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hyperSpec

hyperSpec: Tools for Spectroscopy (R package)

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

Science Score: 23.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
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    .zenodo.json file
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    DOI references
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    Academic publication links
  • ✓
    Committers with academic emails
    1 of 7 committers (14.3%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (11.0%) to scientific vocabulary

Keywords

data-wrangling hyperspectral imaging infrared nmr r-package raman spectroscopy uv-vis xrf
Last synced: 6 months ago · JSON representation

Repository

hyperSpec: Tools for Spectroscopy (R package)

Basic Info
Statistics
  • Stars: 17
  • Watchers: 7
  • Forks: 4
  • Open Issues: 34
  • Releases: 1
Topics
data-wrangling hyperspectral imaging infrared nmr r-package raman spectroscopy uv-vis xrf
Created over 4 years ago · Last pushed over 1 year ago
Metadata Files
Readme Contributing License

README.md

Project Status: Active CRAN status metacran downloads metacran downloads R-CMD-check Codecov Website (pkgdown) <!-- license --> <!-- badges: end -->

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 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:

a. for the released version and b. 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:

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 in CONTRIBUTING.md.

Owner

  • Name: R hyperSpec
  • Login: r-hyperspec
  • Kind: organization

Tools for spectroscopy

GitHub Events

Total
  • Watch event: 5
  • Fork event: 1
Last Year
  • Watch event: 5
  • Fork event: 1

Committers

Last synced: about 2 years ago

All Time
  • Total Commits: 465
  • Total Committers: 7
  • Avg Commits per committer: 66.429
  • Development Distribution Score (DDS): 0.099
Past Year
  • Commits: 22
  • Committers: 4
  • Avg Commits per committer: 5.5
  • Development Distribution Score (DDS): 0.182
Top Committers
Name Email Commits
Vilmantas Gėgžna G****V@g****m 419
Vilmantas Gėgžna v****a@g****t 18
pkg-skeleton Deploy Bot @g****m 10
Bryan h****n@d****u 8
Claudia Beleites C****s@c****h 8
AlreadyTakenJonas j****s@e****e 1
Erick Oduniyi 3****i 1
Committer Domains (Top 20 + Academic)
eichhorn-networks.de: 1 chemometrix.gmbh: 1 depauw.edu: 1 github.com: 1 gmc.vu.lt: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 66
  • Total pull requests: 51
  • Average time to close issues: 3 months
  • Average time to close pull requests: 16 days
  • Total issue authors: 8
  • Total pull request authors: 4
  • Average comments per issue: 1.5
  • Average comments per pull request: 0.43
  • Merged pull requests: 50
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • GegznaV (52)
  • cbeleites (6)
  • wincowgerDEV (2)
  • ADorosz5 (1)
  • olaf-b (1)
  • PAAC1984 (1)
  • henningte (1)
  • BenoitCarreres (1)
Pull Request Authors
  • GegznaV (55)
  • cbeleites (2)
  • AlreadyTakenJonas (1)
  • bryanhanson (1)
Top Labels
Issue Labels
Topic: rename :recycle: (19) Topic: documentation :blue_book: (6) Type: possibly bug :question: (5) Topic: unit test :one: (5) Type: enhancement :balloon: (5) Priority: 3-low (3) Topic: vignette :green_book: (3) Topic: file IO (3) Slot: `@label` (2) Slot: `@wavelength` (2) Type: bug :bomb: (2) Status: under consideration :exclamation: (2) Topic: code :diamond_shape_with_a_dot_inside: (2) Priority: 1-high/urgent (2) Type: new :new: (1) Topic: GHA (1) Topic: datasets :date: (1) Status: confirmed :grey_exclamation: (1) Note: guideline (1) Topic: deprecate/defunct :neckbeard: (1) Topic: plots :chart_with_upwards_trend: (1) Note: R-4.2.0 (1) Topic: CI :cactus: (1) Status: blocked :no_entry: (1)
Pull Request Labels
Topic: rename :recycle: (14) Topic: documentation :blue_book: (6) Topic: vignette :green_book: (5) Type: enhancement :balloon: (4) Topic: unit test :one: (4) Topic: style :pencil2: (2) Type: bug :bomb: (1) Topic: code :diamond_shape_with_a_dot_inside: (1) Topic: plots :chart_with_upwards_trend: (1) Slot: `@wavelength` (1) Topic: file IO (1)

Packages

  • Total packages: 1
  • Total downloads:
    • cran 1,130 last-month
  • Total docker downloads: 21,777
  • Total dependent packages: 7
  • Total dependent repositories: 22
  • Total versions: 18
  • Total maintainers: 1
cran.r-project.org: hyperSpec

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

  • Versions: 18
  • Dependent Packages: 7
  • Dependent Repositories: 22
  • Downloads: 1,130 Last month
  • Docker Downloads: 21,777
Rankings
Dependent repos count: 5.8%
Dependent packages count: 6.6%
Average: 12.1%
Docker downloads count: 12.5%
Downloads: 14.1%
Stargazers count: 16.5%
Forks count: 17.0%
Maintainers (1)
Claudia.Beleites@chemometrix.gmbh
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.6.0 depends
  • ggplot2 >= 2.3.0 depends
  • grid * depends
  • lattice * depends
  • dplyr * imports
  • hySpc.testthat * imports
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  • lazyeval * imports
  • methods * imports
  • rlang * imports
  • utils * imports
  • xml2 * imports
  • MASS * suggests
  • R.matlab * suggests
  • baseline * suggests
  • bookdown * suggests
  • caTools * suggests
  • colorspace * suggests
  • covr * suggests
  • digest * suggests
  • kableExtra * suggests
  • knitr * suggests
  • matrixStats * suggests
  • mvtnorm * suggests
  • plotrix * suggests
  • pls * suggests
  • reshape * suggests
  • reshape2 * suggests
  • rgl * suggests
  • rmarkdown * suggests
  • sessioninfo * suggests
  • sp * suggests
  • styler * suggests
  • tibble * suggests
  • vdiffr >= 1.0.0 suggests
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  • r-lib/actions/setup-r v2 composite
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