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ChemoSpec - Exploratory Chemometrics for Spectroscopy

A collection of functions for top-down exploratory data analysis of spectral data including nuclear magnetic resonance (NMR), infrared (IR), Raman, X-ray fluorescence (XRF) and other similar types of spectroscopy. Includes functions for plotting and inspecting spectra, peak alignment, hierarchical cluster analysis (HCA), principal components analysis (PCA) and model-based clustering. Robust methods appropriate for this type of high-dimensional data are available. ChemoSpec is designed for structured experiments, such as metabolomics investigations, where the samples fall into treatment and control groups. Graphical output is formatted consistently for publication quality plots. ChemoSpec is intended to be very user friendly and to help you get usable results quickly. A vignette covering typical operations is available.

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infrarednmrramanspectroscopyultravioletvisiblexrf

7.27 score 65 stars 50 scripts 1.1k downloads

HiveR - 2D and 3D Hive Plots for R

Creates and plots 2D and 3D hive plots. Hive plots are a unique method of displaying networks of many types in which node properties are mapped to axes using meaningful properties rather than being arbitrarily positioned. The hive plot concept was invented by Martin Krzywinski at the Genome Science Center (www.hiveplot.net/). Keywords: networks, food webs, linnet, systems biology, bioinformatics.

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6.84 score 75 stars 2 dependents 62 scripts 673 downloads

readJDX - Import Data in the JCAMP-DX Format

Import data written in the JCAMP-DX format. This is an instrument-independent format used in the field of spectroscopy. Examples include IR, NMR, and Raman spectroscopy. See the vignette for background and supported formats. The official JCAMP-DX site is <http://www.jcamp-dx.org/>.

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jcamp-dx-formatspectroscopy

6.48 score 8 stars 5 dependents 8 scripts 828 downloads

LearnPCA - Functions, Data Sets and Vignettes to Aid in Learning Principal Components Analysis (PCA)

Principal component analysis (PCA) is one of the most widely used data analysis techniques. This package provides a series of vignettes explaining PCA starting from basic concepts. The primary purpose is to serve as a self-study resource for anyone wishing to understand PCA better. A few convenience functions are provided as well.

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6.05 score 14 stars 456 downloads

ChemoSpec2D - Exploratory Chemometrics for 2D Spectroscopy

A collection of functions for exploratory chemometrics of 2D spectroscopic data sets such as COSY (correlated spectroscopy) and HSQC (heteronuclear single quantum coherence) 2D NMR (nuclear magnetic resonance) spectra. 'ChemoSpec2D' deploys methods aimed primarily at classification of samples and the identification of spectral features which are important in distinguishing samples from each other. Each 2D spectrum (a matrix) is treated as the unit of observation, and thus the physical sample in the spectrometer corresponds to the sample from a statistical perspective. In addition to chemometric tools, a few tools are provided for plotting 2D spectra, but these are not intended to replace the functionality typically available on the spectrometer. 'ChemoSpec2D' takes many of its cues from 'ChemoSpec' and tries to create consistent graphical output and to be very user friendly.

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2d-spectranmrspectroscopy

4.34 score 4 stars 11 scripts 583 downloads

ChemoSpecUtils - Functions Supporting Packages ChemoSpec and ChemoSpec2D

Functions supporting the common needs of packages 'ChemoSpec' and 'ChemoSpec2D'.

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4.31 score 4 stars 2 dependents 17 scripts 668 downloads

roxut - Document Unit Tests Roxygen-Style

Much as 'roxygen2' allows one to document functions in the same file as the function itself, 'roxut' allows one to write the unit tests in the same file as the function. Once processed, the unit tests are moved to the appropriate directory. Currently supports 'testthat' and 'tinytest' frameworks. The 'roxygen2' package provides much of the infrastructure.

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3.60 score 8 stars 411 downloads

LindenmayeR - Functions to Explore L-Systems (Lindenmayer Systems)

L-systems or Lindenmayer systems are parallel rewriting systems which can be used to simulate biological forms and certain kinds of fractals. Briefly, in an L-system a series of symbols in a string are replaced iteratively according to rules to give a more complex string. Eventually, the symbols are translated into turtle graphics for plotting. Wikipedia has a very good introduction: en.wikipedia.org/wiki/L-system This package provides basic functions for exploring L-systems.

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3.60 score 8 stars 6 scripts 262 downloads

exCon - Interactive Exploration of Contour Data

Interactive tools to explore topographic-like data sets. Such data sets take the form of a matrix in which the rows and columns provide location/frequency information, and the matrix elements contain altitude/response information. Such data is found in cartography, 2D spectroscopy and chemometrics. The functions in this package create interactive web pages showing the contoured data, possibly with slices from the original matrix parallel to each dimension. The interactive behavior is created using the 'D3.js' 'JavaScript' library by Mike Bostock.

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3.30 score 4 stars 1 scripts 307 downloads

SpecHelpers - Spectroscopy Related Utilities

Utility functions for spectroscopy. 1. Functions to simulate spectra for use in teaching or testing. 2. Functions to process files created by 'LoggerPro' and 'SpectraSuite' software.

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3.22 score 3 stars 11 scripts 302 downloads