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prospectr

R package: Misc. Functions for Processing and Sample Selection of Spectroscopic Data

https://github.com/l-ramirez-lopez/prospectr

Science Score: 36.0%

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
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 12 committers (8.3%) from academic institutions
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  • ○
    Scientific vocabulary similarity
    Low similarity (14.2%) to scientific vocabulary

Keywords

chemometrics derivatives infrared near-infrared nir pedometrics preprocessing r r-package resample sampling signal soil-spectroscopy spectroscopy
Last synced: 6 months ago · JSON representation

Repository

R package: Misc. Functions for Processing and Sample Selection of Spectroscopic Data

Basic Info
Statistics
  • Stars: 44
  • Watchers: 5
  • Forks: 21
  • Open Issues: 8
  • Releases: 7
Topics
chemometrics derivatives infrared near-infrared nir pedometrics preprocessing r r-package resample sampling signal soil-spectroscopy spectroscopy
Created almost 6 years ago · Last pushed 6 months ago
Metadata Files
Readme Changelog License

README.Rmd 

---
title: "README"
output: md_document
date: "2022-09-18"
---

# prospectr

[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/prospectr)](https://CRAN.R-project.org/package=prospectr)
[![Downloads](https://cranlogs.r-pkg.org/badges/prospectr)](https://cranlogs.r-pkg.org/badges/prospectr)






 Misc. Functions for Processing and Sample Selection of Spectroscopic Data 

_Antoine Stevens & Leo Ramirez-Lopez_

_Last update: `r Sys.Date()`_


Version: `r paste(prospectr:::pkg_info()[1:2], collapse =  " \U002D\U002D ")`

`prospectr` is becoming more and more used in spectroscopic applications, which 
is evidenced by the number of scientific publications citing the package. 
This package is very useful for signal processing and chemometrics in general as 
it provides various utilities for pre--processing and sample selection 
of spectral data. While similar functions are available in other packages, like 
[`signal`](https://CRAN.R-project.org/package=signal), the 
functions in this package works indifferently for `data.frame`, `matrix` and 
`vector` inputs. Besides, several functions are optimized for speed and use 
C++ code through the [`Rcpp`](https://CRAN.R-project.org/package=Rcpp) 
and [`RcppArmadillo`](https://CRAN.R-project.org/package=RcppArmadillo)
packages.

## Installing it from GitHub

Install this package from github by:

```
remotes::install_github("l-ramirez-lopez/prospectr")
```
NOTE: in some MAC Os it is still recommended to install `gfortran` and `clang`
from [here](https://cran.r-project.org/bin/macosx/tools/). Even for R >= 4.0. 
For more info, check this [issue](https://github.com/tidyverts/fable/issues/193).  


## News

Check the NEWS document for new functionality and general changes in the package.


## Vignette

A vignette for `prospectr` explaining its core functionality is available at [https://CRAN.R-project.org/package=prospectr/vignettes/prospectr.html](https://CRAN.R-project.org/package=prospectr/vignettes/prospectr.html).


## Core functionality

A vignette gives an overview of the main functions of the package. Just
type `vignette("prospectr-intro")` in the console to access it. Currently, the
following preprocessing functions are available:

- `resample()`              : resample a signal to new coordinates by linear or spline interpolation

- `resample2()`             : resample a signal to new coordinates using FWHM values

- `movav()`                 : moving average

- `standardNormalVariate()` : standard normal variate

- `msc()`                   : multiplicative scatter correction

- `detrend()`               : detrend normalization

- `baseline()`              : baseline removal/correction

- `blockScale()`            : block scaling

- `blockNorm()`             : sum of squares block weighting

- `binning()`               : average in column--wise subsets

- `savitzkyGolay()`         : Savitzky-Golay filter (smoothing and derivatives)                      

- `gapDer()`                : gap-segment derivative

- `continuumRemoval()`      : continuum-removed absorbance or reflectance values

The selection of representative samples/observations for calibration of spectral
models can be achieved with one of the following functions:

- `naes()`      : k-means sampling

- `kenStone()`  : CADEX (Kennard--Stone) algorithm

- `duplex()`    : DUPLEX algorithm

- `shenkWest()` : SELECT algorithm

- `puchwein()`  : Puchwein sampling

- `honigs()`    : Unique-sample selection by spectral subtraction

Other useful functions are also available:


- `read_nircal()`      : read binary files exported from BUCHI NIRCal software

- `readASD()`          : read binary or text files from an ASD instrument (Indico Pro format)         

- `spliceCorrection()` : correct spectra for steps at the splice of detectors in an ASD FieldSpec Pro

- `cochranTest()`      : detects replicate outliers with the Cochran _C_ test

## Citing the package
Antoine Stevens and Leornardo Ramirez-Lopez (2025). An introduction to the prospectr package. R package
Vignette R package version 0.2.8.
A BibTeX entry for LaTeX users is:

```
 @Manual{stevens2022prospectr,
    title = {An introduction to the prospectr package},
    author = {Antoine Stevens and Leornardo Ramirez-Lopez},
    publication = {R package Vignette},
    year = {2025},
    note = {R package version 0.2.8},
  }
```
## Bug report and development version

You can send an email to the package maintainer () 
or create an [issue](https://github.com/l-ramirez-lopez/prospectr/issues) on github.
To install the development version of `prospectr`, simply install [`devtools`](https://CRAN.R-project.org/package=devtools) from
CRAN then run `install_github("l-ramirez-lopez/prospectr")`.

Owner

  • Name: Leonardo Ramirez-Lopez
  • Login: l-ramirez-lopez
  • Kind: user
  • Location: Switzerland
  • Company: BUCHI Labortechnik AG

Social coding ☆ Favourite colour: infrared

GitHub Events

Total
  • Create event: 3
  • Release event: 1
  • Issues event: 2
  • Watch event: 4
  • Push event: 14
  • Pull request review event: 4
  • Pull request event: 12
  • Fork event: 4
Last Year
  • Create event: 3
  • Release event: 1
  • Issues event: 2
  • Watch event: 4
  • Push event: 14
  • Pull request review event: 4
  • Pull request event: 12
  • Fork event: 4

Committers

Last synced: over 1 year ago

All Time
  • Total Commits: 598
  • Total Committers: 12
  • Avg Commits per committer: 49.833
  • Development Distribution Score (DDS): 0.156
Past Year
  • Commits: 13
  • Committers: 2
  • Avg Commits per committer: 6.5
  • Development Distribution Score (DDS): 0.077
Top Committers
Name Email Commits
Leonardo Ramirez-Lopez r****o@g****m 505
antoinestevens a****s@u****e 48
antoinestevens a****s@h****m 18
l-ramirez-lopez l****3@i****k 12
Philipp Baumann b****p@p****e 6
Kirill Müller k****r@m****g 2
Ramirez-Lopez Leonardo r****l@b****m 2
Guillaume Hans g****s@h****m 1
Leonardo Ramirez-Lopez l****z@w****h 1
Matt m****0@g****m 1
Ramirez-Lopez Leonardo R****L@b****m 1
antoinestevens a****s@g****m 1
Committer Domains (Top 20 + Academic)
buchi.com: 2 wsl.ch: 1 mailbox.org: 1 proton.me: 1 imperial.ac.uk: 1 uclouvain.be: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 24
  • Total pull requests: 54
  • Average time to close issues: about 1 month
  • Average time to close pull requests: 7 days
  • Total issue authors: 10
  • Total pull request authors: 7
  • Average comments per issue: 1.38
  • Average comments per pull request: 0.2
  • Merged pull requests: 52
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 3
  • Pull requests: 7
  • Average time to close issues: N/A
  • Average time to close pull requests: 3 days
  • Issue authors: 3
  • Pull request authors: 3
  • Average comments per issue: 0.67
  • Average comments per pull request: 0.0
  • Merged pull requests: 6
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • l-ramirez-lopez (12)
  • philipp-baumann (2)
  • zecojls (2)
  • aloboa (2)
  • AgroSimi (1)
  • ncudlenco (1)
  • sdroldan (1)
  • georgejr45 (1)
  • soottikkal (1)
  • A-Pai (1)
Pull Request Authors
  • l-ramirez-lopez (56)
  • orellano-c (4)
  • skylogic004 (2)
  • krlmlr (2)
  • philipp-baumann (1)
  • pbulsink (1)
  • guifh (1)
Top Labels
Issue Labels
bug (2) help wanted (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 1,054 last-month
  • Total docker downloads: 21,777
  • Total dependent packages: 3
  • Total dependent repositories: 9
  • Total versions: 12
  • Total maintainers: 1
cran.r-project.org: prospectr

Miscellaneous Functions for Processing and Sample Selection of Spectroscopic Data

  • Versions: 12
  • Dependent Packages: 3
  • Dependent Repositories: 9
  • Downloads: 1,054 Last month
  • Docker Downloads: 21,777
Rankings
Docker downloads count: 1.2%
Forks count: 4.6%
Average: 7.8%
Stargazers count: 8.9%
Dependent repos count: 9.9%
Dependent packages count: 10.6%
Downloads: 11.3%
Maintainers (1)
ramirez.lopez.leo@gmail.com
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.5.0 depends
  • Rcpp >= 1.0.1 imports
  • foreach * imports
  • iterators * imports
  • lifecycle >= 0.2.0 imports
  • mathjaxr >= 1.0 imports
  • bookdown * suggests
  • formatR * suggests
  • knitr * suggests
  • rmarkdown * suggests
  • testthat * suggests