aggplot {pavo}

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)))