surveySpectra {ChemoSpec} | R Documentation |
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
the most.
surveySpectra( spectra, method = c("sd", "sem", "sem95", "mad", "iqr"), by.gr = TRUE, ... ) surveySpectra2( spectra, method = c("sd", "sem", "sem95", "mad", "iqr"), lab.pos = 0.9 * max(spectra$freq), ... )
spectra |
An object of S3 class |
method |
Character. One of |
by.gr |
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. |
lab.pos |
Numeric, giving the frequency where the label should be drawn.
Applies to |
For surveySpectra
the method choice works as follows: sd
plots
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
finally, iqr
plots the median spectrum + the upper hinge and - the
lower hinge.
For surveySpectra2
, the spectra are mean centered and plotted. Below
that, the relative summary statistic is plotted, offset, but on the same
scale.
The returned value depends on the graphics option selected (see GraphicsOptions
).
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 ggplot2
manner.
surveySpectra
: Spectral survey emphasizing mean or median spectrum, optionally by group.
surveySpectra2
: Spectral survey emphasizing variation among spectra.
Bryan A. Hanson (DePauw University), Tejasvi Gupta.
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") p1 <- p1 + ggtitle(myt) p1 p2 <- surveySpectra2(SrE.IR, method = "iqr") p2 <- p2 + ggtitle(myt) p2