ChemoSpec: surveySpectra – R documentation

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surveySpectra

Plot Measures of Central Tendency and Spread for a Spectra Object

Description

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.

Usage

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),
  ...
)

Arguments

`spectra`	An object of S3 class `Spectra` to be analyzed.
`method`	Character. One of `c("sd", "sem", "sem95", "mad", "iqr")`.
`by.gr`	Logical, indicating if the analysis is to be done by group or not. Applies to `surveySpectra` only.
`...`	Additional parameters to be passed to the plotting routines.
`lab.pos`	Numeric, giving the frequency where the label should be drawn. Applies to `surveySpectra2` only.

Details

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.

Value

None; side effect is a plot

Functions

surveySpectra: Spectral survey emphasizing mean or median spectrum, optionally by group.
surveySpectra2: Spectral survey emphasizing variation among spectra.

Author(s)

Bryan A. Hanson, DePauw University.

Examples

data(SrE.IR)
myt <- expression(bolditalic(Serenoa) ~ bolditalic(repens) ~ bold(Extract ~ IR ~ Spectra))
surveySpectra(SrE.IR, method = "iqr", main = myt)
surveySpectra2(SrE.IR, method = "iqr", main = myt)

ChemoSpec

Exploratory Chemometrics for Spectroscopy

v5.3.11

GPL-3

Authors

Bryan A. Hanson [aut, cre] (<https://orcid.org/0000-0003-3536-8246>), Mike Bostock [cph, ctb] (author of the d3.js library used by plotSpectraJS, http://d3js.org), Matt Keinsley [ctb] (author of initial AOV-PCA code)

Initial release

2021-03-24