R: Latent Variable Plot for RR-VGLMs

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, show.plot = 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 = rownames(Cmat), 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 = rownames(x2mat), ...)

### 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.
`show.plot` | 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

    nn <- nrow(pneumo)  # x1, x2 and x3 are some unrelated covariates
    pneumo <- transform(pneumo, slet = scale(log(exposure.time)),
                                  x1 = rnorm(nn), x2 = rnorm(nn), x3 = rnorm(nn))
    fit <- rrvglm(cbind(normal, mild, severe) ~ slet + x1 + x2 + x3,
                  multinomial, data = pneumo, Rank = 2,
                  Corner = FALSE, Uncorrel = 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 1.0-3 Index]