VGAM (version 1.1-14)

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", asp = NULL, check.ok = TRUE, ...)

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).

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.

References

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

See Also

cqo, par, title.

Examples

if (FALSE)  set.seed(111)  # Leads to the global solution
# hspider[,1:6] <- scale(hspider[,1:6])  # Stdze the environ vars
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")  # Ref. line