plot.mat: Plot diagnostics for a mat object

In analogue: Analogue and Weighted Averaging Methods for Palaeoecology

Plot diagnostics for a mat object

Description

Five plots (selectable by which) are currently available: a plot of estimated against observed values, a plot of residuals against estimated values, and screeplots of the apparent RMSE, average bias and maximum bias for MAT models of size k, where k = 1, \dots, n. By default, the first three and ‘5’ are provided.

Usage

## S3 method for class 'mat'
plot(x,
     which = c(1:3, 5),
     weighted = FALSE,
     k,
     caption = c("Inferred vs Observed", "Residuals vs Fitted",
                 "Leave-one-out errors", "Average bias",
                 "Maximum bias"),
     max.bias = TRUE,
     n.bias = 10,
     restrict = 20,
     sub.caption = NULL,
     main = "",
     ask = prod(par("mfcol")) < length(which) &&
                                  dev.interactive(),
     ...,
     panel = if (add.smooth) panel.smooth else points,
     add.smooth = getOption("add.smooth"))

Arguments

x	an object of class "mat".
which	which aspects of the "mat" object to plot if a subset of the plots is required, specify a subset of the numbers 1:5.
weighted	logical; should the analysis use weighted mean of env data of analogues as fitted/estimated values?
k	numeric; the number of analogues to use. If missing k is chosen automatically as the k that achieves lowest RMSE.
caption	captions to appear above the plots.
max.bias	logical, should max bias lines be added to residuals.
n.bias	numeric, number of sections to calculate maximum bias for.
restrict	logical; restrict comparison of k-closest model to k \le restrict.
sub.caption	common title-above figures if there are multiple; used as ‘sub’ (s.‘title’) otherwise. If NULL, as by default, a possibly shortened version of deparse(x$call) is used.
main	title to each plot-in addition to the above caption.
ask	logical; if TRUE, the user is asked before each plot, see par(ask=.).
...	graphical arguments passed to other graphics functions.
panel	panel function. The useful alternative to points, panel.smooth, can be chosen by add.smooth = TRUE.
add.smooth	logical indicating if a smoother should be added to fitted & residuals plots; see also panel above.

Details

This plotting function is modelled closely on plot.lm and many of the conventions and defaults for that function are replicated here.

sub.caption - by default the function call - is shown as a subtitle (under the x-axis title) on each plot when plots are on separate pages, or as a subtitle in the outer margin (if any) when there are multiple plots per page.

Value

One or more plots, drawn on the current device.

Author(s)

Gavin L. Simpson. Code borrows heavily from plot.lm.

See Also

mat

Examples

## Imbrie and Kipp example
## load the example data
data(ImbrieKipp)
data(SumSST)
data(V12.122)

## merge training and test set on columns
dat <- join(ImbrieKipp, V12.122, verbose = TRUE)

## extract the merged data sets and convert to proportions
ImbrieKipp <- dat[[1]] / 100
V12.122 <- dat[[2]] / 100

## MAT
ik.mat <- mat(ImbrieKipp, SumSST, method = "chord")

## summary plot of MAT model
layout(matrix(1:4, ncol = 2, byrow = TRUE))
plot(ik.mat)
layout(1)

analogue documentation built on Sept. 30, 2024, 9:41 a.m.