screeplot: Screeplots of model results

In analogue: Analogue and Weighted Averaging Methods for Palaeoecology

Screeplots of model results

Description

Draws screeplots of performance statistics for models of varying complexity.

Usage

## S3 method for class 'mat'
screeplot(x, k, restrict = 20,
          display = c("rmsep", "avg.bias",
                      "max.bias", "r.squared"),
          weighted = FALSE,  col = "red", xlab = NULL,
          ylab = NULL, main = NULL, sub = NULL, ...)

## S3 method for class 'bootstrap.mat'
screeplot(x, k, restrict = 20,
          display = c("rmsep","avg.bias","max.bias",
                      "r.squared"),
          legend = TRUE, loc.legend = "topright",
          col = c("red", "blue"),
          xlab = NULL, ylab = NULL,
          main = NULL, sub = NULL,
          ...,
          lty = c("solid","dashed"))

Arguments

x	object of class mat and bootstrap.mat.
k	number of analogues to use. If missing 'k' is chosen automatically as the 'k' that achieves lowest RMSE.
restrict	logical; restrict comparison of k-closest model to k <= restrict.
display	which aspect of x to plot? Partial match.
weighted	logical; should the analysis use weighted mean of env data of analogues as fitted/estimated values?
xlab, ylab	x- and y-axis labels respectively.
main, sub	main and subtitle for the plot.
legend	logical; should a legend be displayed on the figure?
loc.legend	character; a keyword for the location of the legend. See legend for details of allowed keywords.
col	Colours for lines drawn on the screeplot. Method for class "bootstrap.mat" takes a vector of two colours.
lty	vector detailing the line type to use in drawing the screeplot of the apparent and bootstrap statistics, respectively. Code currently assumes that length(lty) is 2.
...	arguments passed to other graphics functions.

Details

Screeplots are often used to graphically show the results of cross-validation or other estimate of model performance across a range of model complexity.

Four measures of model performance are currently available: i) root mean square error of prediction (RMSEP); ii) average bias — the mean of the model residuals; iii) maximum bias — the maximum average bias calculated for each of n sections of the gradient of the environmental variable; and v) model R^2.

For the maximum bias statistic, the response (environmental) gradient is split into n = 10 sections.

For the bootstrap method, apparent and bootstrap versions of these statistics are available and plotted.

Note

Currently only models of class mat and bootstrap.mat are supported.

Author(s)

Gavin Simpson

See Also

screeplot

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

## fit the MAT model using the chord distance measure
(ik.mat <- mat(ImbrieKipp, SumSST, method = "chord"))

screeplot(ik.mat)

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