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https://github.com/r-hyperspec/hyperSpec

hyperSpec: Tools for Spectroscopy (R package)
https://github.com/r-hyperspec/hyperSpec

data-wrangling hyperspectral imaging infrared nmr r-package raman spectroscopy uv-vis xrf

Last synced: 26 days ago
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hyperSpec: Tools for Spectroscopy (R package)

Host: GitHub
URL: https://github.com/r-hyperspec/hyperSpec
Owner: r-hyperspec
License: gpl-3.0
Created: 2021-07-14T15:47:53.000Z (almost 3 years ago)
Default Branch: develop
Last Pushed: 2024-05-27T17:10:41.000Z (about 1 month ago)
Last Synced: 2024-05-28T01:57:04.981Z (about 1 month ago)
Topics: data-wrangling, hyperspectral, imaging, infrared, nmr, r-package, raman, spectroscopy, uv-vis, xrf
Language: R
Homepage: https://r-hyperspec.github.io/hyperSpec/
Size: 107 MB
Stars: 12
Watchers: 8
Forks: 3
Open Issues: 34
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE

Lists

awesome-chemometrics - hyperSpec - 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 as obtained during XRF, UV/VIS, Fluorescence, AES, NIR, IR, Raman, NMR, MS, etc. spectroscopy measurements. (R)

README

        

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# R Package **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**](https://www.r-project.org/) package **hyperSpec** is the main package in the [**`r-hyperspec`**](https://r-hyperspec.github.io/) 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](https://en.wikipedia.org/wiki/X-ray_fluorescence),

[UV/VIS](https://en.wikipedia.org/wiki/Ultraviolet%E2%80%93visible_spectroscopy), 

[Fluorescence](https://en.wikipedia.org/wiki/Fluorescence_spectroscopy),

[AES](https://en.wikipedia.org/wiki/Auger_electron_spectroscopy),

[NIR](https://en.wikipedia.org/wiki/Near-infrared_spectroscopy),

[IR](https://en.wikipedia.org/wiki/Infrared_spectroscopy), 

[Raman](https://en.wikipedia.org/wiki/Raman_spectroscopy), 

[NMR](https://en.wikipedia.org/wiki/Nuclear_magnetic_resonance_spectroscopy), 

[MS](https://en.wikipedia.org/wiki/Mass_spectrometry),

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:

a. for the [released version](https://r-hyperspec.github.io/hyperSpec/) and

b. for the [in-development version](https://r-hyperspec.github.io/hyperSpec/dev/) of **hyperSpec**.

The documentation of the other **`r-hyperspec`** family packages can be found at [r-hyperspec.github.io](https://r-hyperspec.github.io/).

## Issues, Bug Reports and Feature Requests

Issues, bug reports, and feature requests should go [here](https://github.com/r-hyperspec/hyperSpec/issues)!

## Installation

### Install from CRAN

You can install the **released** version of **hyperSpec** from [CRAN](https://cran.r-project.org/package=hyperSpec) with:

```r

install.packages("hyperSpec")

```

### Install from CRAN-like Repository

The **recommended** way to install the in-development version:

```r

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](https://github.com/r-hyperspec/hyperSpec) too:

```r

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](https://cran.r-project.org/bin/windows/Rtools/)) 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](https://r-hyperspec.github.io/) or build the package from source (see the next section).

### Install from Source

Install from Source (details)

1. From the **hyperSpec**'s GitHub [repository](https://github.com/r-hyperspec/hyperSpec):

    - 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.  

![image](https://user-images.githubusercontent.com/12725868/89338263-ffa1dd00-d6a4-11ea-94c2-fa36ee026691.png)

2. 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 ![image](https://user-images.githubusercontent.com/12725868/89340903-26621280-d6a9-11ea-8299-0ec5e9cf7e3e.png) in the directory), then the working directory is set correctly by default.

3. In the RStudio 'Console' window, run the code (provided below) to:

    a. Install packages **remotes** and **devtools**.

    b. Install **hyperSpec**'s dependencies.

    c. Create **hyperSpec**'s documentation.

    d. Install package **hyperSpec**.

```r

# 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](https://cran.r-project.org/bin/windows/Rtools/)) to make the code above work.

## For Developers

Developers can find information about automatic deployment from this repo to `pkg-repo` [here](https://github.com/r-hyperspec/pkg-repo) in `CONTRIBUTING.md`.