aggplot: Plot aggregated reflectance spectra

In pavo: Perceptual Analysis, Visualization and Organization of Spectral Colour Data

Plot aggregated reflectance spectra

Description

Combines and plots spectra (by taking the average and the standard deviation, for example) according to an index or a vector of identities.

Usage

aggplot(
  rspecdata,
  by = NULL,
  FUN.center = mean,
  FUN.error = sd,
  lcol = NULL,
  shadecol = NULL,
  alpha = 0.2,
  legend = FALSE,
  ...
)

Arguments

rspecdata	(required) a data frame, possibly of class rspec, which contains a column containing a wavelength range, named 'wl', and spectra data in remaining columns.
by	(required) either a single value specifying the range of spectra within the data frame to be combined (for example, by = 3 indicates the function will be applied to groups of 3 consecutive columns in the spectra data frame); a vector containing identifications for the columns in the spectra data frame (in which case the function will be applied to each group of spectra sharing the same identification); or a list of vectors, e.g., by = list(sex, species).
FUN.center	the function to be applied to the groups of spectra, calculating a measure of central tendency (defaults to base::mean()).
FUN.error	the function to be applied to the groups of spectra, calculating a measure of variation (defaults to stats::sd()).
lcol	colour of plotted lines indicating central tendency.
shadecol	colour of shaded areas indicating variance measure.
alpha	transparency of the shaded areas.
legend	automatically add a legend.
...	additional graphical parameters to be passed to plot.

Value

Plot containing the lines and shaded areas of the groups of spectra.

Author(s)

Rafael Maia [e-mail]

Chad Eliason [e-mail]

References

Montgomerie R (2006) Analyzing colors. In: Hill G, McGraw K (eds) Bird coloration. Harvard University Press, Cambridge, pp 90-147.

Examples

# Load reflectance data
data(sicalis)

# Create grouping variable based on spec names
bysic <- gsub("^ind[0-9].", "", names(sicalis)[-1])

# Plot using various error functions and options
aggplot(sicalis, bysic)
aggplot(sicalis, bysic, FUN.error = function(x) quantile(x, c(0.0275, 0.975)))
aggplot(sicalis, bysic, shadecol = spec2rgb(sicalis), lcol = 1)
aggplot(sicalis, bysic, lcol = 1, FUN.error = function(x) sd(x) / sqrt(length(x)))

pavo documentation built on Sept. 24, 2023, 5:06 p.m.