Description Usage Arguments Details Value Author(s) See Also Examples
Draws a caterpillar plot of the weighted average optima and tolerance range for each of the species in a data set.
1 2 3 4 5 6 7 8 9 10 | ## Default S3 method:
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 class 'data.frame'
caterpillarPlot(x, env, useN2 = TRUE, xlab, ...)
## S3 method for class 'wa'
caterpillarPlot(x, type = c("observed","model"), ...)
|
x |
For the |
tol |
numeric; vector of species tolerances. |
env |
numeric; variable for which optima and tolerances are required. |
useN2 |
logical; should Hill's N2 values be used to produce un-biased tolerances? |
decreasing |
logical; should the sort order of the species be increasing or decreasing? |
mult |
numeric; multiplication factor for species' tolerances. |
labels |
character; vector of labels for the species names with
which to annotate the y-axis. If missing, |
xlab |
character; the x-axis label. If |
pch, bg, col |
The plotting character to use and its background and
foreground colour. See |
lcol, lwd |
The colour and line width to use for the tolerance range. |
type |
character; |
frame.plot |
logical; should a box be drawn round the plot? |
... |
Additional graphical arguments to be passed on to plotting functions. |
The function may also be called using the short form name
caterpillar
:
1 2 | caterpillar(x, ...)
|
The function results in a plot on the currently active device. A data
frame with components Optima
and Tolerance
is returned
invisibly.
Gavin L. Simpson
For the underlying computations optima
and
tolerance
.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | 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)
|
Loading required package: vegan
Loading required package: permute
Loading required package: lattice
This is vegan 2.4-4
analogue version 0.17-0
Optima Tolerance
P.obliq 26.94320 1.554762
G.duter 26.49014 1.998304
C.nitid 26.41005 1.461725
G.rubes 26.27479 1.968294
G.saccu 26.18001 1.979651
G.mentu 26.13778 2.386584
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