NONLINEAR TIME SERIES ANALYSIS
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More informationNONLINEAR TIME SERIES ANALYSISThis book represents a modern approach to time series analysis which is based onthe theory of dynamical systems.It starts from a sound outline of the underlyingtheory to arrive at very practical issues,which are illustrated using a large number ofempirical data sets taken from variousfields.This book will hence be highly usefulfor scientists and engineers from all disciplines who study time variable signals,including the earth,life and social sciences.The paradigm of deterministic chaos has influenced thinking in manyfields ofscience.Chaotic systems show rich and surprising mathematical structures.In theapplied sciences,deterministic chaos provides a striking explanation for irregulartemporal behaviour and anomalies in systems which do not seem to be inherentlystochastic.The most direct link between chaos theory and the real world is the anal-ysis of time series from real systems in terms of nonlinear dynamics.Experimentaltechnique and data analysis have seen such dramatic progress that,by now,mostfundamental properties of nonlinear dynamical systems have been observed in thelaboratory.Great efforts are being made to exploit ideas from chaos theory where-ver the data display more structure than can be captured by traditional methods.Problems of this kind are typical in biology and physiology but also in geophysics,economics and many other sciences.This revised edition has been significantly rewritten an expanded,includingseveral new chapters.In view of applications,the most relevant novelties will be thetreatment of non-stationary data sets and of nonlinear stochastic processes insidethe framework of a state space reconstruction by the method of delays.Hence,non-linear time series analysis has left the rather narrow niche of strictly deterministicsystems.Moreover,the analysis of multivariate data sets has gained more atten-tion.For a direct application of the methods of this book to the reader’s own datasets,this book closely refers to the publicly available software package TISEAN.The availability of this software will facilitate the solution of the exercises,so thatreaders now can easily gain their own experience with the analysis of data sets.Holger Kantz,born in November1960,received his diploma in physics fromthe University of Wuppertal in January1986with a thesis on transient chaos.InJanuary1989he obtained his Ph.D.in theoretical physics from the same place,having worked under the supervision of Peter Grassberger on Hamiltonian many-particle dynamics.During his postdoctoral time,he spent one year on a Marie Curiefellowship of the European Union at the physics department of the University ofMore informationFlorence in Italy.In January1995he took up an appointment at the newly foundedMax Planck Institute for the Physics of Complex Systems in Dresden,where heestablished the research group‘Nonlinear Dynamics and Time Series Analysis’.In1996he received his venia legendi and in2002he became adjunct professorin theoretical physics at Wuppertal University.In addition to time series analysis,he works on low-and high-dimensional nonlinear dynamics and its applications.More recently,he has been trying to bridge the gap between dynamics and statis-tical physics.He has(co-)authored more than75peer-reviewed articles in scien-tific journals and holds two international patents.For up-to-date information seehttp://www.mpipks-dresden.mpg.de/mpi-doc/kantzgruppe.html.Thomas Schreiber,born1963,did his diploma work with Peter Grassberger atWuppertal University on phase transitions and information transport in spatio-temporal chaos.He joined the chaos group of Predrag Cvitanovi´c at the Niels BohrInstitute in Copenhagen to study periodic orbit theory of diffusion and anomaloustransport.There he also developed a strong interest in real-world applications ofchaos theory,leading to his Ph.D.thesis on nonlinear time series analysis(Univer-sity of Wuppertal,1994).As a research assistant at Wuppertal University and duringseveral extended appointments at the Max Planck Institute for the Physics of Com-plex Systems in Dresden he published numerous research articles on time seriesmethods and applications ranging from physiology to the stock market.His habil-itation thesis(University of Wuppertal)appeared as a review in Physics Reportsin1999.Thomas Schreiber has extensive experience teaching nonlinear dynamicsto students and experts from variousfields and at all levels.Recently,he has leftacademia to undertake industrial research.NONLINEAR TIME SERIES ANALYSIS HOLGER KANTZ AND THOMAS SCHREIBERMax Planck Institute for the Physics of Complex Systems,DresdenMore informationMore informationpublished by the press syndicate of the university of cambridgeThe Pitt Building,Trumpington Street,Cambridge,United Kingdomcambridge university pressThe Edinburgh Building,Cambridge CB22RU,UK40West20th Street,New York,NY10011–4211,USA477Williamstown Road,Port Melbourne,VIC3207,AustraliaRuiz de Alarc´o n13,28014Madrid,SpainDock House,The Waterfront,Cape Town8001,South AfricaC Holger Kantz and Thomas Schreiber,2000,2003This book is in copyright.Subject to statutory exceptionand to the provisions of relevant collective licensing agreements,no reproduction of any part may take place withoutthe written permission of Cambridge University Press.First published2000Second edition published2003Printed in the United Kingdom at the University Press,CambridgeTypeface Times11/14pt.System L A T E X2ε[tb]A catalogue record for this book is available from the British LibraryLibrary of Congress Cataloguing in Publication dataKantz,Holger,1960–Nonlinear time series analysis/Holger Kantz and Thomas Schreiber.–[2nd ed.].p.cm.Includes bibliographical references and index.ISBN0521821509–ISBN0521529026(paperback)1.Time-series analysis.2.Nonlinear theories.I.Schreiber,Thomas,1963–II.TitleQA280.K3552003519.5 5–dc212003044031ISBN0521821509hardbackISBN0521529026paperbackThe publisher has used its best endeavours to ensure that the URLs for external websites referred to in this bookare correct and active at the time of going to press.However,the publisher has no responsibility for the websites and can make no guarantee that a site will remain live or that the content is or will remain appropriate.More informationContentsPreface to thefirst edition page xiPreface to the second edition xiiiAcknowledgements xvI Basic topics11Introduction:why nonlinear methods?32Linear tools and general considerations132.1Stationarity and sampling132.2Testing for stationarity152.3Linear correlations and the power spectrum182.3.1Stationarity and the low-frequency component in thepower spectrum232.4Linearfilters242.5Linear predictions273Phase space methods303.1Determinism:uniqueness in phase space303.2Delay reconstruction353.3Finding a good embedding363.3.1False neighbours373.3.2The time lag393.4Visual inspection of data393.5Poincar´e surface of section413.6Recurrence plots434Determinism and predictability484.1Sources of predictability484.2Simple nonlinear prediction algorithm504.3Verification of successful prediction534.4Cross-prediction errors:probing stationarity564.5Simple nonlinear noise reduction58vMore informationvi Contents5Instability:Lyapunov exponents655.1Sensitive dependence on initial conditions655.2Exponential divergence665.3Measuring the maximal exponent from data696Self-similarity:dimensions756.1Attractor geometry and fractals756.2Correlation dimension776.3Correlation sum from a time series786.4Interpretation and pitfalls826.5Temporal correlations,non-stationarity,and space timeseparation plots876.6Practical considerations916.7A useful application:determination of the noise level using thecorrelation integral926.8Multi-scale or self-similar signals956.8.1Scaling laws966.8.2Detrendedfluctuation analysis1007Using nonlinear methods when determinism is weak1057.1Testing for nonlinearity with surrogate data1077.1.1The null hypothesis1097.1.2How to make surrogate data sets1107.1.3Which statistics to use1137.1.4What can go wrong1157.1.5What we have learned1177.2Nonlinear statistics for system discrimination1187.3Extracting qualitative information from a time series1218Selected nonlinear phenomena1268.1Robustness and limit cycles1268.2Coexistence of attractors1288.3Transients1288.4Intermittency1298.5Structural stability1338.6Bifurcations1358.7Quasi-periodicity139II Advanced topics1419Advanced embedding methods1439.1Embedding theorems1439.1.1Whitney’s embedding theorem1449.1.2Takens’s delay embedding theorem1469.2The time lag148More informationContents vii9.3Filtered delay embeddings1529.3.1Derivative coordinates1529.3.2Principal component analysis1549.4Fluctuating time intervals1589.5Multichannel measurements1599.5.1Equivalent variables at different positions1609.5.2Variables with different physical meanings1619.5.3Distributed systems1619.6Embedding of interspike intervals1629.7High dimensional chaos and the limitations of the time delayembedding1659.8Embedding for systems with time delayed feedback17110Chaotic data and noise17410.1Measurement noise and dynamical noise17410.2Effects of noise17510.3Nonlinear noise reduction17810.3.1Noise reduction by gradient descent17910.3.2Local projective noise reduction18010.3.3Implementation of locally projective noise reduction18310.3.4How much noise is taken out?18610.3.5Consistency tests19110.4An application:foetal ECG extraction19311More about invariant quantities19711.1Ergodicity and strange attractors19711.2Lyapunov exponents II19911.2.1The spectrum of Lyapunov exponents and invariantmanifolds20011.2.2Flows versus maps20211.2.3Tangent space method20311.2.4Spurious exponents20511.2.5Almost two dimensionalflows21111.3Dimensions II21211.3.1Generalised dimensions,multi-fractals21311.3.2Information dimension from a time series21511.4Entropies21711.4.1Chaos and theflow of information21711.4.2Entropies of a static distribution21811.4.3The Kolmogorov–Sinai entropy22011.4.4The -entropy per unit time22211.4.5Entropies from time series data226More informationviii Contents11.5How things are related22911.5.1Pesin’s identity22911.5.2Kaplan–Yorke conjecture23112Modelling and forecasting23412.1Linear stochastic models andfilters23612.1.1Linearfilters23712.1.2Nonlinearfilters23912.2Deterministic dynamics24012.3Local methods in phase space24112.3.1Almost model free methods24112.3.2Local linearfits24212.4Global nonlinear models24412.4.1Polynomials24412.4.2Radial basis functions24512.4.3Neural networks24612.4.4What to do in practice24812.5Improved cost functions24912.5.1Overfitting and model costs24912.5.2The errors-in-variables problem25112.5.3Modelling versus prediction25312.6Model verification25312.7Nonlinear stochastic processes from data25612.7.1Fokker–Planck equations from data25712.7.2Markov chains in embedding space25912.7.3No embedding theorem for Markov chains26012.7.4Predictions for Markov chain data26112.7.5Modelling Markov chain data26212.7.6Choosing embedding parameters for Markov chains26312.7.7Application:prediction of surface wind velocities26412.8Predicting prediction errors26712.8.1Predictability map26712.8.2Individual error prediction26812.9Multi-step predictions versus iterated one-step predictions27113Non-stationary signals27513.1Detecting non-stationarity27613.1.1Making non-stationary data stationary27913.2Over-embedding28013.2.1Deterministic systems with parameter drift28013.2.2Markov chain with parameter drift28113.2.3Data analysis in over-embedding spaces283More informationContents ix13.2.4Application:noise reduction for human voice28613.3Parameter spaces from data28814Coupling and synchronisation of nonlinear systems29214.1Measures for interdependence29214.2Transfer entropy29714.3Synchronisation29915Chaos control30415.1Unstable periodic orbits and their invariant manifolds30615.1.1Locating periodic orbits30615.1.2Stable/unstable manifolds from data31215.2OGY-control and derivates31315.3Variants of OGY-control31615.4Delayed feedback31715.5Tracking31815.6Related aspects319A Using the TISEAN programs321A.1Information relevant to most of the routines322A.1.1Efficient neighbour searching322A.1.2Re-occurring command options325A.2Second-order statistics and linear models326A.3Phase space tools327A.4Prediction and modelling329A.4.1Locally constant predictor329A.4.2Locally linear prediction329A.4.3Global nonlinear models330A.5Lyapunov exponents331A.6Dimensions and entropies331A.6.1The correlation sum331A.6.2Information dimension,fixed mass algorithm332A.6.3Entropies333A.7Surrogate data and test statistics334A.8Noise reduction335A.9Finding unstable periodic orbits336A.10Multivariate data336B Description of the experimental data sets338B.1Lorenz-like chaos in an NH3laser338B.2Chaos in a periodically modulated NMR laser340B.3Vibrating string342B.4Taylor–Couetteflow342B.5Multichannel physiological data343More informationx ContentsB.6Heart rate during atrialfibrillation343B.7Human electrocardiogram(ECG)344B.8Phonation data345B.9Postural control data345B.10Autonomous CO2laser with feedback345B.11Nonlinear electric resonance circuit346B.12Frequency doubling solid state laser348B.13Surface wind velocities349References350Index365More informationPreface to thefirst editionThe paradigm of deterministic chaos has influenced thinking in manyfields of sci-ence.As mathematical objects,chaotic systems show rich and surprising structures.Most appealing for researchers in the applied sciences is the fact that determinis-tic chaos provides a striking explanation for irregular behaviour and anomalies insystems which do not seem to be inherently stochastic.The most direct link between chaos theory and the real world is the analysis oftime series from real systems in terms of nonlinear dynamics.On the one hand,experimental technique and data analysis have seen such dramatic progress that,by now,most fundamental properties of nonlinear dynamical systems have beenobserved in the laboratory.On the other hand,great efforts are being made to exploitideas from chaos theory in cases where the system is not necessarily deterministicbut the data displays more structure than can be captured by traditional methods.Problems of this kind are typical in biology and physiology but also in geophysics,economics,and many other sciences.In all thesefields,even simple models,be they microscopic or phenomenological,can create extremely complicated dynamics.How can one verify that one’s model isa good counterpart to the equally complicated signal that one receives from nature?Very often,good models are lacking and one has to study the system just from theobservations made in a single time series,which is the case for most non-laboratorysystems in particular.The theory of nonlinear dynamical systems provides new toolsand quantities for the characterisation of irregular time series data.The scope ofthese methods ranges from invariants such as Lyapunov exponents and dimensionswhich yield an accurate description of the structure of a system(provided thedata are of high quality)to statistical techniques which allow for classification anddiagnosis even in situations where determinism is almost lacking.This book provides the experimental researcher in nonlinear dynamics with meth-ods for processing,enhancing,and analysing the measured signals.The theorist willbe offered discussions about the practical applicability of mathematical results.ThexiMore informationxii Preface to thefirst editiontime series analyst in economics,meteorology,and otherfields willfind inspira-tion for the development of new prediction algorithms.Some of the techniquespresented here have also been considered as possible diagnostic tools in clinical re-search.We will adopt a critical but constructive point of view,pointing out ways ofobtaining more meaningful results with limited data.We hope that everybody whohas a time series problem which cannot be solved by traditional,linear methodswillfind inspiring material in this book.Dresden and WuppertalNovember1996More informationPreface to the second editionIn afield as dynamic as nonlinear science,new ideas,methods and experimentsemerge constantly and the focus of interest shifts accordingly.There is a continuousstream of new results,and existing knowledge is seen from a different angle aftervery few years.Five years after thefirst edition of“Nonlinear Time Series Analysis”we feel that thefield has matured in a way that deserves being reflected in a secondedition.The modification that is most immediately visible is that the program listingshave been be replaced by a thorough discussion of the publicly available softwareTISEAN.Already a few months after thefirst edition appeared,it became clearthat most users would need something more convenient to use than the bare libraryroutines printed in the book.Thus,together with Rainer Hegger we prepared stand-alone routines based on the book but with input/output functionality and advancedfeatures.Thefirst public release was made available in1998and subsequent releasesare in widespread use now.Today,TISEAN is a mature piece of software thatcovers much more than the programs we gave in thefirst edition.Now,readerscan immediately apply most methods studied in the book on their own data usingTISEAN programs.By replacing the somewhat terse program listings by minuteinstructions of the proper use of the TISEAN routines,the link between book andsoftware is strengthened,supposedly to the benefit of the readers and users.Hencewe recommend a download and installation of the package,such that the exercisescan be readily done by help of these ready-to-use routines.The current edition has be extended in view of enlarging the class of data sets to betreated.The core idea of phase space reconstruction was inspired by the analysis ofdeterministic chaotic data.In contrast to many expectations,purely deterministicand low-dimensional data are rare,and most data fromfield measurements areevidently of different nature.Hence,it was an effort of our scientific work over thepast years,and it was a guiding concept for the revision of this book,to explore thepossibilities to treat other than purely deterministic data sets.xiiiMore informationxiv Preface to the second editionThere is a whole new chapter on non-stationary time series.While detectingnon-stationarity is still briefly discussed early on in the book,methods to deal withmanifestly non-stationary sequences are described in some detail in the secondpart.As an illustration,a data source of lasting interest,human speech,is used.Also,a new chapter deals with concepts of synchrony between systems,linear andnonlinear correlations,information transfer,and phase synchronisation.Recent attempts on modelling nonlinear stochastic processes are discussed inChapter12.The theoretical framework forfitting Fokker–Planck equations to datawill be reviewed and evaluated.While Chapter9presents some progress that hasbeen made in modelling input–output systems with stochastic but observed inputand on the embedding of time delayed feedback systems,the chapter on mod-elling considers a data driven phase space approach towards Markov chains.Windspeed measurements are used as data which are best considered to be of nonlinearstochastic nature despite the fact that a physically adequate mathematical model isthe deterministic Navier–Stokes equation.In the chapter on invariant quantities,new material on entropy has been included,mainly on the -and continuous entropies.Estimation problems for stochastic ver-sus deterministic data and data with multiple length and time scales are discussed.Since more and more experiments now yield good multivariate data,alternativesto time delay embedding using multiple probe measurements are considered at var-ious places in the text.This new development is also reflected in the functionalityof the TISEAN programs.A new multivariate data set from a nonlinear semicon-ductor electronic circuit is introduced and used in several places.In particular,adifferential equation has been successfully established for this system by analysingthe data set.Among other smaller rearrangements,the material from the former chapter“Other selected topics”,has been relocated to places in the text where a connectioncan be made more naturally.High dimensional and spatio-temporal data is now dis-cussed in the context of embedding.We discuss multi-scale and self-similar signalsnow in a more appropriate way right after fractal sets,and include recent techniquesto analyse power law correlations,for example detrendedfluctuation analysis.Of course,many new publications have appeared since1997which are potentiallyrelevant to the scope of this book.At least two new monographs are concerned withthe same topic and a number of review articles.The bibliography has been updatedbut remains a selection not unaffected by personal preferences.We hope that the extended book will prove its usefulness in many applicationsof the methods and further stimulate thefield of time series analysis.DresdenDecember2002More informationAcknowledgementsIf there is any feature of this book that we are proud of,it is the fact that almost allthe methods are illustrated with real,experimental data.However,this is anythingbut our own achievement–we exploited other people’s work.Thus we are deeplyindebted to the experimental groups who supplied data sets and granted permissionto use them in this book.The production of every one of these data sets requiredskills,experience,and equipment that we ourselves do not have,not forgetting thehours and hours of work spent in the laboratory.We appreciate the generosity ofthe following experimental groups:NMR laser.Our contact persons at the Institute for Physics at Z¨u rich University were Leci Flepp and Joe Simonet;the head of the experimental group is E.Brun.(See AppendixB.2.)Vibrating string.Data were provided by Tim Molteno and Nick Tufillaro,Otago University, Dunedin,New Zealand.(See Appendix B.3.)Taylor–Couetteflow.The experiment was carried out at the Institute for Applied Physics at Kiel University by Thorsten Buzug and Gerd Pfister.(See Appendix B.4.) Atrialfibrillation.This data set is taken from the MIT-BIH Arrhythmia Database,collected by G.B.Moody and R.Mark at Beth Israel Hospital in Boston.(See Appendix B.6.) Human ECG.The ECG recordings we used were taken by Petr Saparin at Saratov State University.(See Appendix B.7.)Foetal ECG.We used noninvasively recorded(human)foetal ECGs taken by John F.Hofmeister as the Department of Obstetrics and Gynecology,University of Colorado,Denver CO.(See Appendix B.7.)Phonation data.This data set was made available by Hanspeter Herzel at the Technical University in Berlin.(See Appendix B.8.)Human posture data.The time series was provided by Steven Boker and Bennett Bertenthal at the Department of Psychology,University of Virginia,Charlottesville V A.(SeeAppendix B.9.)xvMore informationxvi AcknowledgementsAutonomous CO2laser with feedback.The data were taken by Riccardo Meucci and Marco Ciofini at the INO in Firenze,Italy.(See Appendix B.10.)Nonlinear electric resonance circuit.The experiment was designed and operated by M.Diestelhorst at the University of Halle,Germany.(See Appendix B.11.)Nd:YAG laser.The data we use were recorded in the University of Oldenburg,where we wish to thank Achim Kittel,Falk Lange,Tobias Letz,and J¨u rgen Parisi.(See AppendixB.12.)We used the following data sets published for the Santa Fe Institute Time SeriesContest,which was organised by Neil Gershenfeld and Andreas Weigend in1991:NH3laser.We used data set A and its continuation,which was published after the contest was closed.The data was supplied by U.H¨u bner,N.B.Abraham,and C.O.Weiss.(SeeAppendix B.1.)Human breath rate.The data we used is part of data set B of the contest.It was submitted by Ari Goldberger and coworkers.(See Appendix B.5.)During the composition of the text we asked various people to read all or part of themanuscript.The responses ranged from general encouragement to detailed technicalcomments.In particular we thank Peter Grassberger,James Theiler,Daniel Kaplan,Ulrich Parlitz,and Martin Wiesenfeld for their helpful remarks.Members of ourresearch groups who either contributed by joint work to our experience and knowl-edge or who volunteered to check the correctness of the text are Rainer Hegger,Andreas Schmitz,Marcus Richter,Mario Ragwitz,Frank Schm¨u ser,RathinaswamyBhavanan Govindan,and Sharon Sessions.We have also considerably profited fromcomments and remarks of the readers of thefirst edition of the book.Their effortin writing to us is gratefully appreciated.Last but not least we acknowledge the encouragement and support by SimonCapelin from Cambridge University Press and the excellent help in questions ofstyle and English grammar by Sheila Shepherd.。