1. Introduction
Linear inverse modeling (LIM) is an empirical technique of estimating the best linear stochastic model consistent with a set of multivariate data (Penland 1989; Penland and Sardeshmukh 1995a). As with autoregressive processes, LIM combines the lagged and contemporaneous covariance matrices to estimate the relevant product matrices. However, unlike autoregressive processes, LIM estimates the operator in a continuous stochastic differential equation as well as the correlation structure of the driving white noise. These operators can then be used to diagnose whether or not the governing dynamical system may be described as a linear stochastic differential equation with constant coefficients. Once linearity has been established, forecasts with a theoretically estimated error can be made, and a variety of analyses can be performed to investigate the dynamical relationships between the constituent variables. Of course, these analyses depend on the fidelity of a linear model to the real dynamical system; the mechanics of the analysis, after all, can be applied to any multivariate time series, regardless of the underlying dynamics.
Assessing this fidelity requires a strict test for the validity of LIM, and LIM is valid for time series generated by dynamical systems on a time scale where nonlinear interactions are so fast and so chaotic that they may be approximated by Gaussian white noise terms in a limiting differential equation. That is, the ultimate source of what a coarse-grained system sees as Gaussian white noise may be neither Gaussian nor white at some (unresolved) time scale. The integrated effect of rapidly varying nonlinearities is subject to the central limit theorem, so that a more slowly varying component of the multiscale system cannot be distinguished from a process driven by Gaussian white noise when represented by a coarse-grained time series (Papanicolaou and Kohler 1974; Hasselmann 1976).
As time series analysis is inherently statistical, testing for linearity is also statistical. Ideally, this test would pass only when the generating dynamical system is linear and fail only when it is not. In practice, however, statistical tests have a (hopefully small) probability of delivering a false result. Here we consider a test for linearity, the “tau test“ (e.g., Penland 1989), against a null hypothesis that the dynamical system generating a multivariate time series is nonlinear on the time scales of interest, that is, that nonlinearities cannot be estimated as a linear process with either additive or multiplicative Gaussian white noise. The tau test consists of estimating linear operators based on the lagged covariance matrices at a variety of lags τo (e.g., Penland and Sardeshmukh 1995a; Winkler et al. 2001; Shin et al. 2010; Liu et al. 2012a,b). Linear operators so estimated are expected to be independent of τo. This tau test is generally trustworthy when it passes; Penland and Sardeshmukh (1995a), for example, have shown the spectacular failures of this test when applied to the Lorenz (1963) system in its chaotic regime. Unfortunately, the tau test is notorious for also failing in some cases when the underlying dynamics should indeed be approximated as linear.
It has been shown that the tau test can spuriously fail for several reasons. If the statistics are nonstationary, the tau test will fail (Penland and Sardeshmukh 1995a). If the state vector under consideration does not represent all of the important variables, the tau test will fail (Penland and Ghil 1993). If the time series is seriously corrupted with observation errors, the tau test will fail (Penland 1998). Perhaps the most frustrating cause of tau-test failure, however, is the near inevitability of “Nyquist lags” (Penland and Sardeshmukh 1995a, their appendix B). A Nyquist lag occurs when the lag τo of the covariance matrix used to estimate the linear operator is near half the period of an intrinsic oscillatory mode of the system. Then, that mode cannot be accurately resolved numerically. If this mode is an important constituent of the dynamics, the numerically estimated linear operator is significantly corrupted, and the tau test fails.
When LIM is applied to geophysically relevant datasets, the large number of degrees of freedom requires numerical eigenanalysis, and the Nyquist problem is inevitable. It is the purpose of this article to discuss the Nyquist problem in LIM and to show how it can be resolved in a system that is simple enough to be solved analytically, but where the presence of multiple oscillatory modes requires a sequential, mode-by-mode method of handling the problem. We do not claim to solve the problem in such a general way that it is easy to automate. However, as shown below, this solution can be useful for real world problems, such with a reduced model of El Niño. We first review LIM and present the difficulties associated with the Nyquist problem. This section includes a possible solution to the problem described step by step for a single modal pair. The next section, example 1, shows how the mode-by-mode procedure can be applied to a simple four-dimensional system (two modal pairs) where the analytical solution is known. This section describes in detail both how the estimated linear operator can be corrupted when the unmodified modes are combined and how the linear operator is recovered by proper adjustment of the modes. We also show the kind of evidence that would suggest there is a Nyquist problem in the first place. Finally, to illustrate practical problems, we apply the Nyquist correction to a reduced, empirically derived model of El Niño. The formalism and terminology throughout this article are similar to those used in many previous publications by the American Meteorological Society (e.g., Farrell and Ioannou 1993; Penland and Sardeshmukh 1995a,b; DelSole 1996; Sheshadri et al. 2018, and references therein). Relevant theoretical details concerning matrix methods, for example, the Cayley–Hamilton theorem referenced below, may be found in the textbook by Bronson (1970).
2. Review of LIM and the Nyquist problem

























































It is here that the Nyquist issue arises. The eigenvalues
At first, the situation does not seem so grave. After all, if the eigenmode and adjoint do not change, it seems that all one would have to do is adjust the eigenvalue appropriately and proceed with the expansion Eq. (4b). However, things are a little more complicated. Once τo is big enough to change the sign of
3. Example 1: Two noninteracting oscillators







The multivariate time series was generated using a stochastic Euler scheme (Rümelin 1982) with a time step of (1/120) time units and output was sampled every time unit, that is, every 120 time steps, for a total of 50 000 samples. To test for any sampling issues, calculations were performed with a time series half this long and yielded similar results. Sampling issues have been discussed elsewhere (Penland and Sardeshmukh 1995b; Penland and Matrosova 2001).
This operator
LIM was applied to this output using 15 values of

Specified Euclidean norm of matrix
Citation: Monthly Weather Review 147, 4; 10.1175/MWR-D-18-0104.1

Specified Euclidean norm of matrix
Citation: Monthly Weather Review 147, 4; 10.1175/MWR-D-18-0104.1
Specified Euclidean norm of matrix
Citation: Monthly Weather Review 147, 4; 10.1175/MWR-D-18-0104.1

Comparison of raw estimation of LIM eigenvalues (blue dots) with adjustment of imaginary parts, first by subtracting the estimated value from 2π (red dots) and then by adding the estimated value to 2π (purple dots). (a) Decay rate and frequency of first modal pair. (b) Decay rate and frequency of second modal pair.
Citation: Monthly Weather Review 147, 4; 10.1175/MWR-D-18-0104.1

Comparison of raw estimation of LIM eigenvalues (blue dots) with adjustment of imaginary parts, first by subtracting the estimated value from 2π (red dots) and then by adding the estimated value to 2π (purple dots). (a) Decay rate and frequency of first modal pair. (b) Decay rate and frequency of second modal pair.
Citation: Monthly Weather Review 147, 4; 10.1175/MWR-D-18-0104.1
Comparison of raw estimation of LIM eigenvalues (blue dots) with adjustment of imaginary parts, first by subtracting the estimated value from 2π (red dots) and then by adding the estimated value to 2π (purple dots). (a) Decay rate and frequency of first modal pair. (b) Decay rate and frequency of second modal pair.
Citation: Monthly Weather Review 147, 4; 10.1175/MWR-D-18-0104.1
Turning to the modes, we compare the estimated

Real (blue lines) and imaginary parts (red lines) of mode u1 estimated using (a) τo = 3, (b) τo = 8, and (c) τo = 15. The analytically derived, normalized value of mode u1 is (1 − i, 1 + i, 0, 0)T/2.
Citation: Monthly Weather Review 147, 4; 10.1175/MWR-D-18-0104.1

Real (blue lines) and imaginary parts (red lines) of mode u1 estimated using (a) τo = 3, (b) τo = 8, and (c) τo = 15. The analytically derived, normalized value of mode u1 is (1 − i, 1 + i, 0, 0)T/2.
Citation: Monthly Weather Review 147, 4; 10.1175/MWR-D-18-0104.1
Real (blue lines) and imaginary parts (red lines) of mode u1 estimated using (a) τo = 3, (b) τo = 8, and (c) τo = 15. The analytically derived, normalized value of mode u1 is (1 − i, 1 + i, 0, 0)T/2.
Citation: Monthly Weather Review 147, 4; 10.1175/MWR-D-18-0104.1
The same type of behavior is noted for

As in Fig. 3, but for u3. The derived value of u3 is (0, 0, 1 + i, 1 − i)/2.
Citation: Monthly Weather Review 147, 4; 10.1175/MWR-D-18-0104.1

As in Fig. 3, but for u3. The derived value of u3 is (0, 0, 1 + i, 1 − i)/2.
Citation: Monthly Weather Review 147, 4; 10.1175/MWR-D-18-0104.1
As in Fig. 3, but for u3. The derived value of u3 is (0, 0, 1 + i, 1 − i)/2.
Citation: Monthly Weather Review 147, 4; 10.1175/MWR-D-18-0104.1
Fortunately, the recombination of the operator

Bubble plots representing specified [Eq. (7a)], estimated, and adjusted matrices
Citation: Monthly Weather Review 147, 4; 10.1175/MWR-D-18-0104.1

Bubble plots representing specified [Eq. (7a)], estimated, and adjusted matrices
Citation: Monthly Weather Review 147, 4; 10.1175/MWR-D-18-0104.1
Bubble plots representing specified [Eq. (7a)], estimated, and adjusted matrices
Citation: Monthly Weather Review 147, 4; 10.1175/MWR-D-18-0104.1
Again, the results of this section were obtained with very long time series, and we note here the findings of Penland and Sardeshmukh (1995b) that recombined products of the eigenanalysis performed with LIM on time series of more usual length are more accurate than any of the individual modal products themselves.
4. Example 2: A reduced model of El Niño
Penland and Matrosova (2006) showed that El Niño as represented in sea surface temperature (SST) data could be well approximated as a six-component system consisting of three empirical eigenmode pairs. This six-component system, a subset of modes estimated using LIM applied to SSTs in the tropical belt, described the nonnormal evolution from an optimal initial condition to a mature El Niño pattern. It is not the purpose of this article to consider the El Niño phenomenon; rather, this six-component system is an ideal showcase for the uncertainties and Nyquist issues encountered when LIM is applied in a realistic situation.
LIM was applied to three-month running mean SST anomalies from the Comprehensive Ocean–Atmosphere Data Set (COADS) monthly SST data between 1950 and 1997 (Woodruff et al. 1993), concatenated with three years (1998–2000) of a real-time surface marine data product from the National Centers for Environmental Prediction (NCEP), for a total of 598 samples. The running mean was required to allow subsurface dynamical information time to migrate into the SST while maintaining a time series long enough to perform the LIM procedure. (Modern applications of LIM to El Niño take advantage of subsurface reanalyses which were not available to Penland and Sardeshmukh in 1995, on which the 2006 study was based.) Details of the data analysis are found in Penland and Matrosova (2006). The characteristics of this three-modal pair system as estimated using
Time scales of empirically derived modes.



Euclidean norm of an operator representing a reduced model of El Niño.
Citation: Monthly Weather Review 147, 4; 10.1175/MWR-D-18-0104.1

Euclidean norm of an operator representing a reduced model of El Niño.
Citation: Monthly Weather Review 147, 4; 10.1175/MWR-D-18-0104.1
Euclidean norm of an operator representing a reduced model of El Niño.
Citation: Monthly Weather Review 147, 4; 10.1175/MWR-D-18-0104.1
To test the vagaries of LIM applied to a time series of typical length, we use the constant matrices

As in Fig. 6, but on a log plot showing Euclidean norms from a numerically generated ensemble of 50 Ornstein–Uhlenbeck processes evaluated using τo = 4 months (crosses) and τo = 10 months (filled symbols).
Citation: Monthly Weather Review 147, 4; 10.1175/MWR-D-18-0104.1

As in Fig. 6, but on a log plot showing Euclidean norms from a numerically generated ensemble of 50 Ornstein–Uhlenbeck processes evaluated using τo = 4 months (crosses) and τo = 10 months (filled symbols).
Citation: Monthly Weather Review 147, 4; 10.1175/MWR-D-18-0104.1
As in Fig. 6, but on a log plot showing Euclidean norms from a numerically generated ensemble of 50 Ornstein–Uhlenbeck processes evaluated using τo = 4 months (crosses) and τo = 10 months (filled symbols).
Citation: Monthly Weather Review 147, 4; 10.1175/MWR-D-18-0104.1
One implication of this result is that there is no simple way to adjust the modes estimated with values in the vicinity of the Nyquist lag when the time series is short enough to make those modes highly uncertain. What we can do is look at the time scales associated with the eigenvalues. Figure 8 shows the decay time and period of the most rapidly varying mode as estimated by LIM from the COADS data as function of

Raw estimation (blue) of decay times (circles) and periods (squares) in months from COADS data using LIM as a function of τo. Also shown are the periods resulting from subtracting the estimated angular frequency from 2π (red squares). The Nyquist lag at 11 months is indicated by the vertical line.
Citation: Monthly Weather Review 147, 4; 10.1175/MWR-D-18-0104.1

Raw estimation (blue) of decay times (circles) and periods (squares) in months from COADS data using LIM as a function of τo. Also shown are the periods resulting from subtracting the estimated angular frequency from 2π (red squares). The Nyquist lag at 11 months is indicated by the vertical line.
Citation: Monthly Weather Review 147, 4; 10.1175/MWR-D-18-0104.1
Raw estimation (blue) of decay times (circles) and periods (squares) in months from COADS data using LIM as a function of τo. Also shown are the periods resulting from subtracting the estimated angular frequency from 2π (red squares). The Nyquist lag at 11 months is indicated by the vertical line.
Citation: Monthly Weather Review 147, 4; 10.1175/MWR-D-18-0104.1
5. Conclusions
LIM has been shown to be a useful diagnostic and predictive tool in geophysics specialties as diverse as megadroughts (e.g., Ault et al. 2018, summarized in Physics Today 2018), anthropogenic forcing of global change (e.g., Frankignoul et al. 2017), planetary turbulence (e.g., DelSole and Farrell 1996), monsoon precipitation (e.g., Priya et al. 2015), ocean–atmosphere coupling (e.g., Smirnov et al. 2014), El Niño (e.g., Penland and Sardeshmukh 1995a), and midlatitude low-frequency variability (e.g., Penland and Ghil 1993). An integral part of LIM concerns validation of its underlying assumption of linearity. Since the definition of an exponential function is the unique solution of a linear equation, establishment that the autocovariance matrix function of a dataset follows an exponential law is strong indication of linearity. The test for this exponential law is called the “tau test,” and, although this test may generally be trusted when it passes, this test has been shown to fail sometimes when it ought to pass.
There are several reasons why failure can occur even when the linearity assumption is true, the most pernicious of which may be the Nyquist issue. Unfortunately, in spite of repeated warnings in the literature, the Nyquist issue in LIM is often underappreciated to the extent that some practitioners of the method have lately expressed some surprise when apprised of it. This article discusses the issue in detail and presents a possible solution when the time series is long enough to apply it; that is, when the time series and the dynamical decay times associated with it are long enough to identify the modes uniquely.
As with all analyses, the LIM technique has its drawbacks, and the Nyquist issue is one of them. The Nyquist issue plagues not only LIM, but other techniques such as generalized equilibrium feedback analysis (GEFA; Liu et al. 2012a) and, as is well known, Fourier analysis. It is as tempting to ignore the limitations of a powerful technique when one uses it as it is to emphasize them when the results are unpopular. Dispassionate analysis requires careful consideration of the techniques used, and we hope that awareness of the Nyquist issue in LIM will help researchers to avoid misinterpretation of LIM results.
Acknowledgments
The author is indebted to the reviewers of this manuscript for their accurate and useful comments.
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