Journal of Petrology Advance Access originally published online on March 22, 2006
Journal of Petrology 2006 47(6):1255-1259; doi:10.1093/petrology/egl013
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TECHNICAL NOTE |
Interpretation of Whole-rock Geochemical Data in Igneous Geochemistry: Introducing Geochemical Data Toolkit (GCDkit)
CH JANOU
EK1,2,*CH ERBAN1
1 CZECH GEOLOGICAL SURVEY, KLÁROV 3/131, 118 21 PRAGUE 1, CZECH REPUBLIC
2 INSTITUTE OF PETROLOGY AND STRUCTURAL GEOLOGY, CHARLES UNIVERSITY, ALBERTOV 6, 128 43 PRAGUE 2, CZECH REPUBLIC
3 UNIVERSITY OF GLASGOW COMPUTING SERVICE, GLASGOW G12 8QQ, UK
RECEIVED NOVEMBER 3, 2004; ACCEPTED FEBRUARY 16, 2006
ABSTRACT
Geochemical Data Toolkit (GCDkit) is a program for handling and recalculation of geochemical data from igneous and metamorphic rocks. It is built using the Windows version of R, which provides a flexible and comprehensive language and environment for data analysis and graphics. GCDkit was designed to eliminate routine and tedious operations involving large collections of whole-rock data and, at the same time, provide access to the wealth of statistical functions built into R. Data management tools include import and export of data files in a number of formats, data editing, searching, grouping and generation of subsets. Included are a variety of calculation and normative schemes, for instance CIPW and Mesonorm, as are the common geochemical graphs (e.g. binary and ternary graphs, Harker plots, spider plots, and several dozens of classification and geotectonic discrimination diagrams). The graphical output is publication ready but can be further retouched if required. The system can be further expanded by means of plug-in modules that provide specialist applications. GCDkit is available as Free Software under the terms of the Free Software Foundation's GNU General Public License and can be downloaded from http://www.gla.ac.uk/gcdkit. The product is actively maintained and updated to provide additional functionality; Unix/Linux and Mac OS versions are being developed.
KEY WORDS: igneous rocks; geochemistry; norms; graphs; software; MS Windows; R language
INTRODUCTION
The challenge: geochemical recalculations and plotting
The need to quantify aspects of the world in which we live is inherent in contemporary scientific thinking. Such an approach leads inevitably to a flood of numerical data, which have to be analysed by an appropriate software tool.
The interpretation of whole-rock geochemical data is not different, as it requires complex and time-consuming calculations, which on PC compatible computers are mainly performed using dedicated, stand-alone programs (e.g. NewPet—Clarke et al., 1994
; IgPet—Carr, 1995; MinPet—Richard, 1995; PetroGraph—Petrelli et al., 2005). An alternative preferred by many researchers are spreadsheets, sometimes aided by special macros (Sidder, 1994; Su et al., 2003). Most of these otherwise useful programs are, however, not well suited to management and interpretation of larger datasets. In addition, the usability of many of these tools is hindered by the fact that it is often difficult to determine exactly which algorithm has been employed, because documentation is not detailed enough and it is not a common practice to make the source code available. Even if it is, any modifications or additions to the original program can be tedious, or impossible for legal reasons. Concerning spreadsheets, they have low efficiency for repeated tasks, poor quality of graphic output, as well as limited protection of the primary data. For more complicated calculations the worksheet soon becomes too complex and prone to errors.
The solution: Geochemical Data Toolkit (GCDkit)
To address the major drawbacks of the existing geochemical software, we have developed a new package called Geochemical Data Toolkit for R (GCDkit). GCDkit is a program for management and recalculation of whole-rock geochemical data for igneous and metamorphic rocks. It is built using the open-source (freeware) R language, version for Windows, which in itself provides a flexible and comprehensive environment for efficient data processing, visualization and statistical analysis (Ihaka & Gentleman, 1996; Grunsky, 2002; R Development Core Team, 2005).
GCDkit provides:
- a graphical user interface aiding the user with pull-down menus and dialogue boxes (Fig. 1);
- user-friendly front-end to the powerful statistical and graphical functions of R;
- core routines for effortless import, modification, searching, subsetting, classification and output of the geochemical data;
- calculation and plotting tools designed specifically for igneous geochemists;
- flexible and high-level graphical functions with an output into widely used graphical formats;
- no licensing problems, as it is distributed free via the WWW.
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PROGRAM DESCRIPTION
Data management
The main area of application for GCDkit is the interpretation of larger datasets. Accordingly, great emphasis has been put on data management tools (loading and saving data files, data editing, together with searching and generation of subsets).
GCDkit can read plain text files, including the variants represented by the NewPet (*.ROC) and PetroGraph (*.PEG) files as well as the outputs from WWW-based databases such as GEOROC (http://georoc.mpch-mainz.gwdg.de/georoc) and PETDB (http://www.petdb.org). Data can be imported from Microsoft Excel (*.XLS), Access (*.MDB), or dBase (*.DBF) formats, the latter being the native format for IgPet (Carr, 1995) or MinPet (Richard, 1995) packages. As an alternative, the data can be pasted, via the clipboard, from any Windows-based software, including popular spreadsheets. In any case the data are freeform, which means that the columns can be given in an arbitrary order and missing values are allowed.
Grouping of data is a key part of data management, controlling the output of calculations and the graphical routines. Analyses may be grouped on the basis of various criteria including sample attributes, so-called labels (locality, rock type, etc.), numerical variable, cluster analysis or selected classification diagram (e.g. total alkali–silica). For greatest flexibility queries may be logically combined, allowing, for example, selection based on rock type and contents of particular elements. Interactive selection from classification diagrams is also supported.
Calculations
New variables can be calculated by mathematical expressions including constants, brackets, arithmetic operators and the whole spectrum of R functions. Statistical functions include descriptive statistics, box-and-whiskers and correlation plots or multivariate methods. Also implemented are a variety of calculation schemes used in igneous geochemistry, for instance CIPW norm, Catanorm, Niggli's cationic values, multicationic parameters of De La Roche et al. (1980) and Debon & Le Fort (1983), and improved Mesonorm for granitoid rocks (Mielke & Winkler, 1979). Given major-element analyses of a rock and its main mineral constituents, the best approximation of the modal composition, using either unconstrained or constrained least-squares methods (Albarède, 1995), may be calculated.
The results of all calculations can be appended to the current dataset for further processing (e.g. CIPW-normative albite, quartz and orthoclase to be plotted on a Ab–Qz–Or ternary diagram) or copied to a clipboard, saved or exported to HTML, DBF, XLS, MDB or text files.
Plotting
The main strength of GCDkit is arguably the wealth of built-in publication-quality plots that can be exported into a number of data formats (including PostScript, WMF, JPG, PNG and BMP). The available graphs involve user-defined binary, ternary and multiple binary diagrams (such as Harker plots) as well as a wide palette of classification and geotectonic discrimination diagrams. Three variables can be displayed in pseudo three-dimensional plots, or on binary diagrams in which the size and colour of the plotted symbols correspond to the third variable (Fig. 2a).
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Nd values (y-axis).All plots are publication ready but most can be customized with the included plot editing facilities. The system permits zooming and scaling of the diagrams, editing of the text, font, size and colour of the titles and axis labels, and of the colour, size and symbol for the data points, together with colour, type and width of the lines. Moreover, there is a function for interactive labelling of individual analyses (typically by sample names but other labels can be specified). The graph templates can be used also as a basis for classification. Put simply, the classification algorithm looks for the name of the polygon within the diagram, into which the rock analysis falls according to its x–y coordinates.
GCDkit offers normalization of trace-element data by any chosen standard and the ability to generate normalized multielement diagrams, otherwise called ‘spider plots’. One special feature are the ‘spider boxplots’, in which no individual patterns are drawn. Instead, the statistical distribution of each element is portrayed by a box-and-whiskers plot of normalized concentrations (Fig. 2b). The standard compositions used for normalization can be readily edited and new schemes added. For visualization of larger datasets there are contour and frequency plots (Fig. 2c).
Expandability
The open architecture and simplicity mean that users will readily be able to further enhance the capabilities of the system, by modifying existing functions or creating new ones. The system incorporates a plug-in mechanism whereby new calculation or plotting code is automatically loaded and made accessible through the menu system.
Included with the current version are plug-in modules to calculate saturation temperatures of accessory minerals (Janou
ek, 2006) as well as for interpretation of Sr–Nd isotopic data (Fig. 2d).
CONCLUDING REMARKS
GCDkit will run on any IBM PC compatible computer with Windows 98/ME/2000/NT/XP (but latest versions are strongly recommended). The program with corresponding documentation is available free of charge at http://www.gla.ac.uk/gcdkit and is easy to install.
Our mission is to develop and release a platform-independent system, for Windows, Unix/Linux and Macintosh (System X). In the shorter-term perspective, new plug-ins for direct and inverse modelling of major petrogenetic processes in igneous geochemistry are under development.
The whole system, which is modular and straightforward to modify, provides a practical solution to the needs of petrologists and geochemists. If current modules do not meet requirements, or new techniques evolve, it is hoped that the open source availability of the code will encourage its onward development by users. In this context any feedback (bug reports, suggestions for further development, and pieces of contributed code or even ready plug-ins) would be highly appreciated.
ACKNOWLEDGEMENTS
We are indebted to Jakub míd for much of the ternary plotting function, the Core Team and the whole community for their sterling efforts in continuous developing of R—GCDkit is often merely an interface to their functions. Thanks are specifically due to Friedrich Leisch (Technische Universität Wien) and Duncan Murdoch (University of Western Ontario) for their invaluable advice. Last but not least, we thank beta testers (in particular Pavel Han
l and Bernhard Humer) for their courage and patience, and the students in Prague, Brno and Salzburg for asking nasty questions. This paper and the program itself has benefited from extensive testing, detailed comments and words of encouragement of J.-F. Moyen. Also, the reviews by R. Giere, D. Geist and T. Barry have helped us to improve aspects of the software. Most of the coding of GCDkit originated during the research stay of V.J. at the Institute of Mineralogy, University of Salzburg, in the framework of the FWF Project 15133-GEO (to Fritz Finger). Support from the Czech Grant Agency (Postdoctoral Grant 205/97/P113) and the Czech Geological Survey (Internal Project 3314) is gratefully acknowledged.
* Corresponding author. Telephone +420 251085308. Fax: +420 251818748. E-mail: janousek{at}cgu.cz
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