# Storing, Manipulating and Analysis Spectroscopy and Associated Data

## Documentation for package ‘spectacles’ version 0.5-5

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

A B C D E F I K L M N O P R S W misc

spectacles-package | Storing, Manipulating and Analysis Spectroscopy and Associated Data in R

## -- A --

aggregate_spectra | Aggregates spectral and data information
aggregate_spectra-method | Aggregates spectral and data information
apply_spectra | Apply a function on the spectra of a Spectra* object
as.data.frame.SpatialSpectra | Spectra* classes
as.data.frame.Spectra | Spectra* classes
as.data.frame.SpectraDataFrame | Spectra* classes
australia | Australia spectra library data set

## -- B --

base_line | Baseline correction using the baseline package
base_line-method | Baseline correction using the baseline package
big.head | Return the First or Last Part of an Object
big.tail | Return the First or Last Part of an Object

## -- C --

continuum_removal | Continuum removal
cut | Manipulating the wavelength range of a 'Spectra' object
cut-method | Manipulating the wavelength range of a 'Spectra' object

## -- D --

dim | Retrieve dimensions of Spectra* objects
dim.Spectra | Retrieve dimensions of Spectra* objects
dimensions | Retrieve dimensions of Spectra* objects

## -- E --

extraction-methods | Extracting and replacing parts of Spectra* objects

## -- F --

features | Retrieves or sets the data slot of a SpectraDataFrame object.
features-method | Retrieves or sets the data slot of a SpectraDataFrame object.
features-methods | Retrieves or sets the data slot of a SpectraDataFrame object.
features<- | Retrieves or sets the data slot of a SpectraDataFrame object.
features<--method | Retrieves or sets the data slot of a SpectraDataFrame object.
fill_spectra | Fill missing wavelengths of a Spectra* object with a given value
fill_spectra-method | Fill missing wavelengths of a Spectra* object with a given value

## -- I --

ids | Retrieves or sets the ids of a 'Spectra*' object.
ids-method | Retrieves or sets the ids of a 'Spectra*' object.
ids<- | Retrieves or sets the ids of a 'Spectra*' object.
ids<--method | Retrieves or sets the ids of a 'Spectra*' object.

## -- K --

kenstone | Kennard-Stone algorithm for optimal calibration set selection.
kenstone-method | Kennard-Stone algorithm for optimal calibration set selection.

## -- L --

length | Retrieve dimensions of Spectra* objects
length.Spectra | Retrieve dimensions of Spectra* objects
load_oz | Load the australia dataset

## -- M --

melt_spectra | Melts the spectra data of a Spectra object and returns it as wide format.
melt_spectra-method | Melts the spectra data of a Spectra object and returns it as wide format.
melt_spectra-methods | Melts the spectra data of a Spectra object and returns it as wide format.
mutate | Mutate a Spectra* object by transforming the spectra values, and/or adding new or replacing existing attributes.
mutate-method | Mutate a Spectra* object by transforming the spectra values, and/or adding new or replacing existing attributes.
mutate.Spectra | Mutate a Spectra* object by transforming the spectra values, and/or adding new or replacing existing attributes.

## -- N --

names.SpectraDataFrame | Spectra* classes
names<-.SpectraDataFrame | Spectra* classes
ncol-method | Retrieve dimensions of Spectra* objects
nrow-method | Retrieve dimensions of Spectra* objects

## -- O --

oz | Australia spectra library data set

## -- P --

plot | Plots an object inheriting from the Spectra class
plot-method | Plots an object inheriting from the Spectra class
plot-Spectra | Plots an object inheriting from the Spectra class
plot.Spectra | Plots an object inheriting from the Spectra class
plot_offset | Offset plot of a collection of spectra
plot_offset-method | Offset plot of a collection of spectra
plot_stack | Stacked plot of a collection of spectra
plot_stack-method | Stacked plot of a collection of spectra
plot_summary | Summary plot of a collection of spectra
plot_summary-method | Summary plot of a collection of spectra
postResampleSpectro | Calculates performance indictors across resamples
print-method | Spectra* classes
print.summary.Spectra | Summary

## -- R --

rbind | Stacking 'Spectra' objects together
rbind.Spectra | Stacking 'Spectra' objects together
rbind.SpectraDataFrame | Stacking 'Spectra' objects together
res | Spectral resolution
res-method | Spectral resolution
rnv | Standard and Robust Normal Variate transformations

## -- S --

separate | Separates a 'Spectra*' object into a calibration and a validation set.
separate-method | Separates a 'Spectra*' object into a calibration and a validation set.
separate.Spectra | Separates a 'Spectra*' object into a calibration and a validation set.
show-method | Spectra* classes
snv | Standard and Robust Normal Variate transformations
spectacles | Spectra* classes
Spectra | Constructor for the Spectra class.
spectra | Retrieves or sets the spectra of a 'Spectra*' objects.
Spectra-class | Spectra* classes
spectra-method | Retrieves or sets the spectra of a 'Spectra*' objects.
spectra-methods | Retrieves or sets the spectra of a 'Spectra*' objects.
spectra<- | Retrieves or sets the spectra of a 'Spectra*' objects.
spectra<--method | Retrieves or sets the spectra of a 'Spectra*' objects.
SpectraDataFrame | Constructor for the SpectraDataFrame class.
SpectraDataFrame-class | Spectra* classes
spectroSummary | Calculates performance indictors across resamples
splice | Splice correction of a spectra collected using ASD hardware
splice-method | Splice correction of a spectra collected using ASD hardware
split | Split a Spectra* object using factors
split-method | Split a Spectra* object using factors
split.Spectra | Split a Spectra* object using factors
subset | Subset SpectraDataFrame object
subset-method | Subset SpectraDataFrame object
subset.SpectraDataFrame | Subset SpectraDataFrame object
summary | Summary
summary.Spectra | Summary

## -- W --

wl | Retrieves or sets the wavelengths of a 'Spectra*' object.
wl-method | Retrieves or sets the wavelengths of a 'Spectra*' object.
wl<- | Retrieves or sets the wavelengths of a 'Spectra*' object.
wl<--method | Retrieves or sets the wavelengths of a 'Spectra*' object.
wl_units | Wavelengths of Spectra* objects
wl_units-method | Wavelengths of Spectra* objects
wl_units<- | Wavelengths of Spectra* objects
wl_units<--method | Wavelengths of Spectra* objects

## -- misc --

$ | Extracting and replacing parts of Spectra* objects
$-method | Extracting and replacing parts of Spectra* objects
$<- | Extracting and replacing parts of Spectra* objects
$<--method | Extracting and replacing parts of Spectra* objects
[ | Extracting and replacing parts of Spectra* objects
[-method | Extracting and replacing parts of Spectra* objects
[<- | Extracting and replacing parts of Spectra* objects
[<--method | Extracting and replacing parts of Spectra* objects
[[ | Extracting and replacing parts of Spectra* objects
[[-method | Extracting and replacing parts of Spectra* objects
[[<- | Extracting and replacing parts of Spectra* objects
[[<--method | Extracting and replacing parts of Spectra* objects