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Introduction to Scientific Programming and Simulation
Using R 1st Edition Owen Jones Digital Instant Download
Author(s): Owen Jones, Robert Maillardet, Andrew Robinson
ISBN(s): 9781420068726, 1420068725
Edition: 1
File Details: PDF, 7.64 MB
Year: 2009
Language: english
 IntroductIon to

Scientific Programming
and Simulation using r

© 2009 by Taylor & Francis Group, LLC

 IntroductIon to

Scientific Programming
and Simulation using r

Owen Jones, Robert Maillardet,

and Andrew Robinson

© 2009 by Taylor & Francis Group, LLC

Chapman & Hall/CRC
Taylor & Francis Group
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© 2009 by Taylor & Francis Group, LLC
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© 2009 by Taylor & Francis Group, LLC

 Preface

This book has two principal aims: to teach scientific programming and to
introduce stochastic modelling. Stochastic modelling in particular, and math-
ematical modelling in general, are intimately linked to scientific programming
because the numerical techniques of scientific programming enable the practi-
cal application of mathematical models to real-world problems. In the context
of stochastic modelling, simulation is the numerical technique that enables us
to analyse otherwise intractable models.
Simulation is also the best way we know of developing statistical intuition.
This book assumes that users have completed or are currently undertaking
a first year university level calculus course. The material is suitable for first
and second year science/engineering/commerce students and masters level stu-
dents in applied disciplines. No prior knowledge of programming or probability
is assumed.
It is possible to use the book for a first course on probability, with an empha-
sis on applications facilitated by simulation. Modern applied probability and
statistics are numerically intensive, and we give an approach that integrates
programming and probability right from the start.
We chose the programming language R because of its programming features.
We do not describe statistical techniques as implemented in R (though many
of them are admittedly quite remarkable), but rather show how to turn algo-
rithms into code. Our intended audience is those who want to make tools, not
just use them.
Complementing the book is a package, spuRs, containing most of the code
and data we use. Instructions for installing it are given in the first chapter. In
the back of the book we also provide an index of the programs developed in
the text and a glossary of R commands.

Course structure options

This book has grown out of the notes prepared for a first year course consist-
ing of 36 lectures, 12 one-hour tutorials, and 12 two-hour lab classes. However
it now contains more material than would fit in such a course, which permits

© 2009 by Taylor & Francis Group, LLC

vi PREFACE
its use for a variety of course structures, for example to meet prerequisite
requirements for follow-on subjects. We found the lab classes to be particu-
larly important pedagogically, as students learn programming through their
own experimentation. Instructors may straightforwardly compile lab classes
by drawing on the numerous examples and exercises in the text, and these are
supplemented by the programming projects contained in Chapter 22, which
are based on assignments we gave our students.

Core content The following chapters contain our core material for a course
on scientific programming and simulation.

Part I: Core knowledge of R and programming concepts. Chapters 1–6.

Part II: Thinking about mathematics from a numerical point of view: applying
Part I concepts to root finding and numerical integration. Chapters 9–11.

Part III: Essentials of probability, random variables, and expectation required

to understand simulation. Chapters 13–15 plus the uniform distribution.

Part IV: Stochastic modelling and simulation: random number generation,

Monte-Carlo integration, case studies and projects. Chapters 18.1–18.2, 19,
21.1–21.2 and 22.

Additional stochastic material The core outlined above only uses discrete
random variables, and for estimation only uses the concept of a sample average
converging to a mean. Chapters 16 and 17 add continuous random variables,
the Central Limit Theorem and confidence intervals. Chapters 18.3–18.5 and
20 then look at simulating continuous random variables and variance reduc-
tion. With some familiarity of continuous random variables the remaining case
studies, Chapter 21.3–21.4, become accessible.

Note that some of the projects in Chapter 22 use continuous random variables,
but can be easily modified to use discrete random variables instead.

Additional programming and numerical material For the core material ba-
sic plotting of output is sufficient, but for those wanting to produce more
professional graphics we provide Chapter 7. Chapter 8, on further program-
ming, acts as a bridge to more specialised texts, for those who wish to pursue
programming more deeply.

Chapter 12 deals with univariate and multivariate optimisation. Sections 12.3–

12.7 on multivariate optimisation, are harder than the rest of the book, and
require a basic familiarity with vector calculus. This material is self-contained,
with the exception of Example 17.1.2, which uses the optim function. However,
if you are prepared to use optim as a black box, then this example is also quite
accessible without reading the multivariate optimisation sections.

© 2009 by Taylor & Francis Group, LLC

PREFACE vii
Chapter outlines

1: Setting up. Here we describe how to obtain and install R, and the package
spuRs which complements the book.
2: R as a calculating environment. This chapter shows you how to use R to
do arithmetic calculations; create and manipulate variables, vectors, and ma-
trices; work with logical expressions; call and get help on built-in R functions;
and to understand the workspace.
3: Basic programming. This chapter introduces a set of basic programming
structures that are the building blocks of many programs. Some structures are
common to numerous programming languages, for example if, for and while
statements. Others, such as vector-based programming, are more specialised,
but are arguably just as important for efficient R coding.
4: Input and output. This chapter describes some of the infrastructure that R
provides for importing data for subsequent analysis, and for displaying and
saving results of that analysis. More details on the construction of graphics
are available in Chapter 7, and we provide more information about importing
data in Chapter 6.
5: Programming with functions. This chapter extends Chapter 3 to include
user-defined functions. We cover the creation of functions, the rules that they
must follow, and how they relate to the environments from which they are
called. We also present some tips on the construction of efficient functions,
with especial reference to how they are treated in R.
6: Sophisticated data structures. In this chapter we study R’s more sophisti-
cated data structures—lists and dataframes—which simplify data representa-
tion, manipulation, and analysis. The dataframe is like a matrix but extended
to allow for different data modes in different columns, and the list is a general
data storage object that can house pretty much any other kind of R object.
We also introduce the factor, which is used to represent categorical objects.
7: Better graphics. This chapter provides a deeper exposition of the graphical
capabilities of R, building on Chapter 4. We explain the individual pieces that
make up the default plot. We discuss the graphics parameters that are used
to fine-tune individual graphs and multiple graphics on a page. We show how
to save graphical objects in various formats. Finally, we demonstrate some
graphical tools for the presentation of multivariate data (lattice graphs), and
3D-graphics.
8: Further programming. This chapter briefly mentions some more advanced
aspects of programming in R. We introduce the management of and interac-
tion with packages. We present details about how R arranges the objects that
we create within the workspace, and within functions that we are running.
We provide further suggestions for debugging your own functions. Finally, we

© 2009 by Taylor & Francis Group, LLC

viii PREFACE
present some of the infrastructure that R provides for object-oriented program-
ming, and for executing code that has been compiled from another computer
language, for example, C.
9: Numerical accuracy and program efficiency. In this chapter we consider
technical details about how computers operate, and their ramifications for
programming practice, particularly within R. We look at how computers rep-
resent numbers, and the effect that this has on the accuracy of computation
results. We also discuss the time it takes to perform a computation, and pro-
gramming techniques for speeding things up. Finally we consider the effects
of memory limitations on computation efficiency.
10: Root-finding. This chapter presents a suite of different techniques for find-
ing roots. We cover fixed-point iteration, the Newton-Raphson method, the
secant method, and the bisection method.
11: Numerical integration. This chapter introduces numerical integration. The
problem with integration is that often a closed form of the antiderivative is not
available. Under such circumstances we can try to approximate the integral
using computational methods. We cover the trapezoidal rule, Simpson’s rule,
and adaptive quadrature.
12: Optimisation. This chapter covers the problem of finding the maximum
or minimum of a possibly multivariate function. We introduce the Newton
method and the golden-section method in the context of a univariate function,
and steepest ascent/descent and Newton’s method for multivariate functions.
We then provide some further information about the optimisation tools that
are available in R.
13: Probability. In this chapter we introduce mathematical probability, which
allows us to describe and think about uncertainty in a precise fashion. We cover
the probability axioms and conditional probability. We also cover the Law of
Total Probability, which can be used to decompose complicated probabilities
into simpler ones that are easier to compute, and Bayes’ theorem, which is
used to manipulate conditional probabilities in very useful ways.
14: Random variables. In this chapter we introduce the concept of a random
variable. We define discrete and continuous random variables and consider
various ways of describing their distributions, including the distribution func-
tion, probability mass function, and probability density function. We define
expectation, variance, independence, and covariance. We also consider trans-
formations of random variables and derive the Weak Law of Large Numbers.
15: Discrete random variables. In this chapter we study some of the most
important discrete random variables, and summarise the R functions relating
to them. We cover the Bernoulli, binomial, geometric, negative binomial, and
the Poisson distribution.
16: Continuous random variables. This chapter presents the theory, applica-
tions of, and R representations of, a number of continuous random variables.

© 2009 by Taylor & Francis Group, LLC

PREFACE ix
We cover the uniform, exponential, Weibull, gamma, normal, χ2 , and t distri-
butions.
17: Parameter estimation. This chapter covers point and interval estimation.
We introduce the Central Limit Theorem, normal approximations, asymptotic
confidence intervals and Monte-Carlo confidence intervals.
18: Simulation. In this chapter we simulate uniformly distributed random vari-
ables and discrete random variables, and describe the inversion and rejection
methods for simulating continuous random variables. We also cover several
techniques for simulating normal random variables.
19: Monte-Carlo integration. This chapter covers simulation-based approaches
to integration. We cover the hit-and-miss method, and the more efficient
Monte-Carlo integration method. We also give some comparative results on
the convergence rate of these two techniques compared with the trapezoid and
Simpson’s rule, which we covered in Chapter 11.
20: Variance reduction. This chapter introduces several sampling-based inno-
vations to the problem of estimation. We cover antithetic sampling, control
variates, and importance sampling. These techniques can vastly increase the
efficiency of simulation exercises when judiciously applied.
21: Case studies. In this chapter we present three case studies, on epidemics,
inventory, and seed dispersal (including an application of object-oriented cod-
ing). These are extended examples intended to demonstrate some of our sim-
ulation techniques.
22: Student projects. This chapter presents a suite of problems that can be
tackled by students. They are less involved than the case studies in the pre-
ceding chapter, but more substantial than the exercises that we have included
in each chapter.

Bibliography/further reading

For those wishing to further their study of scientific programming and simu-
lation, here are some texts that the authors have found useful.
The R language
W.N. Venables and B.D. Ripley, S Programming. Springer, 2000.
W.N. Venables and B.D. Ripley, Modern Applied Statistics with S, Fourth
Edition. Springer, 2002.
J.M. Chambers and T.J. Hastie (Editors), Statistical Models in S.
Brooks/Cole, 1992.
J. Maindonald and J. Braun, Data Analysis and Graphics Using R: An
Example-Based Approach, Second Edition. Cambridge University Press, 2006.
Scientific programming/numerical techniques
W. Cheney and D. Kincaid, Numerical Mathematics And Computing, Sixth

© 2009 by Taylor & Francis Group, LLC

x PREFACE
Edition. Brooks/Cole, 2008.
M.T. Heath, Scientific Computing: An Introductory Survey, Second Edition.
McGraw-Hill, 2002.
W.H. Press, S.A. Teukolsky, W.T. Vetterling and B.P. Flannery, Numerical
Recipes, 3rd Edition: The Art of Scientific Computing. Cambridge University
Press, 2007.
C.B. Moler, Numerical Computing with Matlab, Society for Industrial Mathe-
matics, 2004.
Stochastic modelling and simulation
A.M. Law and W.D. Kelton, Simulation Modeling and Analysis, Third Edition.
McGraw-Hill, 1999.
M. Pidd, Computer Simulation in Management Science, Fifth Edition. Wiley,
2004.
S.M. Ross, Applied Probability Models with Optimization Applications. Dover,
1992.
D.L. Minh, Applied Probability Models. Brooks/Cole, 2001.

Caveat computator

R is under constant review. The core programmers schedule a major release

and a minor release every year. Releases involve many changes and additions,
most of which are small, but some of which are large. However, there is no
guarantee of total backward compatibility, so new releases can break code that
makes assumptions about how the environment should work.
For example, while we were writing this book, the upgrade from version 2.7.1 to
2.8.0. changed the default behaviour of var, to return an NA where previously
it returned an error, if any of the input were NA. Happily, we had time to
rewrite the material that presumed that an error would be returned.
We conclude that R changes, and we note that this book was written for
version 2.8.0. The spuRs package will include a list of errata.

Thanks

Much of this book is based on a course given by the first two authors at the
University of Melbourne. The course was developed over many years, and we
owe much to previous lecturers for its fundamental structure, in particular
Steve Carnie and Chuck Miller. We are also indebted to our proof readers and
reviewers: Gad Abraham, Paul Blackwell, Steve Carnie, Alan Jones, David
Rolls, and especially Phil Spector. Olga Borovkova helped with some of the
coding, and we thank John Maindonald for drawing our attention to playwith.
We would like to acknowledge the dedication and the phenomenal achievement

© 2009 by Taylor & Francis Group, LLC

PREFACE xi
of the community that has provided the tools that we used to produce this
book. We are especially grateful to R-core, to the LATEX community, the GNU
community, and to Friedrich Leisch for Sweave.
Of course we could not have written the book without the support of our
partners, Charlotte, Deborah, and Grace, or the bewilderment of our offspring,
Indigo, Simone, André, and Felix.
ODJ
RJM
APR
October 2008

© 2009 by Taylor & Francis Group, LLC

 Contents

Preface v

I Programming 1

1 Setting up 3
1.1 Installing R 3
1.2 Starting R 3
1.3 Working directory 4
1.4 Writing scripts 5
1.5 Help 5
1.6 Supporting material 5

2 R as a calculating environment 11
2.1 Arithmetic 11
2.2 Variables 12
2.3 Functions 13
2.4 Vectors 15
2.5 Missing data 18
2.6 Expressions and assignments 19
2.7 Logical expressions 20
2.8 Matrices 23
2.9 The workspace 25
2.10 Exercises 25

xiii

© 2009 by Taylor & Francis Group, LLC

xiv CONTENTS
3 Basic programming 29
3.1 Introduction 29
3.2 Branching with if 31
3.3 Looping with for 33
3.4 Looping with while 36
3.5 Vector-based programming 38
3.6 Program flow 39
3.7 Basic debugging 41
3.8 Good programming habits 42
3.9 Exercises 43

4 I/O: Input and Output 49

4.1 Text 49
4.2 Input from a file 51
4.3 Input from the keyboard 53
4.4 Output to a file 55
4.5 Plotting 56
4.6 Exercises 58

5 Programming with functions 63

5.1 Functions 63
5.2 Scope and its consequences 68
5.3 Optional arguments and default values 70
5.4 Vector-based programming using functions 70
5.5 Recursive programming 74
5.6 Debugging functions 76
5.7 Exercises 78

6 Sophisticated data structures 85

6.1 Factors 85
6.2 Dataframes 88
6.3 Lists 94
6.4 The apply family 98
6.5 Exercises 105

© 2009 by Taylor & Francis Group, LLC

CONTENTS xv
7 Better graphics 109
7.1 Introduction 109
7.2 Graphics parameters: par 111
7.3 Graphical augmentation 113
7.4 Mathematical typesetting 114
7.5 Permanence 118
7.6 Grouped graphs: lattice 119
7.7 3D-plots 123
7.8 Exercises 124

8 Pointers to further programming techniques 127

8.1 Packages 127
8.2 Frames and environments 132
8.3 Debugging again 134
8.4 Object-oriented programming: S3 137
8.5 Object-oriented programming: S4 141
8.6 Compiled code 144
8.7 Further reading 146
8.8 Exercises 146

II Numerical techniques 149

9 Numerical accuracy and program efficiency 151

9.1 Machine representation of numbers 151
9.2 Significant digits 154
9.3 Time 156
9.4 Loops versus vectors 158
9.5 Memory 160
9.6 Caveat 161
9.7 Exercises 162

© 2009 by Taylor & Francis Group, LLC

xvi CONTENTS
10 Root-finding 167
10.1 Introduction 167
10.2 Fixed-point iteration 168
10.3 The Newton-Raphson method 173
10.4 The secant method 176
10.5 The bisection method 178
10.6 Exercises 181

11 Numerical integration 187

11.1 Trapezoidal rule 187
11.2 Simpson’s rule 189
11.3 Adaptive quadrature 194
11.4 Exercises 198

12 Optimisation 201
12.1 Newton’s method for optimisation 202
12.2 The golden-section method 204
12.3 Multivariate optimisation 207
12.4 Steepest ascent 209
12.5 Newton’s method in higher dimensions 213
12.6 Optimisation in R and the wider world 218
12.7 A curve fitting example 219
12.8 Exercises 220

III Probability and statistics 225

13 Probability 227
13.1 The probability axioms 227
13.2 Conditional probability 230
13.3 Independence 232
13.4 The Law of Total Probability 233
13.5 Bayes’ theorem 234
13.6 Exercises 235

© 2009 by Taylor & Francis Group, LLC

CONTENTS xvii
14 Random variables 241
14.1 Definition and distribution function 241
14.2 Discrete and continuous random variables 242
14.3 Empirical cdf’s and histograms 245
14.4 Expectation and finite approximations 246
14.5 Transformations 251
14.6 Variance and standard deviation 256
14.7 The Weak Law of Large Numbers 257
14.8 Exercises 261

15 Discrete random variables 267

15.1 Discrete random variables in R 267
15.2 Bernoulli distribution 268
15.3 Binomial distribution 268
15.4 Geometric distribution 270
15.5 Negative binomial distribution 273
15.6 Poisson distribution 274
15.7 Exercises 277

16 Continuous random variables 281

16.1 Continuous random variables in R 281
16.2 Uniform distribution 282
16.3 Lifetime models: exponential and Weibull 282
16.4 The Poisson process and the gamma distribution 287
16.5 Sampling distributions: normal, χ2 , and t 292
16.6 Exercises 297

17 Parameter Estimation 303

17.1 Point Estimation 303
17.2 The Central Limit Theorem 309
17.3 Confidence intervals 314
17.4 Monte-Carlo confidence intervals 321
17.5 Exercises 322

© 2009 by Taylor & Francis Group, LLC

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suis le plus grand homme de lettres actuellement vivant, disait-il, mais
ce n’est pas moi qu’il faut louer, c’est Dieu, qui m’a fait ainsi.» (Revue
bleue, 20 septembre 1879, p. 273.)

[25] «La gloire veut qu’on l’aide auprès des hommes; elle n’aime pas
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internationale, 1869; in-18.)

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année 1883, t. VI, p. 269): «C’est chez moi une occupation perpétuelle à
me continuer après ma mort, à me survivre, à laisser des images de ma
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l’infinité, l’immensité, l’éternité, et remplissant l’indigence de son maistre
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[27] Voir, par exemple, ce que dit Cicéron dans Le Songe de Scipion,
livre VI, chap. XIV, XV et XVIII, sur la gloire humaine: «... Quelle gloire
digne de tes vœux peux-tu acquérir parmi les hommes? Tu vois quelles
rares et étroites contrées ils occupent sur le globe terrestre... Retranche
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Hachette, 1866): «A quoi bon faire des livres pour cette petite terre, qui
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vie me fait tomber le livre ou la plume des mains, toutes les fois que
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extravagance c’est de croire qu’il y a une réputation qui nous
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164). «... Nous ressemblons tous à une suite de naufragés qui essaient
de se sauver les uns les autres, pour périr eux-mêmes l’instant d’après.»
(Id., Portraits littéraires, t. III, p. 128.) «... Un peu plus tôt, un peu plus
tard, nous y passerons tous. Chacun a la mesure de sa pleine eau. L’un
va jusqu’à Saint-Cloud, l’autre va jusqu’à Passy.» (Id., Nouvelle
Correspondance, p. 157.)
Sur l’aléa et l’inanité de la gloire littéraire, voir, dans le Mercure de
France de novembre 1900, un article abondamment documenté et des
plus judicieux de Remy de Gourmont.

[28] Parmi les curiosités ou les monstruosités littéraires, la phrase du

chapeau, de l’académicien Patin (1793-1876), est légitimement célèbre.
«C’est, a dit Robert de Bonnières (Mémoires d’aujourd’hui, 2e série p.
88), le plus mémorable exemple du plus joyeux galimatias.» Voici cette
perle:
 «Disons-le en passant, ce chapeau fort classique, porté ailleurs par
Oreste et Pylade, arrivant d’un voyage, dont Callimaque a décrit les
larges bords dans des vers conservés, précisément à l’occasion du
passage qui nous occupe, par le scoliaste, que chacun a pu voir
suspendu au cou et s’étalant sur le dos de certains personnages de bas-
reliefs, a fait de la peine à Brumoy qui l’a remplacé par un parasol.»
(Patin, Études sur les tragiques grecs, t. I, p. 114; édit. de 1842.)
«Cette phrase du chapeau était jusqu’à présent réputée comme
typique et inimitable, lit-on dans la Revue encyclopédique du 15 mars
1892 (col. 473); Léon Cladel (1834-1902) l’a de beaucoup surpassée
dans la suivante, qui sert de début à l’un de ses contes, Don Peyrè (dans
le volume de Léon Cladel, Urbains et Ruraux, p. 107 et suiv.; Ollendorff,
1884):
«A peine eut-elle débouché des gorges de Saint-Yrieix sur le plateau
marneux qui les surplombe et d’où l’on découvre, à travers l’immense
plaine s’étendant du dernier chaînon des Cévennes aux assises des
Pyrénées, ces montagnes dont la beauté grandiose arracha jadis des cris
d’enthousiasme au peu sensible Béarnais, déjà roi de Navarre, et faillit le
rendre aussi troubadour que bien longtemps avant lui l’avait été Richard
Cœur de Lion, alors simple duc du Pays des Eaux, où l’on trouve encore
quelques vestiges des monuments érigés en l’honneur de ce descendant
de Geoffroy, comte d’Anjou, lequel seigneur, aucun historien n’a su
pourquoi ni comment, ornait en temps de paix sa toque, en temps de
guerre son haubert d’une branche de genêt, habitude qui lui valut le
surnom de Plantagenet, porté plus tard par toute la famille française à
laquelle le trône anglo-saxon, après la mort d’Étienne de Blois, le dernier
héritier de Guillaume de Normandie, avait été dévolu, ma monture prit
peur et manqua de me désarçonner.»
Patin s’était contenté d’égayer çà et là sa phrase de quelques
incidentes bizarres; «dans celle de Léon Cladel, ajoute la Revue
encyclopédique, entre le sujet et le verbe, qui n’arrive qu’au bout d’une
vingtaine de lignes, se trouve intercalée une bonne partie de l’histoire de
France et d’Angleterre! C’est un véritable tour de force.»
Le Larousse mensuel (juin 1913, Petite correspondance, col. 3)
reproduit une phrase de Ferdinand Brunetière (1849-1907), digne
pendant des précédentes, et dont je me borne à citer le début: «Il n’en
est pas de même des Mémoires de Mme de Caylus, ni des Lettres de
cette bonne Mme de Sévigné, dont on aurait pourtant tort de croire
qu’elles doivent l’une et l’autre nous inspirer une entière confiance, étant
donné d’une part, en ce qui concerne Mme de Sévigné, que nous avons
affaire à une femme dont il est vrai de dire qu’encore que ses lettres, qui
sont d’un de nos bons écrivains, contiennent de précieux
renseignements sur les événements de la cour de Louis XIV, néanmoins
peu d’auteurs ont été plus légers dans leurs informations, plus
superficiels dans leurs jugements, et plus médisants à cœur-joie qu’elle
ne l’a été pour le plus vif plaisir de son grand malicieux de cousin, Bussy,
comte de Rabutin, et de sa pimbêche de fille, la comtesse de Grignan,»
etc. Je m’arrête, n’étant pas encore arrivé à la moitié de la phrase.

[29] C’est à propos de l’Histoire des Girondins qu’Alexandre Dumas père

disait de Lamartine: «Il a élevé l’histoire à la hauteur du roman». C’est
bien le même Dumas qui disait: «Qu’est-ce que l’histoire? C’est un clou
auquel j’accroche mes tableaux». (Sainte-Beuve, Causeries du lundi, t. XI,
p. 463.)

[30] Théophile Gautier se plaisait à la lecture des dictionnaires (Cf. Les

Jeunes-France, préface, p. 11), et emmagasinait quantité de termes
techniques, rarissimes et incompréhensibles «aux bourgeois» et à tout le
monde, et les glissait dans ses écrits. Voir, par exemple, son roman
Partie carrée (Charpentier, 1889), dont plusieurs épisodes se déroulent, il
est vrai, dans les Indes: surmé, gorotchana, siricha (p. 187); — apsara,
malica, amra (p. 198); — tchampara, kesara, ketoca, bilva, cokila,
tchavatraka (p. 199), etc. Dans Mademoiselle de Maupin (Charpentier,
1866): stymphalide (p. 32); smorfia (p. 150); une robe de byssus (p.
200); nagassaris, angsoka (p. 246), etc.

[31] Comparer cette orthographe Qaïn à celle d’Yaqoub, un des

personnages du drame de Charles VII d’Alexandre Dumas père, qui écrit
toujours Yaqoub et non Yacoub. (Cf. Théâtre complet d’Alexandre
Dumas, t. II, p. 231 et suiv., Michel Lévy, 1873.)

[32] Je rencontre les mêmes pensées ou des pensées analogues dans

une très belle lettre de M. Edmond Haraucourt adressée à M. Julien
Larroche, le 30 novembre 1907, en tête du recueil de vers Les Voix du
tombeau, par Julien Larroche (Lemerre, 1908): «... Ni dithyrambes ni
réclames ne valent cette paix sereine qui se devine au fond de vous.
Gardez-la comme le trésor unique, et n’enviez personne, même si le
silence des critiques accueille vos poèmes: vos poèmes vous ont réjoui
ou consolé, n’attendez rien de plus, et dites-vous qu’au temps où nous
sommes les poètes dont on redit le nom et ceux dont on ne parle pas
sont, en dépit des apparences, confondus fraternellement dans le même
dédain des foules, car on ne lit les vers ni des uns ni des autres.»
N’empêche que poètes et poétesses, tout comme leurs confrères en
prose d’ailleurs, ne se montrent pas, d’ordinaire, si philosophes et ne se
désintéressent pas aussi facilement du succès et de la célébrité.
[33] Voir ci-dessus (p. 25) Corneille disant, à propos de certains de ses
vers peu intelligibles: «Tel qui ne les entendra pas les admirera»; — et
(p. 94) Théophile Gautier à qui l’on attribue cette sentence: «Il faut que,
dans chaque page, il y ait une dizaine de mots que le bourgeois ne
comprend pas». C’était aussi, comme nous le verrons plus loin (p. 181),
l’opinion de Balzac.

[34] Il s’appelait Claude-Marie-Louis-Emmanuel Carbon de Flins des

Oliviers, et la multiplicité de ses noms lui attira cette épigramme de
Lebrun-Pindare:
Carbon de Flins des Oliviers
A plus de noms que de lauriers.
(Cf. Chateaubriand, Mémoires d’outre-tombe, t. I, p. 219, note
1; édit. Biré.)

[35] Aussi des poètes, voire de plus illustres, n’ont-ils pas hésité à faire
ange du féminin:
C’est une femme aussi, c’est une ange charmante.
(Alfred de Vigny, Éloa, Poésies complètes, p. 14; Charpentier,
1882.)

[36] Cf. Victor Hugo, La Pitié suprême, XIV, p. 150 (Hetzel-Quantin, s. d.

in-16):
Être le guérisseur, le bon Samaritain
Des monstres, ces martyrs ténébreux du destin,
Etc., etc.

[37] Une curieuse et amusante aventure arriva à Marmontel,

précisément comme il briguait les suffrages académiques. «... Désirant
avec ardeur une place à l’Académie, Marmontel prit le parti de louer,
dans sa Poétique française, presque tous les académiciens vivants dont il
comptait se concilier la bienveillance et obtenir la voix pour la première
place vacante. Il se fit presque autant de tracasseries qu’il avait fait
d’éloges; personne ne se trouva assez loué, ni loué à son gré. Il avait
cité de Moncrif un couplet avec les plus grands éloges; Moncrif prétendit
qu’il fallait citer et transcrire la chanson tout entière ou ne point s’en
mêler.» (Correspondance de Grimm, t. I, p. 337-338; Buisson, 1812.)

[38] Cf. Chateaubriand (Génie du christianisme, VI, 5; t. I, p. 169;

Didot, 1865): «L’enfant naît, la mamelle est pleine; la bouche du jeune
convive n’est point armée, de peur de blesser la coupe du banquet
maternel.»
[39] Sur les mystifications commises par Charles Nodier, voir mon
ouvrage Mystifications littéraires et théâtrales, p. 89 et suiv.
(Fontemoing, 1913).

[40] Nous avons vu aussi (p. 94 et 135) le même système préconisé

plus ou moins sérieusement par Théophile Gautier: «Il faut, dans chaque
page, une dizaine de mots que le bourgeois ne comprend pas», etc. Et
(déjà cité p. 136) Destouches (La Fausse Agnès, I, 2): «La baronne. Cet
endroit-ci n’est pas clair, mais c’est ce qui en fait la beauté. — Le baron.
Assurément. Quand je lis quelque chose, et que je ne l’entends pas, je
suis toujours dans l’admiration.» Cf. aussi Montaigne, le cardinal de Retz,
La Bruyère, etc., cités par nous p. 135-136.

[41] J.-J. Rousseau, nous l’avons vu (Cf. ci-dessus, p. 172), a encore

été bien plus loin, lui: «... Moi qui me suis cru toujours et qui me crois
encore, à tout prendre, le meilleur des hommes...» (Les Confessions, II,
x; t. VI, p. 85; Hachette, 1864.)

[42] La même anecdote a été appliquée à une autre Sophie, cuisinière

du docteur Véron.

[43] Barbey aimait ces verdicts draconiens et sans appel. De même

qu’il voulait condamner Flaubert à ne plus écrire, il déclarait qu’«à dater
des Contemplations, M. Hugo n’existe plus». C’est fini de lui. (Le
Larousse mensuel, octobre 1912, p. 539.) Voir aussi Barbey d’Aurevilly,
Dernières Polémiques, Un Poète prussien, p. 43-48; Savine, 1891.

[44] Cette phrase comique a été souvent citée, mais parfois altérée et
amplifiée. Poitevin (La Grammaire, les Écrivains et les Typographes, p.
225) la donne ainsi: «Le pépin du mécontentement n’allait pas tarder à
pousser dans son cœur.» Hippolyte Babou (La Vérité sur le cas de M.
Champfleury, p. 31) ajoute tout un membre de phrase qui rend la
métaphore plus grotesque: «Le pépin du mécontentement devait
produire un arbre touffu sous lequel s’abriteraient les mauvaises
langues.»

[45] Voici le texte complet de cette phrase, avec sa ponctuation, tel

qu’on le trouve dans la première édition de Bouvard et Pécuchet, établie
d’après le manuscrit même de Flaubert. Ce texte a été modifié dans des
éditions suivantes: «Mais le plus beau, c’était dans l’embrasure de la
fenêtre, une statue de saint Pierre! Sa main droite couverte d’un gant
serrait la clef du Paradis. De couleur vert-pomme, sa chasuble, que des
fleurs de lis agrémentaient, était bleu-ciel, et sa tiare très jaune, pointue
comme une pagode.»
[46] Girault-Duvivier, qui est loin d’avoir l’esprit large, tolérant, éclairé
et judicieux de Littré, condamne, en effet et bien entendu, et l’Académie
pareillement, les locutions de Flaubert citées ci-dessus: cf. la Grammaire
des Grammaires, principalement les «Remarques détachées», t. II, p.
1051-1291 (Cotelle, 1859).

[47] Berquin (1749-1791) commet, lui, une autre erreur, à propos des
rossignols: il en fait chanter deux ensemble et tout près l’un de l’autre,
ce qui n’a jamais lieu. «Deux rossignols allèrent se percher près de là,
sur le sommet d’un berceau de verdure, pour la réjouir (une jeune fille)
de leurs chansons de l’aurore.» (L’Ami des enfants, Clémentine et
Madelon, p. 28; Lehuby, s. d.)

[48] A propos de Gustave Flaubert, on lit, dans le Journal des Goncourt

(t. V, p. 79), que le futur auteur de Madame Bovary avait composé, étant
encore au collège, un drame sur Louis XI, où un malheureux s’exprimait
en ces termes: «Monseigneur, nous sommes obligés d’assaisonner nos
légumes avec le sel de nos larmes.»

[49] Jean-Jacques Rousseau, né à Genève et dont le français n’était pas

très pur, allait plus loin encore et englobait toute la province dans cet
ostracisme: «Il y a une certaine pureté de goût et une correction de
style qu’on n’atteint jamais dans la province, quelque effort qu’on fasse
pour cela.» (Lettre à M. Vernes, 4 avril 1757: Œuvres complètes de J.-J.
Rousseau, t. VII, p. 67; Hachette, 1864.) Mais ce qui était vrai du temps
de Rousseau ne l’est plus, ou du moins plus autant, de nos jours.

[50] Camille Lemonnier, dans la préface de Héros et Pantins (p. xiii-xiv),

apprécie en ces termes le labeur littéraire de Léon Cladel: «... Il va
jusqu’à épuiser l’artifice des plus subtiles rhétoriques, en variant
incessamment la tournure des phrases et le choix des mots, en ne
permettant pas qu’un même vocable reparaisse dans tout le cours d’un
livre, et d’autres fois en prohibant même, en tête des alinéas, le retour
d’une même lettre initiale. C’est encore là le secret de ces terribles
phrases kilométriques dont se gaussent fort impertinemment des
stylistes sans haleine, las et pantois au bout de dix mots, et qui,
enchevêtrées d’incidentes, avec des circonlocutions nombreuses et des
arabesques emmêlées comme les sinuosités d’un labyrinthe, rampent à
la façon des ronces ou se dressent à la façon des chênes, touffue
végétation du style, où chantent, et sifflent, et chuchotent les idées, ces
oiseaux de l’esprit.» On pourrait d’ailleurs dire de Léon Cladel ce que lui-
même a dit de Baudelaire, dans la dédicace de La Fête votive (p. 6;
Lemerre, 1882): «Un mot le préoccupait au point de l’empêcher de
dormir pendant huit nuits consécutives, une phrase le persécutait un
mois durant, telle page des années; et c’est ainsi qu’au prix des plus
cruels sacrifices, il forma... ligne à ligne sa prose».

[51] Glissons, en bas de page, cette savoureuse anecdote relative à

l’illustre créateur de Rocambole. Ponson du Terrail fit un jour, «contre
Aurélien Scholl, le pari que, dans toutes les petites villes, dans tous les
villages où ils iraient ensemble, ils ne trouveraient personne qui n’eût lu
ses ouvrages, tandis qu’à peine un petit nombre de lettrés connaîtraient
le nom de Flaubert». Et Ponson gagna le pari. (Paul Stapfer, Des
Réputations littéraires, t. II, p. 249.)

[52] Bien des anecdotes et plaisanteries ont été contées à propos de la

Vénus de Milo; en voici quelques-unes:
Un concierge déménage une Vénus de Milo en plâtre et la brise.
Fureur du locataire. «Il n’y a pas tant de mal, riposte le concierge: elle
avait déjà les bras cassés». (Le National, 29 janvier 1885.)
A l’hôtel Drouot, un garçon novice pose sur la table une terre cuite
représentant la fameuse Vénus de Milo, et, s’essuyant les mains, il dit
sans malice au public: «Si l’on trouve les bras, on les donnera.»
(L’Opinion, 13 octobre 1885.)
Un habitant de San Francisco avait commandé à Paris une statue de
la Vénus de Milo. Elle lui fut expédiée. Le destinataire a intenté un
procès à la Central Pacific Company sous le prétexte que la Vénus lui
était parvenue sans bras, c’est-à-dire mutilée. Le plus fort, dit-on, c’est
que le juge a condamné la Compagnie à payer une indemnité à ce
destinataire. (Le Radical, 19 mars 1887.)
 Note de transcription

Les erreurs clairement introduites par le typographe ont été corrigées.

L’orthographe d’origine a été conservée. La ponctuation n’a pas été modifiée
hormis quelques corrections mineures. Les points de suspension ont été
normalisés à trois points.
Les numéros des pages blanches n’ont pas été repris.
Les notes ont été renumérotées et placées à la fin du livre.
À la p. 82, les lignes “Pour touchée.” et la précédente ont été permutées pour
que, comme dans le reste du livre, une ligne d’attribution suive
immédiatement les vers qu’on cite.
À la p. 222, la date de décès d’Émile Zola a été corrigée: la date correcte est
1902, non 1905.
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