reconPlot: Stratigraphic plots of palaeoenvironmental reconstructions

In analogue: Analogue and Weighted Averaging Methods for Palaeoecology

Stratigraphic plots of palaeoenvironmental reconstructions

Description

Draws a palaeoenvironmental reconstruction of predicted environmental values for sub-fossil assemblages.

Usage

reconPlot(x, ...)

## Default S3 method:
reconPlot(x, depths, errors,
          display.error = c("none", "bars", "lines"),
          rev.x = TRUE,
          col.error = "grey", lty.error = "dashed",
          type = "l",
          xlim, ylim,
          xlab = "", ylab = "", main = "",
          ...)

## S3 method for class 'predict.mat'
reconPlot(x, depths, use.labels = FALSE,
          predictions = c("model", "bootstrap"),
          display.error = c("none", "bars", "lines"),
          sample.specific = TRUE, ...)

## S3 method for class 'predict.wa'
reconPlot(x, depths, use.labels = FALSE,
          display.error = c("none", "bars", "lines"),
          sample.specific = TRUE, ...)

Arguments

x	An R object.
depths	numeric; a vector of depths for which predicted values exist or will be generated. Can be missing, in which case, if use.labels = TRUE, the function will attempt to derive suitable values for you. See Details below.
errors	numeric; a vector of errors for plotting error bars or lines.
display.error	character; hown should error bars be drawn on the plot? One of "none", "bars", or "lines". If "bars", error bars are drawn for each sample. If "lines", lines are drawn enclosing the region prediction +/- RMSEP.
rev.x	logical; should the depth/age axis be reversed (drawn from high to low)?
col.error, lty.error	the colour and type of line drawn. See par and arguments "col" and "lty".
type	type of line drawn. See par and argument "type".
xlab, ylab	character; the x- and y-axis labels respectively.
main	character; main title for the plot.
xlim, ylim	numeric, length 2; the x- and y-limits for the plotted axes. If not provided, the function will calculate appropriate values to cover the range of plotted values and any error bars (if requested via "error.bars".
use.labels	logical; should reconPlot attempt to derive values for argument depths from the names of the predicted values? Only use if depths is missing. See Details below.
predictions	character; one of "model" or "bootstrap". Which type of predicted values should be plotted? The model predictions ("model") or the bootstrap-derived predictions ("bootstrap").
sample.specific	logical; should sample specific errors be used? Only for predictions = "bootstrap".
...	arguments passed to other graphics functions.

Details

Conventionally, these plots are drawn on a depth or an age scale. Argument depths is used to provide the depth or age axis, against which the predicted values are plotted.

If depths is not provided, then the function will try to derive the appropriate values from the labels of the predictions if use.labels = TRUE. You must provide depths or set use.labels = TRUE otherwise an error will result. The derived labels will be coerced to numerics. If your labels are not coercible, then you'll either get nonsense on the plot or an error from R. If so, provide suitable values for depths.

Value

A plot on the currently active device.

Author(s)

Gavin L. Simpson

See Also

mat, and predict.mat for MAT transfer functions and wa and predict.wa for WA models.

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

## Reconstruct pH for the RLGH core
v12.pH <- predict(ik.mat, V12.122)

## draw the reconstruction
reconPlot(v12.pH, use.labels = TRUE, display.error = "bars",
          xlab = "Depth", ylab = "Summer Seas-surface Temperature")

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