Publications by R on Chemometrics & Spectroscopy using R
FOSS for Spectroscopy
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 page for details, and please contribute! For this initial version, I searched the CRAN ecosystem via...
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readJDX Overhaul
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: improved documentation the addition of more vignettes improved output when debug > 0 2D NMR files ...
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ChemoSpecUtils Update
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 during data importing. These should be useful to normal-vision individuals when there are a lot of ...
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FOSS for Spectroscopy Update
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 table now gives the date of the most recent update to the project that I can find in an automated way....
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ChemoSpec Update
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 changes were made: Added documentation for updateGroups which has been in ChemoSpecUtils for a while...
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Exploring Github Topics
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 search them. Wait, what? I didn’t know one could add topics to a repo, ...
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ChemoSpec2D Update
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 stabilized and is pretty robust. The main area for future expansion is to add additional data import routi...
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Aligning 2D NMR Spectra Part 1
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...
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Aligning 2D NMR Spectra Part 2
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 is used to report on the quality of the alignment. ...
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Aligning 2D NMR Spectra Part 3
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 are shifted relative to each other. The space potentially covered is -maxF...
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