Articles by R on Chemometrics & Spectroscopy using R

Simulating Spectroscopic Data Part 1

June 27, 2020 | 0 Comments

It is well-recognized that one of the virtues of the R language is the extensive tools it provides for working with distributions. Functions exist to generate random number draws, determine quantiles, and examine the probability density and cumulative distribution curves that describe each distribution. This toolbox gives one the ability ...
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Fortifying hyperSpec: Getting Ready for GSOC

May 6, 2020 | 0 Comments

hyperSpec is an R package for working with hyperspectral data sets. Hyperspectral data can take many forms, but a common application is a series of spectra collected over an x, y grid, for instance Raman imaging of medical specimens. hyperSpec was ... [Read more...]

ChemoSpecUtils Update

April 26, 2020 | 0 Comments

ChemoSpecUtils, a package that supports the common needs of ChemoSpec and ChemoSpec2D, has been updated to fix an unfortunate distance calculation error in version 0.4.38, released in January of this year. From the NEWS file for version 0.4.51: Fu... [Read more...]

Spectral Heatmaps

April 24, 2020 | 0 Comments

Most everyone is familiar with heatmaps in a general way. It’s hard not to run into them. Let’s consider some variations: A heatmap is a 2D array of rectangular cells colored by value. Generally, the rows and columns are ordered in some purposeful manner. These are very commonly ...
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Aligning 2D NMR Spectra Part 3

March 3, 2020 | 0 Comments

This is Part 3 of a series on aligning 2D NMR, as implemented in the package ChemoSpec2D. Part 1 Part2 Let’s get to work. The function to carry out alignment is hats_alignSpectra2D. The arguments maxF1 and maxF2 define the space that will be considered as the two spectra ...
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Aligning 2D NMR Spectra Part 2

March 1, 2020 | 0 Comments

This is Part 2 of a series on aligning 2D NMR, as implemented in the package ChemoSpec2D. Part 1. The HATS-PR Algorithm In Part 1 I briefly mentioned that we would be using the HATS-PR algorithm of Robinette et al. (Robinette et al. 2011). I also discussed the choice of objective function which ... [Read more...]

Aligning 2D NMR Spectra Part 1

February 19, 2020 | 0 Comments

In one-dimensional \(^1\)H NMR spectroscopy, particularly biomolecular NMR, it is frequently necessary to align spectra before chemometric or metabolomics analysis. Poor alignment arises largely from pH and ionic strength induced shifts in aqueous samples. There are a number of published alignment algorithms for the one-dimensional case. In this series of ...
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ChemoSpec2D Update

February 18, 2020 | 0 Comments

I’m pleased to announce that ChemoSpec2D, a package for exploratory data analysis of 2D NMR spectra, has been updated on CRAN and is coming to a mirror near you. Barring user reports to the contrary, I feel like the package has pretty much stabil... [Read more...]

Exploring Github Topics

January 24, 2020 | 0 Comments

As the code driving FOSS for Spectroscopy has matured, I began to think about how to explore Github in a systematic way for additional repositories with tools for spectroscopy. It turns out that a Github repo can have topics assigned to it, and you can use the Github API to ...
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ChemoSpec Update

January 23, 2020 | 0 Comments

ChemoSpec has just been updated to version 5.2.12, and should be available on the mirrors shortly. The most significant user-facing changes are actually in the update to ChemoSpecUtils from a few days ago. In addition, the following documentation c... [Read more...]

ChemoSpecUtils Update

January 21, 2020 | 0 Comments

ChemoSpecUtils, a package that supports the common needs of ChemoSpec and ChemoSpec2D, has been updated on CRAN and is coming to a mirror near you. Noteworthy changes: There are new color options available in addition to the auto color scheme used...
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FOSS for Spectroscopy Update

January 21, 2020 | 0 Comments

FOSS for Spectroscopy has had a significant update! It’s really quite surprising how many projects are out there. There is a lot of variety and not too much overlap. After a lot of wrestling with Github access issues, the Status column in the ta... [Read more...]

readJDX Overhaul

January 1, 2020 | 0 Comments

readJDX reads files in the JCAMP-DX format used in the field of spectroscopy. A recent overhaul has made it much more robust, and as such the version is now at 0.4.29.1 Most of the changes were internal, but three important user-facing changes are:... [Read more...]

FOSS for Spectroscopy

December 31, 2019 | 0 Comments

For this inaugural blog post, I’m pleased to share a project I have been working on recently: FOSS4Spectroscopy is an attempt to catalog FOSS spectroscopy software. The page is designed to be updated easily with new or edited entries – see the ... [Read more...]

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