Work with Hyperspectral Data, i.e. Spectra + Meta Information (Spatial, Time, Concentration, ...) • hyperSpec

Package hyperSpec is under overhaul now.
So this website is still under construction and the contents as well as resources are not fully updated yet.
The documentation of version 0.100.2 is not present here either.

R package hyperSpec is the main package in the r-hyperspec family of packages. The goal of hyperSpec (and whole r-hyperspec) is to make the work with hyperspectral data sets, (i.e. spatially or time-resolved spectra, or spectra with any other kind of information associated with each of the spectra) more comfortable. The spectra can be data obtained during XRF, UV/VIS, Fluorescence, AES, NIR, IR, Raman, NMR, MS, etc. spectroscopy measurements. More generally, any data that is recorded over a discretized variable, e.g. absorbance = f(wavelength), stored as a vector of absorbance values for discrete wavelengths is suitable.

Documentation

There are two versions of hyperSpec online documentation:

for the released version and
for the in-development version of hyperSpec.

The documentation of the other r-hyperspec family packages can be found at r-hyperspec.github.io.

Issues, Bug Reports and Feature Requests

Issues, bug reports, and feature requests should go here!

Installation

Install from CRAN

You can install the released version of hyperSpec from CRAN with:

install.packages("hyperSpec")

Install from CRAN-like Repository

The recommended way to install the in-development version:

repos <- c("https://r-hyperspec.github.io/pkg-repo/", getOption("repos"))
install.packages("hyperSpec", repos = repos)

Install from GitHub

Install from GitHub (details)

You can install the in-development version of the package from GitHub too:

if (!require(remotes)) {install.packages("remotes")}
remotes::install_github("r-hyperspec/hyperSpec")

NOTE 1: Usually, “Windows” users need to download, install, and properly configure Rtools (see these instructions) to make the code above work.

NOTE 2: This method will not install package’s documentation (help pages and vignettes) into your computer. So you can either use the online documentation or build the package from source (see the next section).

Install from Source

Install from Source (details)

From the hyperSpec’s GitHub repository:
- If you use Git, git clone the branch of interest. You may need to fork it before cloning.
- Or just choose the branch of interest (1 in Figure below), download a ZIP archive with the code (2, 3), and unzip it on your computer.
Open the downloaded directory in RStudio (preferably, as an RStudio project).
- The code below works correctly only if your current working directory coincides with the root of the repository, i.e., if it is in the directory that contains file README.md.
- If you open RStudio project correctly (e.g., by clicking project.Rproj icon in the directory), then the working directory is set correctly by default.
In the RStudio ‘Console’ window, run the code (provided below) to:
1. Install packages remotes and devtools.
2. Install hyperSpec’s dependencies.
3. Create hyperSpec’s documentation.
4. Install package hyperSpec.

# Do not abort installation even if some packages are not available
Sys.setenv(R_REMOTES_NO_ERRORS_FROM_WARNINGS = "true")

# Install packages remotes and devtools
install.packages(c("remotes", "devtools"))

# Install hyperSpec's dependencies
remotes::install_deps(dependencies = TRUE)

# Create hyperSpec's documentation
devtools::document()

# Install package hyperSpec
devtools::install(build_vignettes = TRUE)

NOTE 1: Usually, “Windows” users need to download, install, and properly configure Rtools (see these instructions) to make the code above work.