Compute and plot various measures of central tendency and
spread for a
Spectra object. Several different measures/spreads
are available. These are useful as an overview of where a data set varies
An object of S3 class
Spectra to be analyzed.
Character. One of
c("sd", "sem", "sem95", "mad",
Logical, indicating if the analysis is to be done by group or
not. Applies to
Parameters to be passed to the plotting routines. Applies to base graphics only.
Numeric, giving the frequency where the label should be drawn.
The returned value depends on the graphics option selected (see
None. Side effect is a plot.
The plot is displayed, and a
ggplot2 plot object is returned if the
value is assigned. The plot can be modified in the usual
surveySpectra the method choice works as follows:
the mean spectrum +/- the standard deviation,
sem plots the mean
spectrum +/- the standard error of the mean,
sem95 plots the mean
spectrum +/- the standard error at the 95 percent confidence interval,
mad plots the median spectrum +/- the median absolute deviation, and
iqr plots the median spectrum + the upper hinge and - the
surveySpectra2, the spectra are mean centered and plotted. Below
that, the relative summary statistic is plotted, offset, but on the same
surveySpectra: Spectral survey emphasizing mean or median spectrum, optionally by group.
surveySpectra2: Spectral survey emphasizing variation among spectra.
Additional documentation at https://bryanhanson.github.io/ChemoSpec/
# This example assumes the graphics output is set to ggplot2 (see ?GraphicsOptions). library("ggplot2") data(SrE.IR) myt <- expression(bolditalic(Serenoa) ~ bolditalic(repens) ~ bold(Extract ~ IR ~ Spectra)) p1 <- surveySpectra(SrE.IR, method = "iqr") #> #> Group EPO has 3 or fewer members #> so your stats are not very useful... #> This group has been dropped for display purposes! #> #> Group OO has 3 or fewer members #> so your stats are not very useful... #> This group has been dropped for display purposes! p1 <- p1 + ggtitle(myt) p1 p2 <- surveySpectra2(SrE.IR, method = "iqr") p2 <- p2 + ggtitle(myt) p2