Note: Intro -- Eddy Covariance -- Preface -- Contents -- Contributors -- Chapter 1: The Eddy Covariance Method -- 1.1 History -- 1.2 Preliminaries -- 1.2.1 Context of Eddy Covariance Measurements -- 1.2.2 Reynolds Decomposition -- 1.2.3 Scalar Definition -- 1.3 One Point Conservation Equations -- 1.3.1 Dry Air Mass Conservation (Continuity) Equation -- 1.3.2 Momentum Conservation Equation -- 1.3.3 Scalar Conservation Equation -- 1.3.4 Enthalpy Equation -- 1.4 Integrated Relations -- 1.4.1 Dry Air Budget Equation -- 1.4.2 Scalar Budget Equation (Generalized Eddy Covariance Method) -- 1.5 Spectral Analysis -- 1.5.1 Spectral Analysis of Turbulence -- 1.5.2 Spectral Analysis of Atmospheric Turbulence -- 1.5.3 Sensor Filtering -- 1.5.4 Impacts of Measurement Height and Wind Velocity -- References -- Chapter 2: Measurement, Tower, and Site Design Considerations -- 2.1 Introduction -- 2.2 Tower Considerations -- 2.2.1 Theoretical Considerations for Tower Design -- 2.2.1.1 Diverse Ecosystems and Environments -- 2.2.1.2 Physical Effects on Surrounding Flows Due to the Presence of Tower Structure -- 2.2.1.3 Size of Horizontal Supporting Boom -- 2.2.1.4 Tower Deflection and Oscillations -- 2.2.1.5 Recirculation Zone at the Opening in a Tall Canopy -- 2.2.2 Tower Design and Science Requirements -- 2.2.2.1 Tower Location Requirements -- 2.2.2.2 Tower Structure Requirements -- 2.2.2.3 Tower Height Requirements -- 2.2.2.4 Tower Size Requirements -- 2.2.2.5 Instrument Orientation Requirements -- 2.2.2.6 Tower Installation and Site Impact Requirements -- 2.3 Sonic Anemometer -- 2.3.1 General Principles -- 2.3.2 Problems and Corrections -- 2.3.3 Requirements for Sonic Choice, Positioning, and Use -- 2.4 Eddy CO2/H2O Analyzer -- 2.4.1 General Description -- 2.4.2 Closed-Path System -- 2.4.2.1 Absolute and Differential Mode. , 2.4.2.2 Tubing Requirements for Closed-Path Sensors -- 2.4.2.3 Calibration for CO2 -- 2.4.2.4 Water Vapor Calibration -- 2.4.3 Open-Path Systems -- 2.4.3.1 Installation and Maintenance -- 2.4.3.2 Calibration -- 2.4.4 Open and Closed Path Advantages and Disadvantages -- 2.4.5 Narrow-Band Spectroscopic CO2 Sensors -- 2.5 Profile Measurement -- 2.5.1 Requirements for Measurement Levels -- 2.5.2 Requirements for Profile Mixing Ratio Measurement -- References -- Chapter 3: Data Acquisition and Flux Calculations -- 3.1 Data Transfer and Acquisition -- 3.2 Flux Calculation from Raw Data -- 3.2.1 Signal Transformation in Meteorological Units -- 3.2.1.1 Wind Components and Speed of Sound from the Sonic Anemometer -- 3.2.1.2 Concentration from a Gas Analyzer -- 3.2.2 Quality Control of Raw Data -- 3.2.3 Variance and Covariance Computation -- 3.2.3.1 Mean and Fluctuation Computations -- 3.2.3.2 Time Lag Determination -- 3.2.4 Coordinate Rotation -- 3.2.4.1 Requirements for the Choice of the Coordinate Frame and Its Orientation -- 3.2.4.2 Coordinate Transformation Equations -- 3.2.4.3 Determination of Rotation Angles -- 3.3 Flux Determination -- 3.3.1 Momentum Flux -- 3.3.2 Buoyancy Flux and Sensible Heat Flux -- 3.3.3 Latent Heat Flux and Other Trace Gas Fluxes -- 3.3.4 Derivation of Additional Parameters -- References -- Chapter 4: Corrections and Data Quality Control -- 4.1 Flux Data Correction -- 4.1.1 Corrections Already Included into the Raw Data Analysis (Chap. 3) -- 4.1.2 Conversion of Buoyancy Flux to Sensible Heat Flux (SND-correction) -- 4.1.3 Spectral Corrections -- 4.1.3.1 Introduction -- 4.1.3.2 High-Frequency Loss Corrections -- 4.1.3.3 Low-Cut Frequency -- 4.1.4 WPL Corrections -- 4.1.4.1 Introduction -- 4.1.4.2 Open-Path Systems -- 4.1.4.3 WPL and Imperfect Instrumentation -- 4.1.4.4 Closed-Path Systems -- 4.1.5 Sensor-Specific Corrections. , 4.1.5.1 Flow Distortion Correction of Sonic Anemometers -- 4.1.5.2 Correction Due to Sensor Head Heating of the Open-Path Gas Analyzer LiCor 7500 -- 4.1.5.3 Corrections to the Krypton Hygrometer KH20 -- 4.1.5.4 Corrections for CH4 and N2O Analyzers -- 4.1.6 Nonrecommended Corrections -- 4.1.7 Overall Data Corrections -- 4.2 Effect of the Unclosed Energy Balance -- 4.2.1 Reasons for the Unclosed Energy Balance -- 4.2.2 Correction of the Unclosed Energy Balance -- 4.3 Data Quality Analysis -- 4.3.1 Quality Control of Eddy Covariance Measurements -- 4.3.2 Tests on Fulfilment of Theoretical Requirements -- 4.3.2.1 Steady State Tests -- 4.3.2.2 Test on Developed Turbulent Conditions -- 4.3.3 Overall Quality Flag System -- 4.4 Accuracy of Turbulent Fluxes After Correction and Quality Control -- 4.5 Overview of Available Correction Software -- References -- Chapter 5: Nighttime Flux Correction -- 5.1 Introduction -- 5.1.1 History -- 5.1.2 Signs Substantiating the Night Flux Error -- 5.1.2.1 Comparison with Bottom Up Approaches -- 5.1.2.2 Sensitivity of Flux to Friction Velocity -- 5.1.3 The Causes of the Problem -- 5.2 Is This Problem Really Important? -- 5.2.1 In Which Case Should the Night Flux Error Be Corrected? -- 5.2.2 What Is the Role of Storage in This Error? -- 5.2.3 What Is the Impact of Night Flux Error on Long-Term Carbon Sequestration Estimates? -- 5.2.4 What Is the Impact of the Night Flux Error on Functional Relationships? -- 5.2.5 What Is the Impact of the Night Flux Error on Other Fluxes? -- 5.3 How to Implement the Filtering Procedure? -- 5.3.1 General Principle -- 5.3.2 Choice of the Selection Criterion -- 5.3.3 Filtering Implementation -- 5.3.4 Evaluation -- 5.4 Correction Procedures -- 5.4.1 Filtering=+Gap Filling -- 5.4.2 The ACMB Procedure -- 5.4.2.1 History -- 5.4.2.2 Procedure -- 5.4.2.3 Evaluation -- References. , Chapter 6: Data Gap Filling -- 6.1 Introduction -- 6.2 Gap Filling: Why and When Is It Needed? -- 6.3 Gap-Filling Methods -- 6.3.1 Meteorological Data Gap Filling -- 6.3.2 General Rules and Strategies (Long Gaps) -- 6.3.2.1 Sites with Management and Disturbances -- 6.3.3 Methods Description -- 6.3.3.1 Mean Diurnal Variation -- 6.3.3.2 Look-Up Tables -- 6.3.3.3 Artificial Neural Networks -- 6.3.3.4 Nonlinear Regressions -- 6.3.3.5 Process Models -- 6.4 Uncertainty and Quality Flags -- 6.5 Final Remarks -- References -- Chapter 7: Uncertainty Quantification -- 7.1 Introduction -- 7.1.1 Definitions -- 7.1.2 Types of Errors -- 7.1.3 Characterizing Uncertainty -- 7.1.4 Objectives -- 7.2 Random Errors in Flux Measurements -- 7.2.1 Turbulence Sampling Error -- 7.2.2 Instrument Errors -- 7.2.3 Footprint Variability -- 7.2.4 Quantifying the Total Random Uncertainty -- 7.2.5 Overall Patterns of the Random Uncertainty -- 7.2.6 Random Uncertainties at Longer Time Scales -- 7.3 Systematic Errors in Flux Measurements -- 7.3.1 Systematic Errors Resulting from Unmet Assumptions and Methodological Challenges -- 7.3.2 Systematic Errors Resulting from Instrument Calibration and Design -- 7.3.2.1 Calibration Uncertainties -- 7.3.2.2 Spikes -- 7.3.2.3 Sonic Anemometer Errors -- 7.3.2.4 Infrared Gas Analyzer Errors -- 7.3.2.5 High-Frequency Losses -- 7.3.2.6 Density Fluctuations -- 7.3.2.7 Instrument Surface Heat Exchange -- 7.3.3 Systematic Errors Associated with Data Processing -- 7.3.3.1 Detrending and High-Pass Filtering -- 7.3.3.2 Coordinate Rotation -- 7.3.3.3 Gap Filling -- 7.3.3.4 Flux Partitioning -- 7.4 Closing Ecosystem Carbon Budgets -- 7.5 Conclusion -- References -- Chapter 8: Footprint Analysis -- 8.1 Concept of Footprint -- 8.2 Footprint Models for Atmospheric Boundary Layer -- 8.2.1 Analytical Footprint Models -- 8.2.2 Lagrangian Stochastic Approach. , 8.2.3 Forward and Backward Approach by LS Models -- 8.2.4 Footprints for Atmospheric Boundary Layer -- 8.2.5 Large-Eddy Simulations for ABL -- 8.3 Footprint Models for High Vegetation -- 8.3.1 Footprints for Forest Canopy -- 8.3.2 Footprint Dependence on Sensor and Source Heights -- 8.3.3 Influence of Higher-Order Moments -- 8.4 Complicated Landscapes and Inhomogeneous Canopies -- 8.4.1 Closure Model Approach -- 8.4.2 Model Validation -- 8.4.3 Footprint Estimation by Closure Models -- 8.4.4 Footprints over Complex Terrain -- 8.4.5 Modeling over Urban Areas -- 8.5 Quality Assessment Using Footprint Models -- 8.5.1 Quality Assessment Methodology -- 8.5.2 Site Evaluation with Analytical and LS Footprint Models -- 8.5.3 Applicability and Limitations -- 8.6 Validation of Footprint Models -- References -- Chapter 9: Partitioning of Net Fluxes -- 9.1 Motivation -- 9.2 Definitions -- 9.3 Standard Methods -- 9.3.1 Overview -- 9.3.2 Nighttime Data-Based Methods -- 9.3.2.1 Model Formulation: Temperature - Measurements -- 9.3.2.2 Reco Model Formulation -- 9.3.2.3 Challenges: Additional Drivers of Respiration -- 9.3.2.4 Challenges: Photosynthesis - Respiration Coupling and Within-Ecosystem Transport -- 9.3.3 Daytime Data-Based Methods -- 9.3.3.1 Model Formulation: The NEE Light Response -- 9.3.3.2 Challenges: Additional Drivers and the FLUXNET Database Approach -- 9.3.3.3 Unresolved Issues and Future Work -- 9.4 Additional Considerations and New Approaches -- 9.4.1 Oscillatory Patterns -- 9.4.2 Model Parameterization -- 9.4.3 Flux Partitioning Using High-Frequency Data -- 9.4.4 Flux Partitioning Using Stable Isotopes -- 9.4.5 Chamber-Based Approaches -- 9.4.6 Partitioning Water Vapor Fluxes -- 9.5 Recommendations -- References -- Chapter 10: Disjunct Eddy Covariance Method -- 10.1 Introduction -- 10.2 Theory -- 10.2.1 Sample Interval -- 10.2.2 Response Time. , 10.2.3 Definition of DEC.