plot.fi | R Documentation |
This function generates custom plots for FI objects.
## S4 method for signature 'fi'
plot(x, ylim = c(1, 10), yaxp = c(1, 10, 9), xlab = 'Samples',
ylab = 'FORAM Index', pch.urg = 25, pch.mrg = 21, pch.crg = 24,
bg.urg = 'red', bg.mrg = 'yellow', bg.crg = 'green', pt.cex = 1,
limits = TRUE, ...)
x |
an object of class |
ylim |
the y limits (x1, x2) of the plot, defaults to |
yaxp |
a vector of the form c(y1, y2, n) giving the coordinates of the extreme tick marks and the number of intervals between tick-marks, defaults to |
xlab |
a label for the x axis, defaults to |
ylab |
a label for the y axis, defaults to |
pch.urg |
plotting 'character', i.e., symbol to use, prefer one between 21:25, defaults to |
pch.mrg |
plotting 'character', i.e., symbol to use, prefer one between 21:25, defaults to |
pch.crg |
plotting 'character', i.e., symbol to use, prefer one between 21:25, defaults to |
bg.urg |
background (fill) color for the open plot symbols given by |
bg.mrg |
background (fill) color for the open plot symbols given by |
bg.crg |
background (fill) color for the open plot symbols given by |
pt.cex |
character (or symbol) expansion: a numerical vector, defaults to 1. |
limits |
logical; if TRUE, draws lines limiting the three FORAM Index classes and identifies them, defaults to |
... |
other graphical parameters, see |
The plot uses the axis
function, so a complete customization (i.e. side
) of the axes is not possible at this moment, and some other parameters may show improperly if changed.
FI > 4 indicates environment conducive to reef growth (CRG), FI varying between 3 and 5 indicates environmental change (Coefficient of Variation > 0.1), 2 < FI < 4 indicates environment marginal for reef growth (MRG) and unsuitable for recovery and FI < 2 indicates stressed conditions unsuitable for reef growth (UGR).
For more details on other graphic prameters see plot.default
and par
.
Rodrigo Aluizio
Hallock, P., Lidz, B.H., Cockey-Burkhard, E.M. & Donnelly, K.B. (2003). Foraminifera as bioindicators in coral reef assessment and monitoring: The foram index. Environmental monitoring and assessment 81, 221-238.
data(LF)
data(Factors)
MyFI <- fi(LF, Factors)
plot(MyFI)
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