analogue (version 0.17-7)

plot.mat: 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 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"))

Value

One or more plots, drawn on the current device.

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.

Author

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

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.

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)