lvplot.rrvglm {VGAM}R Documentation

Latent Variable Plot for RR-VGLMs

Description

Produces an ordination diagram (also known as a biplot or latent variable plot) for reduced-rank vector generalized linear models (RR-VGLMs). For rank-2 models only, the x- and y-axis are the first and second canonical axes respectively.

Usage

lvplot.rrvglm(object, 
              A = TRUE, C = TRUE, scores = FALSE, plot.it = TRUE,
              groups = rep(1, n), gapC = sqrt(sum(par()$cxy^2)), 
              scaleA = 1, 
              xlab = "Latent Variable 1", ylab = "Latent Variable 2", 
              Alabels = if (length(object@misc$predictors.names)) 
              object@misc$predictors.names else paste("LP", 1:M, sep = ""), 
              Aadj = par()$adj, Acex = par()$cex, Acol = par()$col, 
              Apch = NULL, 
              Clabels = dimnames(Cmat)[[1]], Cadj = par()$adj, 
              Ccex = par()$cex, Ccol = par()$col, Clty = par()$lty, 
              Clwd = par()$lwd, 
              chull.arg = FALSE, ccex = par()$cex, ccol = par()$col, 
              clty = par()$lty, clwd = par()$lwd, 
              spch = NULL, scex = par()$cex, scol = par()$col,
              slabels = dimnames(x2mat)[[1]], ...)

Arguments

object Object of class "rrvglm".
A Logical. Allow the plotting of A?
C Logical. Allow the plotting of C? If TRUE then C is represented by arrows emenating from the origin.
scores Logical. Allow the plotting of the n scores? The scores are the values of the latent variables for each observation.
plot.it Logical. Plot it? If FALSE, no plot is produced and the matrix of scores (n latent variable values) is returned. If TRUE, the rank of object need not be 2.
groups A vector whose distinct values indicate which group the observation belongs to. By default, all the observations belong to a single group. Useful for the multinomial logit model (see multinomial.
gapC The gap between the end of the arrow and the text labelling of C, in latent variable units.
scaleA Numerical value that is multiplied by A, so that C is divided by this value.
xlab Caption for the x-axis. See par.
ylab Caption for the y-axis. See par.
Alabels Character vector to label A. Must be of length M.
Aadj Justification of text strings for labelling A. See the adj argument of par.
Acex Numeric. Character expansion of the labelling of A. See the cex argument of par.
Acol Line color of the arrows representing C. See the col argument of par.
Apch Either an integer specifying a symbol or a single character to be used as the default in plotting points. See par. The pch argument can be of length M, the number of species.
Clabels Character vector to label C. Must be of length p2.
Cadj Justification of text strings for labelling C. See the adj argument of par.
Ccex Numeric. Character expansion of the labelling of C. See the cex argument of par.
Ccol Line color of the arrows representing C. See the col argument of par.
Clty Line type of the arrows representing C. See the lty argument of par.
Clwd Line width of the arrows representing C. See the lwd argument of par.
chull.arg Logical. Plot the convex hull of the scores? This is done for each group (see the group argument).
ccex Numeric. Character expansion of the labelling of the convex hull. See the cex argument of par.
ccol Line color of the convex hull. See the col argument of par.
clty Line type of the convex hull. See the lty argument of par.
clwd Line width of the convex hull. See the lwd argument of par.
spch Either an integer specifying a symbol or a single character to be used as the default in plotting points. See par. The spch argument can be of length M, the number of species.
scex Numeric. Character expansion of the labelling of the scores. See the cex argument of par.
scol Line color of the arrows representing C. See the col argument of par.
slabels Character vector to label the scores. Must be of length n.
... Arguments passed into the plot function when setting up the entire plot. Useful arguments here include xlim and ylim.

Details

For RR-VGLMs, a biplot and a latent variable plot coincide. In general, many of the arguments starting with ``A'' refer to A (of length M), ``C'' to C (of length p2), ``c'' to the convex hull (of length length(unique(groups))), and ``s'' to scores (of length n).

As the result is a biplot, its interpretation is based on the inner product.

Value

The matrix of scores (n latent variable values) is returned regardless of whether a plot was produced or not.

Note

The functions lvplot.rrvglm and biplot.rrvglm are equivalent.

In the example below the predictor variables are centered, which is a good idea.

Author(s)

Thomas W. Yee

References

Yee, T. W. and Hastie, T. J. (2003) Reduced-rank vector generalized linear models. Statistical Modelling, 3, 15–41.

See Also

lvplot, par, rrvglm, Coef.rrvglm, rrvglm.control.

Examples

data(pneumo)
n = nrow(pneumo)  # x1, x2 and x3 are some unrelated covariates
pneumo = transform(pneumo, slet=scale(log(exposure.time)),
                   x1 = rnorm(n), x2 = rnorm(n), x3 = rnorm(n))
fit = rrvglm(cbind(normal, mild, severe) ~ slet + x1 + x2 + x3,
             multinomial, pneumo, Rank=2, Corner=FALSE, Uncor=TRUE)
## Not run: 
lvplot(fit, chull=TRUE, scores=TRUE, clty=2, ccol="blue", scol="red",
       Ccol="darkgreen", Clwd=2, Ccex=2,
       main="Biplot of some fictitional data")
## End(Not run)

[Package VGAM version 0.7-7 Index]