
Draws a caterpillar plot of the weighted average optima and tolerance range for each of the species in a data set.
# S3 method for default
caterpillarPlot(x, tol, mult = 1, decreasing = TRUE,
labels, xlab = NULL, pch = 21, bg = "white",
col = "black", lcol = col, lwd = 2, frame.plot = FALSE, ...)# S3 method for data.frame
caterpillarPlot(x, env, useN2 = TRUE, xlab, ...)
# S3 method for wa
caterpillarPlot(x, type = c("observed","model"), ...)
The function results in a plot on the currently active device. A data
frame with components Optima
and Tolerance
is returned
invisibly.
For the default
method, a numeric vector of species
optima. For the data.frame
method a species data matrix or data
frame. For the wa
method an object of class "wa"
.
numeric; vector of species tolerances.
numeric; variable for which optima and tolerances are required.
logical; should Hill's N2 values be used to produce un-biased tolerances?
logical; should the sort order of the species be increasing or decreasing?
numeric; multiplication factor for species' tolerances.
character; vector of labels for the species names with
which to annotate the y-axis. If missing, names(x)
is used.
character; the x-axis label. If NULL
, the default,
a description of env
is used.
The plotting character to use and its background and
foreground colour. See par
.
The colour and line width to use for the tolerance range.
character; "observed"
uses the actual tolerances
observed from the data. "model"
uses the tolerances used in
the WA model where very small tolerances have been reset for some
definition of small.
logical; should a box be drawn round the plot?
Additional graphical arguments to be passed on to plotting functions.
Gavin L. Simpson
The function may also be called using the short form name
caterpillar
:
caterpillar(x, ...)
For the underlying computations optima
and
tolerance
.
data(ImbrieKipp)
data(SumSST)
## default plot
caterpillar(ImbrieKipp, SumSST)
## customisation
opttol <-
caterpillar(ImbrieKipp, SumSST, col = "red2",
bg = "yellow", lcol = "blue",
xlab = expression(Summer ~ Sea ~ Surface ~
Temperature~(degree*C)))
## invisibly returns the optima and tolerances
head(opttol)
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