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

  by = NULL, = mean,
  FUN.error = sd,
  lcol = NULL,
  shadecol = NULL,
  alpha = 0.2,
  legend = FALSE,



(required) a data frame, possibly of class rspec, which contains a column containing a wavelength range, named 'wl', and spectra data in remaining columns.


(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).

the function to be applied to the groups of spectra, calculating a measure of central tendency (defaults to base::mean()).


the function to be applied to the groups of spectra, calculating a measure of variation (defaults to stats::sd()).


colour of plotted lines indicating central tendency.


colour of shaded areas indicating variance measure.


transparency of the shaded areas.


automatically add a legend.


additional graphical parameters to be passed to plot.


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


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


Rafael Maia

Chad Eliason


# 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)))