plot.fi: Custom plot function for FORAM Index results

In forams: Foraminifera and Community Ecology Analyses

Custom plot function for FORAM Index results

Description

This function generates custom plots for FI objects.

Usage

## 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, ...)

Arguments

x	an object of class fi.
ylim	the y limits (x1, x2) of the plot, defaults to c(1, 10)
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 c(1, 10, 9).
xlab	a label for the x axis, defaults to "Samples".
ylab	a label for the y axis, defaults to "FORAM Index".
pch.urg	plotting 'character', i.e., symbol to use, prefer one between 21:25, defaults to 25
pch.mrg	plotting 'character', i.e., symbol to use, prefer one between 21:25, defaults to 21
pch.crg	plotting 'character', i.e., symbol to use, prefer one between 21:25, defaults to 24
bg.urg	background (fill) color for the open plot symbols given by pch=21:25, defaults to "red".
bg.mrg	background (fill) color for the open plot symbols given by pch=21:25, defaults to "yellow".
bg.crg	background (fill) color for the open plot symbols given by pch=21:25, defaults to "green".
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 TRUE.
...	other graphical parameters, see par for details.

Details

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.

Note

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.

Author(s)

Rodrigo Aluizio

References

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.

Examples

data(LF)
data(Factors)
MyFI <- fi(LF, Factors)
plot(MyFI)

forams documentation built on Aug. 24, 2023, 5:11 p.m.