Tuesday, 27 October 2015

Book on geochemical modelling of magmatic processes in R/GCDkit

We break the two years of our silence with some news potentially interesting to anyone involved in interpretation of whole-rock geochemical data from igneous rocks. We are pleased to announce that, after two years of intense writing, we have finally published a book:

JanouĊĦek, V., Moyen, J. F., Martin, H., Erban, V. & Farrow, C. M. (2016). Geochemical Modelling of Igneous Processes – Principles and Recipes in R Language. Bringing the Power of R to a Geochemical Community. Springer-Verlag, Berlin, Heidelberg, 346 pp. 


 Abstract from the publisher:
"The aim of this book is to unlock the power of the freeware R language to advanced university students and researchers dealing with whole-rock geochemistry of (meta-) igneous rocks. The first part covers data input/output, calculation of commonly used indexes and plotting in R. The core of the book then focuses on the presentation and practical implementations of modelling techniques used for fingerprinting processes such as partial melting, fractional crystallization, binary mixing or AFC using major-, trace-element and radiogenic isotope data. The reader will be given a firm theoretical basis for forward/reverse modelling, followed by exercises dealing with typical problems likely to be encountered in real life, and their solutions using R. The concluding sections GCDkit for interpretation of whole-rock geochemical data from igneous and metamorphic rocks."
demonstrate, using practical examples, how a researcher can proceed in developing a realistic model simulating natural systems. The appendices outline the fundamentals of the R language and provide a quick introduction to the open-source R-package
In more simple words, this book:
  • Provides basics of R language and its application to geochemical problems,
  • Gives the first comprehensive introduction to the GCDkit system,
  • Explains fundamentals of numerical modelling of igneous processes,
  • Shows not only formulae, but also the successful modelling strategies,
  • Includes numerous worked examples how geochemical modelling helps us to understand geological problems.
And its contents are in the nutshell:

Part I: R/GCDkit at work

  • Loading and Manipulating Data
  • Linking Whole-Rock Chemistry with Mineral Stoichiometry
  • Statistics
  • Classification and Grouping
  • Classical Plots
    (binary, Harker, ternary, spider)
  • Specialized Plots
    (log–log, specialized spiderplots, contour plots, anomaly plots…)
  • Radiogenic Isotopes
    (initial ratios, epsilon values, model ages, isochrons…)

Parts II–IV: Majors, traces, radiogenic isotopes

  • Core of the book; explains fundamentals of each direct and reverse modelling, including the relevant formulae
  • Introduces the numerical solution and its implementation in the R language
  • Includes a number of real numerical problems
  • Each is presented as a numerical receipt with solution in R  (± GCDkit )

Part V: Practical Modelling

  • Choosing an Appropriate Model
    (evidence for crystallization, partial melting, magma mixing and assimilation…)
  • Semi-Quantitative Approach
    (assessing the trace-element compatibility, process identification, mixing test…)
  • Constraining a Model
    (using appropriate strategy, obtaining input parameters for the model, partition coefficients, dealing with accessories…)
  • Numerical Tips and Tricks
    (reducing system, colinearity, breaking minerals to end-members, coupling majors and traces…)
  • Common Sense in Action
    (thermodynamic, rheological  constraints, scale and speed of processes, how well can we distinguish between models, dangerous projections…)

Part VI: Worked Examples

  • Differentiation of a Calc-Alkaline Series: Atacazo-Ninahuilca volcanoes, Ecuador
  • Progressive Melting of a Metasedimentary Sequence: the Saint-Malo Migmatitic Complex, France
  • Appendix A: R Syntax in a Nutshell
  • Appendix B: Introduction to GCDkit
  • Appendix C: Solving Systems of Linear Algebraic Equations in R
Courtesy of the publisher, the Appendices explaining the R syntax and the workings of the GCDkit system, are freely available here.
The book can be purchased directly from Springer, either as a hardback (for ca. 85 EUR) or as an e-book (ca. 70 EUR). Alternatively, it can be ordered for instance via Amazon

The datasets, code and further supplementary material is available from book.gcdkit.org.

Please let us know, what do you think about this publication, especially if you spot some errors. Enjoy!

Vojtech (on behalf of all the authors)



2 comments:

  1. For a review by Prof. Hugh Rollinson, see Elements 3/2016:
    http://www.elementsmagazine.org/archives/e12_3/e12_3_dep_bookreview.pdf

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