0, err)
	z.complex <- 0.4*x + - 0.2*x*y + + 0.1*x^2 - 0.03*y^2 + rnorm(n, 0, err)
})

r1 <- RSA(z.sq~x*y, df, models=c("SQD", "full", "IA"))
plot(r1)	# default: model = "full"
plot(r1, model="SQD", points=list(show=TRUE, value="predicted"))

## End(Not run)

RSA documentation built on Jan. 12, 2023, 9:07 a.m.