designDiagram class and some basic methodsObjects of class designDiagram as generated by DD is a list with entries as specified below.
responseLogical stating whether a response variable was present.
termsNamed vector with all terms in the design.
random.termsVector with the random terms in the design.
relationsNamed matrix with relations between variables with the following interpretation: "0"=linear indepent, "<"=row term is a subspace of column, "<-"=row term is a subspace of column term and no other terms are inbetween, ">" and "->" the similar interpretatioin between columns and rows, name=name of minimum between row and column term.
innerNamed matrix of squared inner products of subspaces with nesting subspaces removed. Rounded at order of eps in the call to link{DD}. Used to decide orthogonality of the design.
NparmNamed vector with the number of parameters for the terms.
dfNamed vector with the degrees of freedom for the terms.
SSNamed matrix with Sum-of-Squares if a response variable was specified.
MSSNamed matrix with Mean-Sum-of-Squares if a response variable was specified.
pvalueNamed matrix with p-values for Type-I F-tests. p-values are stated at the collapsed nesting, but F-test are done against the most coarse nested random effect.
sigma2Named vector of random effects variance estimates.
varcovNamed list of variance-covariance matrix for fixed effects relative to each of the random effects. Rounded at order of eps.
coordinatesData frame with node coordinates of the terms. Initialized in Sugiyama layout.
# S3 method for designDiagram
print(x, ...)# S3 method for designDiagram
summary(object, ...)
# S3 method for designDiagram
update(object, ...)
# S3 method for designDiagram
plot(
x,
circle = "none",
pvalue = (circle == "MSS"),
sigma2 = NULL,
kill = ~1,
ca = FALSE,
max.area = NULL,
relative = 0.01,
color = NULL,
circle.scaling = 1,
arrow.type = arrow(angle = 20, length = unit(4, "mm")),
xlim = c(0, 1),
ylim = c(0, 1),
horizontal = TRUE,
...
)
object of class designDiagram
not used.
object of class designDiagram
character specifying which circles to draw at the terms: "none"=no circles, "SS"=a circle with area proportional to the associated Sum-of-Squares, "MSS"=a circle with area proportional to the associated Mean-Sum-of-Squares, "I"=a circle with area proportional to average information, "I2"=a circle with area proportional to average information of the parameter contrasts. Defaults to "none".
boolean specifying whether p-values should be inserted on the graphs. This is only possible if a response variable was specified. Defaults to TRUE is circle="MSS" and FALSE otherwise.
vector of random effects variances. Defaults to NULL, in which case the estimates are used (if present), otherwise all variances are set to 1.
formula specifying which cirlces not to plot. Defaults to ~1 corresponding to not plotting the intercept term (that otherwise may overweight the remaining terms).
boolean deciding whether collinearity analysis is visualized. If NULL then set TRUE for non-orthogonal designs, and to FALSE for orthogonal designs. Defaults to FALSE.
numeric specifying the used maximal area of circles. If NULL then max.area is derived from SS, MSS or I according to value of circle. Defaults to NULL.
positive numeric, which specifies needed relative increase for an area to be visualized in the collinearity analysis. Defaults to 0.01.
color of circles when ca=FALSE. Defaults to NULL corresponding to preassigned choice of colors (see details below).
numeric specifying size scaling of circles. Defaults to 1, which corresponds to the largest circle having a radius that is half of the shortest distance between two nodes.
specifying arrow heads via arrow. Defaults to arrow(angle=20,length=unit(4,"mm")).
x-range of diagram plot. Defaults to c(0,1).
y-range of diagram plot. Defaults to c(0,1).
boolean specifying if the design diagram should be drawn horizontally or vertically. Defaults to TRUE.
For plot.designDiagram the options circle="SS" and circle="MSS" are only available if a response variable was specified for the design.
For circle="I" and circle="I2" the color of the circles visualize the coefficient of variation of the informations. For the computation of the informations the variances of the random effects are either estimated (if a response variable is present), all set to 1 (otherwise), or given via the option sigma2.
If color=NULL and ca=FALSE, then the defaults colors are "lightgreen" for Sum-of-Squares, "lightblue" for Mean-Sum-of-Squares, and a gradient from "limegreen" to "orange" for information spread. To specify a different color gradient in the latter case, then give a vector of two colors.
For update.designDiagram the second argument should be a data frame with new coordinates. This can be usefull for manually setting the coordinates for plotting.
DD