Skip to content
Methods for converting between objects used by R packages HyperSpec and ChemoSpec
Branch: master
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Type Name Latest commit message Commit time
Failed to load latest commit information.
man Updating for R 3.3 in progress - not working yet Jul 27, 2015
.Rbuildignore Updating for R 3.3 in progress - not working yet Jul 27, 2015
NAMESPACE v 1.1.26 see NEWS Jan 26, 2016
gitignore.txt Updating for R 3.3 in progress - not working yet Jul 27, 2015

How to install hyperChemoBridge

NOTE: The repository is named HyperChemoBridge, but the package is hyperChemoBridge (note different capitalization).

To install from Github:

install_github(repo = "Chathurga/HyperChemoBridge@master")

If you use "@some_other_branch" you can get other branches that might be available. They may or may not pass CRAN checks and thus may not install automatically using the method above. Check the NEWS file to see what's up.

License Information

hyperChemoBridge is distributed under the GPL-3 license, as stated in the DESCRIPTION file. For more info, see the GPL site.


A Comparison of the R Packages hyperSpec & ChemoSpec

This page compares these two packages for your convenience. This is not a comprehensive list of functions in each package, only a comparison of frequently needed tasks. See the respective package vignettes, index pages and help pages for details.

hyperSpec ChemoSpec HyperChemoBridge

The focus of hyperSpec is on data handling: it provides methods for manipulating data in preparation for other analyses using functions from base R or other packages. The focus of ChemoSpec, on the other hand, is to provide wrappers to common statistical methods (such as PCA, HCA etc) that permit the user to analyze their data from within ChemoSpec.

For example, hyperSpec uses dedicated method dispatch which makes data handling very straightforward. If, for instance, you want to take the log of your spectral data, new_object <- log(object) will take care of it. hyperSpec automatically accesses just the spectral data contained in the larger structure, and takes the log of that part, then returns the entire object. For ChemoSpec, you would have to dig into the object yourself: object$data <- log(object$data). Another example would be that in hyperSpec, typing the name of the object gives you a summary of the object. Doing so in the ChemoSpec would write the object to the screen, not very desirable. In ChemoSpec, you may wish to do str(object) or, better, sumSpectra(object).

For statistical methods, ChemoSpec provides wrappers. For instance, to carry out PCA, you might choose classPCA which handles most of the details of the prcomp object in the background. In hyperSpec, you'll need to do some of the work yourself (see Section 4.5 of the vignette on the chondro data set, via vignette("chondro").

The following table does not cover every option in each package by any means. See the indices for each package for complete coverage.

task hyperSpec ChemoSpec
package overview & index package?hyperSpec ?ChemoSpec
vignettes vignette("topic") topics: baseline, chondro, fileio, flu, introduction, laser, plotting vignette("ChemoSpec")
import data see vignette("fileio") files2SpectraObject
verify data integrity chk.hy chkSpectra
summarize data type name_of_data_set sumSpectra
baseline correct spectra baselineSpec
normalize spectral data sweep(spc, 1, rowMeans(spc), "/") normSpectra
bin spectral data spc.bin binBuck
align spectral data * clupaSpectra
remove selected samples see ?"[" removeSample
remove selected frequencies see ?"[" removeFreq
remove selected groups see ?"[" removeGroups
split a data set into new groups split splitSpectraGroups
plot spectra by frequency plotspc, plotmap, plotmat, plotc plotSpectra, specSurvey
plot spectra as time series plotc *
compare different data sets Compare *
merge different data sets merge *

* There is no function for this action, it will have to be done manually.

You can’t perform that action at this time.