GCDkit.Mineral – a customizable, platform-independent R-language environment for recalculation, plotting and classification of electron-probe micro-analyses of common rock-forming minerals

Abstract

GCDkit.Mineral is a platform-independent (Windows/Mac/Linux) freeware for recalculation, plotting and statistical treatment of mineral data obtained by microbeam techniques, typically an electron microprobe. It is written in R, a language providing a feature-rich environment for statistics and data visualization.This new program imports compositional data in a variety of commonly used file formats, or retrieves them from the clipboard. Routines are available for data management, i.e. grouping, searching, and generation of subsets, using regular expressions and Boolean logic. Raw compositional data (wt.%) are recalculated to atoms per formula unit (apfu) based on a required number of O equivalents, atoms or charges, with or without, Fe II /Fe III estimation by a variety of methods. Analyses may then be recast to structural formulae; i.e. the atoms are distributed into appropriate crystallographic sites. For minerals forming solid solutions, the molar percentages of end members are computed. All the data may be treated statistically, either by built-in functions for descriptive and multivariate statistics, or using the wealth of tools provided by the wide R community.Raw and recalculated mineral data may be plotted on assorted binary and ternary plots, and boxplots. Most are defined as internal templates that provide a means to make later changes to the plot (zooming and scaling, adding comments or legend, identifying data points, altering the size or color of the plotting symbols, etc.). The publication-ready graphics may be saved into a number of vector-(PostScript, PDF and WMF) and bitmap-based (e.g., PNG, TIF and JPG) formats, ready to be imported into a professional graphical, presentation, or desktop publishing software.Importantly, the graphical templates are used as a basis for classification. The general classification routine looks for the name of the polygon within the diagram (= graphical template), into which the analysis falls according to its x-y coordinates. The outcome may be This is the peer-reviewed, final accepted version for American Mineralogist, published by the Mineralogical Society of America.The published version is subject to change. Cite as Authors (Year) Title. American Mineralogist, in press.