Stratiplot {analogue}R Documentation

Palaeoecological stratigraphic diagrams

Description

Draws palaeoecological stratigraphic diagrams of one or more variables as a function of depth/age, with the time dimension flowing from the bottom to the top of the y-axis, using the Lattice graphics package.

Usage

Stratiplot(x, ...)

## Default S3 method:
Stratiplot(x, y, type = "l", ylab = "", xlab = "",
           pages = 1, ...)

## S3 method for class 'formula':
Stratiplot(formula, data, subset, na.action, type = "l",
           ylab = "", xlab = "", pages = 1, ...)

Arguments

x matrix-like object; the variables to be plotted.
y numeric vector of depths/ages corresponding to rows in x. Length of y must be the same as nrow(x) or exactly equal to nrow(x) / ncol(x). See Details.
formula an object of class "formula" (or one that can be coerced to that class): a symbolic description of the model to be fitted. The details of plot specification are given under ‘Details’.
type character; The type of plotting. Can be a vector. Note that not all Lattice ‘type’s are supported and some new types are allowed. See panel.Stratiplot for further details.
data an optional data frame, list or environment (or object coercible by as.data.frame to a data frame) containing the variables to plot. If not found in data, the variables are taken from environment(formula), typically the environment from which Stratiplot is called.
subset an optional vector specifying a subset of observations to be used in the fitting process.
na.action a function which indicates what should happen when the data contain NAs. The default is set by the na.action setting of options, and is na.fail if that is unset. The ‘factory-fresh’ default is na.omit. Another possible value is NULL, no action. Value na.exclude can be useful.
ylab, xlab the x- and y-axis labels.
pages numeric; the number of pages to draw the plot over. May be useful for data sets with many species.
... additional arguments passed to panel.Stratiplot and the underlying xyplot function.

Details

Currently the function is designed for relative abundance data only. Greater flexibility is planned in a future version.

Plots can be specified symbolically using a formula. A typical model has the form Y ~ variables, where Y is either the core depths or sample ages/dates (to be plotted on the y-axis) and variables is a series of terms which specifies the variables to plot against Y. Terms should be specified with the form var1 + var2 + var3 to plot only those variables. Other, standard, notation for formulae apply, such as model formulae used in lm.

Note that formula is not passed on to xyplot. Instead, the formula is parsed and evaluated within Stratiplot and an appropriate data structure formed to facilitate plotting via xyplot. As such, the special features of Lattice formulae cannot be used.

Value

Returns a Lattice plot object of class "trellis".

Note

The function currently doesn't know about ages/dates and will interpret these as ‘depths’ instead. This will be fixed in a future version.

Author(s)

Gavin L. Simpson.

See Also

xyplot', panel.Stratiplot, panel.Loess.

Examples

data(V12.122)
depths <- as.numeric(rownames(V12.122))

(plt <- Stratiplot(depths ~ O.univ + G.ruber + G.tenel + G.pacR,
                   data = V12.122,
                   type = c("h","l","g","smooth")))

(plt2 <- Stratiplot(depths ~ O.univ + G.ruber + G.tenel + G.pacR,
                    data = V12.122,
                    type = c("poly","g")))

(plt3 <- Stratiplot(depths ~ O.univ + G.ruber + G.tenel + G.pacR,
                    data = V12.122,
                    type = c("h")))

spp.want <- c("O.univ","G.ruber","G.tenel","G.pacR")
(plt4 <- Stratiplot(V12.122[, spp.want], y = depths,
                    type = c("poly", "g")))

[Package analogue version 0.6-6 Index]