VGAM: trplot.qrrvglm – R documentation

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trplot.qrrvglm

Trajectory plot for QRR-VGLMs

Description

Produces a trajectory plot for quadratic reduced-rank vector generalized linear models (QRR-VGLMs). It is only applicable for rank-1 models with argument noRRR = ~ 1.

Usage

trplot.qrrvglm(object, which.species = NULL, add = FALSE, show.plot = TRUE,
               label.sites = FALSE, sitenames = rownames(object@y),
               axes.equal = TRUE, cex = par()$cex,
               col = 1:(nos * (nos - 1)/2), log = "",
               lty = rep_len(par()$lty, nos * (nos - 1)/2),
               lwd = rep_len(par()$lwd, nos * (nos - 1)/2),
               tcol = rep_len(par()$col, nos * (nos - 1)/2),
               xlab = NULL, ylab = NULL,
               main = "", type = "b", check.ok = TRUE, ...)

Arguments

`object`	Object of class `"qrrvglm"`, i.e., a CQO object.
`which.species`	Integer or character vector specifying the species to be plotted. If integer, these are the columns of the response matrix. If character, these must match exactly with the species' names. The default is to use all species.
`add`	Logical. Add to an existing plot? If `FALSE` (default), a new plot is made.
`show.plot`	Logical. Plot it?
`label.sites`	Logical. If `TRUE`, the points on the curves/trajectories are labelled with the `sitenames`.
`sitenames`	Character vector. The names of the sites.
`axes.equal`	Logical. If `TRUE`, the x- and y-axes will be on the same scale.
`cex`	Character expansion of the labelling of the site names. Used only if `label.sites` is `TRUE`. See the `cex` argument in `par`.
`col`	Color of the lines. See the `col` argument in `par`. Here, `nos` is the number of species.
`log`	Character, specifying which (if any) of the x- and y-axes are to be on a logarithmic scale. See the `log` argument in `par`.
`lty`	Line type. See the `lty` argument of `par`.
`lwd`	Line width. See the `lwd` argument of `par`.
`tcol`	Color of the text for the site names. See the `col` argument in `par`. Used only if `label.sites` is `TRUE`.
`xlab`	Character caption for the x-axis. By default, a suitable caption is found. See the `xlab` argument in `plot` or `title`.
`ylab`	Character caption for the y-axis. By default, a suitable caption is found. See the `xlab` argument in `plot` or `title`.
`main`	Character, giving the title of the plot. See the `main` argument in `plot` or `title`.
`type`	Character, giving the type of plot. A common option is to use `type="l"` for lines only. See the `type` argument of `plot`.
`check.ok`	Logical. Whether a check is performed to see that `noRRR = ~ 1` was used. It doesn't make sense to have a trace plot unless this is so.
`...`	Arguments passed into the `plot` function when setting up the entire plot. Useful arguments here include `xlim` and `ylim`.

Details

A trajectory plot plots the fitted values of a ‘second’ species against a ‘first’ species. The argument which.species must therefore contain at least two species. By default, all of the species that were fitted in object are plotted. With more than a few species the resulting plot will be very congested, and so it is recommended that only a few species be selected for plotting.

In the above, M is the number of species selected for plotting, so there will be M*(M-1)/2 curves/trajectories in total.

A trajectory plot will be fitted only if noRRR = ~ 1 because otherwise the trajectory will not be a smooth function of the latent variables.

Value

A list with the following components.

`species.names`	A matrix of characters giving the ‘first’ and ‘second’ species. The number of different combinations of species is given by the number of rows. This is useful for creating a legend.
`sitenames`	A character vector of site names, sorted by the latent variable (from low to high).

Note

Plotting the axes on a log scale is often a good idea. The use of xlim and ylim to control the axis limits is also a good idea, so as to limit the extent of the curves at low abundances or probabilities. Setting label.sites = TRUE is a good idea only if the number of sites is small, otherwise there is too much clutter.

Author(s)

Thomas W. Yee

References

Yee, T. W. (2020). On constrained and unconstrained quadratic ordination. Manuscript in preparation.

Examples

## Not run:  set.seed(111)  # This leads to the global solution
# hspider[,1:6] <- scale(hspider[,1:6])  # Standardize the environmental variables
p1 <- cqo(cbind(Alopacce, Alopcune, Alopfabr, Arctlute, Arctperi, Auloalbi,
                Pardlugu, Pardmont, Pardnigr, Pardpull, Trocterr, Zoraspin) ~
          WaterCon + BareSand + FallTwig + CoveMoss + CoveHerb + ReflLux,
          poissonff, data = hspider, trace = FALSE)

trplot(p1, which.species = 1:3, log = "xy", type = "b", lty = 1,
       main = "Trajectory plot of three hunting spiders species",
       col = c("blue","red","green"), lwd = 2, label = TRUE) -> ii
legend(0.00005, 0.3, lwd = 2, lty = 1, col = c("blue", "red", "green"),
       with(ii, paste(species.names[,1], species.names[,2], sep = " and ")))
abline(a = 0, b = 1, lty = "dashed", col = "grey")  # Useful reference line

## End(Not run)

VGAM

Vector Generalized Linear and Additive Models

v1.1-5

GPL-3

Authors

Thomas Yee [aut, cre], Cleve Moler [ctb] (author of several LINPACK routines)

Initial release

2021-01-13