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Geochemical Modelling of Igneous Processes Principles And Recipes in R Language: Bringing the Power of R to a Geochemical Community Softcover reprint of the original 1st ed. 2016 [Pehme köide]

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  • Formaat: Paperback / softback, 346 pages, kõrgus x laius: 235x155 mm, kaal: 5679 g, 86 Illustrations, color; 246 Illustrations, black and white; XXVIII, 346 p. 332 illus., 86 illus. in color., 1 Paperback / softback
  • Sari: Springer Geochemistry
  • Ilmumisaeg: 29-Oct-2016
  • Kirjastus: Springer-Verlag Berlin and Heidelberg GmbH & Co. K
  • ISBN-10: 366251687X
  • ISBN-13: 9783662516874
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Geochemical Modelling of Igneous Processes Principles And Recipes in R Language: Bringing the Power of R to a Geochemical Community Softcover reprint of the original 1st ed. 2016Suurem pilt
  • Formaat: Paperback / softback, 346 pages, kõrgus x laius: 235x155 mm, kaal: 5679 g, 86 Illustrations, color; 246 Illustrations, black and white; XXVIII, 346 p. 332 illus., 86 illus. in color., 1 Paperback / softback
  • Sari: Springer Geochemistry
  • Ilmumisaeg: 29-Oct-2016
  • Kirjastus: Springer-Verlag Berlin and Heidelberg GmbH & Co. K
  • ISBN-10: 366251687X
  • ISBN-13: 9783662516874
Teised raamatud teemal:
Püsilink: https://www.kriso.ee/db/9783662516874.html
Märksõnad:

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 focusses 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 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 GCDkit for interpretation of whole-rock geochemical data from igneous and metamorphic rocks.

Arvustused

It is a textbook which discusses the theory of geochemical modelling as applied to whole-rock major and trace element data and to radiogenic isotopes . A starting graduate student in geochemistry would benefit from spending time with this book. It is well produced, the text is clear and the coding sections are printed in a different font for clarity, it is well illustrated with excellent diagrams, some of which are in colour, and each chapter is thoroughly referenced. (Hugh Rollinson, Elements, elementsmagazine.org, June, 2016)

1 Introduction
1(10)
1.1 Causes of Whole-Rock Chemical Variation in Igneous Suites
1(2)
1.2 Conventional Software for Igneous Geochemistry
3(1)
1.2.1 Spreadsheets
3(1)
1.2.2 Dedicated Programs (PC Compatibles)
4(1)
1.3 A Revolution? The R Language
4(2)
1.3.1 What is R?
4(1)
1.3.2 Geochemical Data Toolkit (GCDkit)
5(1)
References
6(5)
Part I R/GCDkit at Work
2 Data Manipulation and Simple Calculations
11(16)
2.1 Loading and Manipulating Data
11(2)
2.2 Linking Whole-Rock Chemistry with Mineral Stoichiometry
13(5)
2.2.1 Basic Indexes
14(2)
2.2.2 Cationic Parameters
16(1)
2.2.3 Normative Calculations and Classification of Igneous Rocks
17(1)
2.3 Statistics
18(1)
2.4 Classification and Grouping---Using Factors
19(5)
2.4.1 Statistical Examination of Complex Data Sets
20(2)
2.4.2 Conversion of Numeric Vectors to Factors
22(1)
2.4.3 Frequency (Contingency) Tables
23(1)
References
24(3)
3 Classical Plots
27(18)
3.1 Binary Plots
27(4)
3.1.1 Plotting Simple Binary Plots
27(3)
3.1.2 Constant Sum Effect (Closure)
30(1)
3.2 Harker Plots and Other Basic Multiple Plots
31(1)
3.3 Ternary Plots
32(2)
3.4 Classification Plots in GCDkit
34(1)
3.5 Geotectonic Diagrams
35(1)
3.6 Spiderplots
36(4)
3.7 Multiple Plots by Groups
40(1)
References
41(4)
4 Specialized Plots
45(8)
4.1 Log-Log Binary Plots
45(1)
4.2 Specialized Spiderplots
46(2)
4.2.1 Double-Normalized Spiderplots
47(1)
4.2.2 Spider Boxplots, Spider Box and Percentile Plots
47(1)
4.3 Contour Plots
48(1)
4.4 Anomaly Plots
49(1)
4.5 Stripplots and Strip Boxplots
50(1)
References
51(2)
5 Radiogenic Isotopes
53(16)
5.1 Recalculation of Elemental to Isotopic Ratios
53(2)
5.2 Calculation of Initial Ratios or Ages
55(2)
5.3 Epsilon, Delta and Gamma Values
57(3)
5.4 Model Ages
60(3)
5.4.1 Single-Stage Nd Model Ages
60(1)
5.4.2 Two-Stage Nd Model Ages
61(2)
5.5 Isochron Ages
63(2)
References
65(4)
Part II Modelling Major Elements
6 Direct Models
69(12)
6.1 Mass Balance During Crystallization
69(6)
6.1.1 Graphical Solutions
70(1)
6.1.2 Cumulate Composition
71(1)
6.1.3 Analytical Formulation
72(1)
6.1.4 Generating a Magmatic Series Through Crystallization
73(2)
6.2 Partial Melting
75(1)
6.3 Peritectic Reactions
76(2)
6.4 Mixing
78(1)
6.5 Crystallization and Partial Melting---Are These Just Special Cases of Mixing?
79(1)
Reference
80(1)
7 Reverse Models
81(4)
7.1 An Under-Determined Problem
81(1)
7.2 Least-Square Solution to Crystallization/Melting Problems
82(1)
7.3 Least-Square Solution to Mixing Problems
83(1)
References
83(2)
8 Forward Modelling in R
85(8)
References
92(1)
9 Reverse Modelling in R
93(8)
Part III Modelling Trace Elements
10 Dilute Trace Elements: Partition Coefficients
101(4)
10.1 Crystal Networks and Substitutions
101(1)
10.2 Partition Coefficients
101(1)
10.3 Controls on the Values of Partition Coefficients
102(1)
10.4 Bulk Distribution Coefficients
103(1)
References
104(1)
11 Direct (Dilute) Trace-Element Models
105(20)
11.1 Crystallization
106(4)
11.1.1 Batch Crystallization
106(1)
11.1.2 Fractional Crystallization
106(3)
11.1.3 Comparing Different Models
109(1)
11.2 Melting
110(4)
11.2.1 Batch Melting
110(1)
11.2.2 Fractional Melting
110(1)
11.2.3 Comparing Different Models
111(1)
11.2.4 Alternative Formulations of the Melting Equations
111(3)
11.3 Mixing
114(3)
11.3.1 Ratio of Two Elements During Binary Mixing
114(1)
11.3.2 Mixing Hyperbolae in Ratio-Ratio Plots
114(3)
11.4 Assimilation and Fractional Crystallization (AFC)
117(2)
11.5 Composite Models
119(4)
11.5.1 Crystallization with Incomplete Crystal Separation (Batch Crystallization + Binary Mixing)
120(1)
11.5.2 Fluxed Melting (Binary Mixing + Batch Melting)
121(2)
References
123(2)
12 Reverse (Dilute) Trace-Element Models
125(4)
12.1 Reverse Fractional Crystallization (Using Rayleigh's Law)
125(2)
12.2 Reverse Batch Partial Melting
127(1)
12.3 Reverse Mixing
128(1)
References
128(1)
13 Trace Elements as Essential Structural Constituents of Accessory Minerals: the Solubility Concept
129(12)
13.1 Solubility Formulae for Common Accessory Minerals
129(7)
13.1.1 Zircon, ZrSiO4
129(2)
13.1.2 Monazite, (LREE)PO4
131(3)
13.1.3 Apatite, Ca5(PO4)3(F,Cl,OH)
134(2)
13.2 Evolution Through Saturation
136(3)
References
139(2)
14 Forward Modelling in R
141(12)
References
152(1)
15 Reverse Modelling in R
153(6)
Part IV Radiogenic Isotopes
16 Direct Models
159(8)
16.1 Binary Mixing
159(4)
16.1.1 Single Isotopic Ratio
159(2)
16.1.2 Pair of Isotopic Ratios
161(2)
16.2 AFC Formulation for Isotopes
163(3)
References
166(1)
17 Reverse Models
167(2)
17.1 Binary Mixing
167(1)
17.2 AFC
167(1)
References
168(1)
18 Forward Modelling in R
169(6)
18.1 Binary Mixing
169(4)
18.2 AFC
173(2)
19 Reverse Modelling in R
175(6)
Reference
177(4)
Part V Practical Modelling
20 Choosing an Appropriate Model
181(10)
20.1 Evidence for Crystallization
181(2)
20.1.1 Final Solidification During Emplacement
181(1)
20.1.2 Fractional Crystallization at Depth
182(1)
20.2 Evidence For Melting
183(2)
20.2.1 Crustal Anatexis
183(1)
20.2.2 Melting of the Mantle
184(1)
20.3 Magma Mixing and Assimilation
185(2)
20.3.1 Mixing and Mingling of Magmas
185(1)
20.3.2 Assimilation
186(1)
References
187(4)
21 Semi-Quantitative Geochemical Approach
191(14)
21.1 Assessing Trace-Element Compatibility
191(1)
21.2 Order of (In)Compatibility
192(3)
21.3 Process Identification
195(4)
21.3.1 Mixing vs. Crystallization/Melting
195(1)
21.3.2 Crystallization vs. Melting in a Log-Log Diagram
195(3)
21.3.3 Crystallization vs. Melting Using Incompatible Elements
198(1)
21.4 Mixing Test
199(3)
21.5 Identifying Fractionating Minerals Using Log-Log Plots
202(1)
References
203(2)
22 Constraining a Model
205(20)
22.1 Choosing an Appropriate Strategy
205(1)
22.2 Constraining a Fractionation or Melting Model
206(6)
22.2.1 The Differentiated Liquid(s)/Melt: CL
206(1)
22.2.2 The Primitive Liquid/Source: C0
206(2)
22.2.3 Composition of the Solid Phases (Cumulate/Restite)
208(3)
22.2.4 Partition Coefficients
211(1)
22.3 Dealing with Accessory Minerals
212(9)
22.3.1 Assessing the Role of Accessory Minerals
212(2)
22.3.2 Modelling with Accessories
214(7)
22.4 Constraining the End-Members of a Mixing Model
221(1)
References
222(3)
23 Numerical Tips and Tricks
225(6)
23.1 The Size of the Geochemical Space
225(2)
23.2 Reducing the System
227(1)
23.3 Colinearity
227(1)
23.4 Breaking Minerals into End Members
228(1)
23.5 Coupling Majors and Traces
228(1)
23.6 This Space Left Blank for Your Own Tricks
229(1)
References
229(2)
24 Common Sense in Action
231(14)
24.1 Physical Constraints
231(3)
24.1.1 Thermodynamic Constraints
231(1)
24.1.2 Mechanical (Rheological) Constraints
232(2)
24.2 Scale and Speed of Processes---Approach to Equilibrium
234(1)
24.3 Is Your Model Worth Your Efforts?
235(4)
24.3.1 How Well Can We Discriminate Between Models?
236(1)
24.3.2 Dangerous Projections
237(1)
24.3.3 KD vs. C0---What Should You Improve First?
238(1)
24.4 Back to the Field!
239(1)
References
240(5)
Part VI Worked Examples
25 Differentiation of a Calc-Alkaline Series: Example of the Atacazo-Ninahuilca volcanoes, Ecuador
245(16)
25.1 Geological Setting
245(1)
25.2 Data Exploration and Implications
246(4)
25.2.1 Isotopic Data
246(1)
25.2.2 Major Elements
247(1)
25.2.3 Trace Elements
248(2)
25.3 Geochemical Modelling
250(8)
25.3.1 First Step: Atacazo
252(4)
25.3.2 Second Step: Ninahuilca
256(2)
25.4 Summary
258(2)
References
260(1)
26 Progressive Melting of a Metasedimentary Sequence: the Saint-Malo Migmatitic Complex, France
261(16)
26.1 Geological Setting
261(1)
26.2 Major and Trace Elements
262(2)
26.3 Geochemical Modelling
264(11)
26.3.1 Mode Evolution During melting
265(3)
26.3.2 Major and Trace Elements
268(3)
26.3.3 Zircon
271(4)
References
275(2)
Appendix A R Syntax in a Nutshell
1 Direct Mode
277(18)
1.1 Basic Operations
277(2)
1.1.1 Starting and Terminating the R Session
277(1)
1.1.2 Seeking Help and Documentation
278(1)
1.2 Fundamental Objects of the R Language
279(3)
1.2.1 Commands
279(2)
1.2.2 Handling Objects in Memory
281(1)
1.2.3 Attributes to Objects
282(1)
1.3 Numeric Vectors
282(2)
1.3.1 Assignment
282(1)
1.3.2 Vector Arithmetic
282(1)
1.3.3 Names
283(1)
1.3.4 Generating Regular Sequences
283(1)
1.3.5 Functions to Manipulate Numeric Vectors
284(1)
1.4 Character Vectors
284(1)
1.5 Logical Vectors
285(1)
1.5.1 Logical Operators
285(1)
1.5.2 Missing Values (NA, NaN)
286(1)
1.6 Arrays, Matrices, Data Frames
286(2)
1.6.1 Matrix/Data Frame Operations
287(1)
1.7 Indexing/Subsetting of Vectors, Arrays and Data Frames
288(2)
1.7.1 Vectors
289(1)
1.7.2 Matrices/Data Frames
289(1)
1.8 Lists
290(1)
1.9 Coercion of Individual Object Types
291(1)
1.10 Factors
292(1)
1.10.1 Basic Usage of Factors
292(1)
1.10.2 Conversion of Numeric Vectors to Factors
292(1)
1.10.3 Frequency Tables
293(1)
1.10.4 Using Factors to Handle Complex Datasets
293(1)
1.11 Data Input/Output, Files
293(2)
1.11.1 Reading Data
293(2)
1.11.2 Sample Data Sets
295(1)
1.11.3 Saving Data
295(1)
2 Graphics
295(14)
2.1 Obtaining and Annotating Binary Plots
295(7)
2.2 Additional High-Level Plotting Functions
302(3)
2.3 Creating Custom Layouts and Axes
305(3)
2.4 Exporting Graphs from R and Graphical Devices
308(1)
2.5 Interaction with Plots
308(1)
3 Programming in R
309(6)
3.1 Input and Output
309(1)
3.2 Conditional Execution
310(1)
3.3 Loops
310(1)
3.4 User-Defined Functions
311(2)
3.4.1 Arguments to Functions
311(1)
3.4.2 Assignments in Functions
312(1)
3.5 An Alternative to Loops---sapply
313(1)
References
313(2)
Appendix B Introduction to GCDkit
1 First Steps with GCDkit
315(17)
1.1 Installation
315(1)
1.2 GCDkit Overview: The User Interface
316(2)
1.3 Working with Data
318(5)
1.3.1 Data Format
318(1)
1.3.2 Loading Data
319(2)
1.3.3 Merging Data
321(1)
1.3.4 Choosing Data
322(1)
1.3.5 Grouping
322(1)
1.4 Plotting
323(6)
1.4.1 Plot Settings
326(1)
1.4.2 Single Plot Editing
327(1)
1.4.3 Plates and Plate Editing
328(1)
1.4.4 Spiderplots
328(1)
1.4.5 Classification and Geotectonic Diagrams
329(1)
1.5 Calculations
329(2)
1.6 Exporting from GCDkit
331(1)
2 Under the Bonnet: GCDkit Internals
332(5)
2.1 R language and GCDkit
332(1)
2.2 Data Variables
333(1)
2.3 System Variables
333(1)
2.4 Tailoring GCDkit to Suit your Needs
334(1)
2.5 Plugins
334(2)
References
336(1)
Appendix C Solving Systems of Linear Algebraic Equations in R
1.1 Linear Algebraic Equation Systems (Single Solution)
337(1)
1.2 Overdetermined Systems (Unconstrained Least-Square Method)
338(1)
1.3 Constrained Least-Square Method
339(1)
References
340(1)
Index 341
Vojtch Janouek (*1968) is associate professor at the Charles University in Prague, employed in the radiogenic isotopes laboratory of the Czech Geological Survey. He received a MSci from the Charles University and a PhD in geochemistry from the University of Glasgow. His research focusses on igneous geochemistry, geochronology and numerical modelling as well as computing in geosciences. He is editor-in-chief of open-access Journal of Geosciences.

Jean-François Moyen is professor at the University of Saint-Etienne, France. He obtained a PhD in petrology and geochemistry at the University of Clermont-Ferrand (France), and was a post-doc and then lecturer in Stellenbosch, South Africa (20032009). His research interests include geochemical modelling, igneous petrology and geochemistry.

Hervé Martin is Professor at the University Blaise Pascal in Clermont-Ferrand, France, where he works in the Laboratoire Magmas et Volcans. The research that he develops consists inmodeling the geochemical behaviour of major and trace elements in order to constrain the petrogenesis of the Earths primitive continental crust, as well as magma genesis in modern subduction zones.

Vojtch Erban is working at the Radiogenic Isotopes Laboratory of the Czech Geological Survey in Prague. His professional interests comprise geochemistry, isotope analytics and geochemical modelling.

Colin Farrow is an IT specialist and former member of the Department of Geology & Applied Geology, University of Glasgow with an interest in developing software for geological data analysis.