reconPlot {analogue} | R Documentation |
Draws a palaeoenvironmental reconstruction of predicted environmental values for sub-fossil assemblages.
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, ...)
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. |
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
.
A plot on the currently active device.
Gavin L. Simpson
mat
, and predict.mat
for MAT
transfer functions and wa
and predict.wa
for WA models.
## Continue example from ?join example(join) ## Fit a MAT model swap.mat <- mat(swapdiat, swappH, method = "SQchord") swap.mat ## Reconstruct pH for the RLGH core rlgh.pH <- predict(swap.mat, rlgh) ## draw the reconstruction reconPlot(rlgh.pH, use.labels = TRUE, display.error = "bars", xlab = "Depth", ylab = "pH")