Stratiplot {analogue} | R Documentation |
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.
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, ...)
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 NA s. 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. |
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.
Returns a Lattice plot object of class "trellis"
.
The function currently doesn't know about ages/dates and will interpret these as ‘depths’ instead. This will be fixed in a future version.
Gavin L. Simpson.
xyplot
',
panel.Stratiplot
, panel.Loess
.
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")))