Publications by R on Chemometrics & Spectroscopy using R
Spectral Heatmaps
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 encountered in microarrays for example. An image is a type of h...
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ChemoSpecUtils Update
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: Function rowDist, which supports a number of functions, was overhauled to address confusion in the doc...
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Fortifying hyperSpec: Getting Ready for GSOC
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 originally written by Claudia Beleites and she currently guides a core group of contributors.1 Claud...
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Simulating Spectroscopic Data Part 1
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 to creat...
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GSOC Wrap Up
Well, things have been busy lately! As reported back in May, I’ve been participating in Google Summer of Code which has now wrapped up. This was very rewarding for me, but today I want to share a guest post by Erick Oduniyi, the very talented student on the project. Bryan Checking in from Kansas! This past summer (2020) I had the amazing oppor...
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Interfacing ChemoSpec to PLS
The ChemoSpec package carries out exploratory data analysis (EDA) on spectroscopic data. EDA is often described as “letting that data speak”, meaning that one studies various descriptive plots, carries out clustering (HCA) as well as dimension reduction (e.g. PCA), with the ultimate goal of finding any natural structure in the data. As such,...
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Spectroscopy Suite Update
My suite of spectroscopy R packages has been updated on CRAN. There are only a few small changes, but they will be important to some of you: ChemoSpecUtils now provides a set of colorblind-friendly colors, see ?colorSymbol. These are available for use in ChemoSpec and ChemoSpec2D. At the request of several folks, readJDX now includes a function,...
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Using Github Actions & drat to Deploy R Packages
Last summer, a GSOC project was approved for work on the hyperSpec package which had grown quite large and hard to maintain.1 The essence of the project was to break the original hyperSpec package into smaller packages.2 As part of that project, we needed to be able to: Provide development versions of packages Provide large data-only packages (p...
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Automatically Searching Github Repos by Topic
One of the projects I maintain is the FOSS for Spectroscopy web site. The table at that site lists various software for use in spectroscopy. Historically, I have used the Github or Python Package Index search engines to manually search by topic such as “NMR” to find repositories of interest. Recently, I decided to try to automate at least som...
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GSOC 2021: hyperSpec and ChemoSpec!
I’m really happy to announce that this summer I’ll be a co-mentor on two Google Summer of Code spectroscopy projects: Once again, I’ll co-mentor with Claudia and Vilmantas to continue the work Erick started last summer on hyperSpec (see here for Erick’s wrap up blog post at the end of last year). Sang Truong is the very talented student ...
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