Stochastic Pdes and Markov Random Fields with Ecological Applications
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Intro SPDE GMRF Examples Boundaries Excursions References Stochastic PDEs and Markov random fields with ecological applications Finn Lindgren Spatially-varying Stochastic Differential Equations with Applications to the Biological Sciences OSU, Columbus, Ohio, 2015 Finn Lindgren - [email protected] Stochastic PDEs and Markov random fields with ecological applications Intro SPDE GMRF Examples Boundaries Excursions References “Big” data Z(Dtrn) 20 15 10 5 Illustration: Synthetic data mimicking satellite based CO2 measurements. Iregular data locations, uneven coverage, features on different scales. Finn Lindgren - [email protected] Stochastic PDEs and Markov random fields with ecological applications Intro SPDE GMRF Examples Boundaries Excursions References Sparse spatial coverage of temperature measurements raw data (y) 200409 kriged (eta+zed) etazed field 20 15 15 10 10 10 5 5 lat lat lat 0 0 0 −10 −5 −5 44 46 48 50 52 44 46 48 50 52 44 46 48 50 52 −20 2 4 6 8 10 14 2 4 6 8 10 14 2 4 6 8 10 14 lon lon lon residual (y − (eta+zed)) climate (eta) eta field 20 2 15 18 10 16 1 14 5 lat 0 lat lat 12 0 10 −1 8 −5 44 46 48 50 52 6 −2 44 46 48 50 52 44 46 48 50 52 2 4 6 8 10 14 2 4 6 8 10 14 2 4 6 8 10 14 lon lon lon Regional observations: ≈ 20,000,000 from daily timeseries over 160 years Finn Lindgren - [email protected] Stochastic PDEs and Markov random fields with ecological applications Intro SPDE GMRF Examples Boundaries Excursions References Spatio-temporal modelling framework Spatial statistics framework ◮ Spatial domain D, or space-time domain D × T, T ⊂ R. ◮ Random field u(s), s ∈ D, or u(s, t), (s, t) ∈ D × T. ◮ Observations yi . In the simplest setting, yi = u(si )+ ǫi , but more generally yi ∼ GLMM, with u(·) as a structured random effect. ◮ Needed: models capturing stochastic dependence on multiple scales ◮ Partial solution: Basis function expansions, with large scale functions and covariates to capture static and slow structures, and small scale functions for more local variability Two basic model and method components ◮ Stochastic models for u(·). ◮ Computationally efficient (i.e. avoid MCMC whenever possible) inference methods for the posterior distribution of u(·) given data y. Finn Lindgren - [email protected] Stochastic PDEs and Markov random fields with ecological applications Intro SPDE GMRF Examples Boundaries Excursions References Covariance functions and stochastic PDEs The Matérn covariance family on Rd 21−ν Cov(u(0), u(s)) = σ2 (κksk)ν K (κksk) Γ(ν) ν Scale κ> 0, smoothness ν > 0, variance σ2 > 0 Whittle (1954, 1963): Matérn as SPDE solution Matérn fields are the stationary solutions to the SPDE α/2 κ2 −∇·∇ u(s)= W(s), α = ν + d/2 2 d ∂ 2 Γ(ν) W(·) white noise, ∇·∇ = i 2 , σ = 2ν d/2 =1 ∂si Γ(α)κ (4π) P Questions: What is “white noise”? How can we define fractional operators? How can we deal with SPDEs in hierarchical models? Why do we want to? Finn Lindgren - [email protected] Stochastic PDEs and Markov random fields with ecological applications Intro SPDE GMRF Examples Boundaries Excursions References Generalised Spectrum Markov White noise on continuous domains, and Brownian motion ∗ Let W (f ) be a Gaussian random measure for functions f ∈ L2(D), such that ∗ ∗ ∗ E(W (1A)) = 0, Cov(W (1A), W (1B )) = |A ∩ B|Leb(D). for all Lebesgue-measurable A, B ⊆ D. Gaussian white noise W(s) is then formally defined by defining ∗ hf , WiD ≡W (f ), so that E(hf , WiD ) = 0, s s s Cov(hf , WiD , hg, WiD )= hf , giD ≡ f ( )g( )d , ZD hf , WiD ∼N (0, hf , f iD ) The Brownian motion Wt on R and the associated stochastic differential ∗ dWt from Radu’s lectures are related to W and W via ∗ Wt = W (1[0,t]) dWt = W(t)dt Finn Lindgren - [email protected] Stochastic PDEs and Markov random fields with ecological applications Intro SPDE GMRF Examples Boundaries Excursions References Generalised Spectrum Markov A Gaussian random field u : D 7→ R is defined via E(u(s)) = m(s), Cov(u(s), u(s′)) = K (s, s′), u(si ), i = 1,..., n ∼N (m = m(si ), i = 1,..., n , Σ s s = K ( i , j ), i, j = 1,..., n ) for all finite location sets {s1,..., sn }, and K (·, ·) symmetric positive definite. A generalised Gaussian random field u : D 7→ R is defined via a random ∗ R measure, hf , uiD = u (f ): HR(D) 7→ , s s s E(hf , uiD )= hf , miD = f ( )m( )d , ZD s s s′ s′ s s′ Cov(hf , uiD , hg, uiD )= hf , RgiD ≡ f ( )K ( , )g( )d d , ZZD×D hf , uiD ∼N (hf , miD , hf , Rf iD ) R for all f , g ∈ HR(D) ≡ {f : D 7→ ; hf , Rf iD < ∞}. This allows for singular covariance kernels K (·, ·). Finn Lindgren - [email protected] Stochastic PDEs and Markov random fields with ecological applications Intro SPDE GMRF Examples Boundaries Excursions References Generalised Spectrum Markov White noise vs independent noise Gaussian white noise on continuous domains Standard Gaussian white noise W(·) is a generalised random field, with s s s′ s′ m( ) = 0, K ( , )= δs( ), hf , WiD ∼N (0, hf , f iD ), s for all f ∈ L2(D). Since hδs,δsiD = ∞ for all ∈ D, W(·) does not have pointwise meaning. We can only do calculus! Independent Gaussian noise Spatially independent Gaussian noise w(·) is a random field, with ′ m(s) = 0, K (s, s )= 1{s=s′}, w(s) ∼N (0, 1), ′ for all s, s ∈ D. However, for every set A ⊂ D with |A|Leb(D) > 0, P(sup w(s)= ∞)= P(inf w(s)= −∞) = 1, s s∈A ∈A and the generalised calculus is not applicable. Finn Lindgren - [email protected] Stochastic PDEs and Markov random fields with ecological applications Intro SPDE GMRF Examples Boundaries Excursions References Generalised Spectrum Markov Spectral properties Bochner’s theorem on Rd A symmetric kernel K (s, s′), s, s′ ∈ Rd , is a positive (semi-)definite stationary covariance kernel if and only if there exists a non-negative spectral measure S ∗(ω) such that K (s, s′)= exp(i(s′ − s) · ω)dS ∗(ω) Rd Z If the measure has a density S(ω), K (s, s′)= exp(i(s′ − s) · ω)S(ω)dω Rd Z 1 s s s S(ω)= d exp(−i · ω)K (0, )d (2π) Rd Z d d White noise on R has spectral density SW (ω) = 1/(2π) . Finn Lindgren - [email protected] Stochastic PDEs and Markov random fields with ecological applications Intro SPDE GMRF Examples Boundaries Excursions References Generalised Spectrum Markov Rd s s s Let D = , and f (ω)=(Ff )(ω)= Rd exp(i · ω)f ( )d . Very informally, S (ω)= E(|u(ω)|2). u R Differential operatorsb can also be interpreted spectrally: Lf b f ∇f −∇·∇f Lα/2f Lf ≡ F(Lf ) f iωf kωk2f |L|α/2f The rightmost column is a definition of a fractional operator! For the Whittle-Matérnbb SPDE, informally,b b b b b (κ2 −∇·∇)α/2u(s)= W(s) (κ2 + kωk2)α/2u(ω)= W(ω) E(|(κ2 + kωk2)α/2u(ω)|2)= E(|W(ω)|2) c 2 2 α b (κ + kωk ) Su (ω)= SW (ω) c b 1 S (ω)= u (2π)d (κ2 + kωk2)α ′ Whittle (1954, 1963) showed that (FSu (·))(s − s) is equal to the Matérn covariance (up to a known scaling constant), with smoothness ν = α − d/2. Finn Lindgren - [email protected] Stochastic PDEs and Markov random fields with ecological applications Intro SPDE GMRF Examples Boundaries Excursions References Generalised Spectrum Markov Simple heat equation d For space-time fields, we write u(s, t), (s, t) ∈ R × R, and Su (k,ω), (k,ω) ∈ Rd × R. We drive a heat equation with a noise process E that is white noise in time and Matérn noise in space, with parameters matching the heat operator: ∂ γ + κ2 −∇ ·∇ u(s)= E(s, t), ∂t s s 2 α/2 (κ −∇s ·∇s ) E(s, t)= W(s, t). The Fourier domain version is iγω + κ2 + kkk2 u(k,ω)= E(k,ω), (κ2 + kkk2)α/ 2E(k,ω)= W(k,ω), b b and b c 1 S (k,ω)= u (2π)d+1(γ2ω2 +(κ2 + kkk2)2)(κ2 + kkk2)α How differentiable are the realisations? Finn Lindgren - [email protected] Stochastic PDEs and Markov random fields with ecological applications Intro SPDE GMRF Examples Boundaries Excursions References Generalised Spectrum Markov Simple heat equation (cont) Using that, in the standardised Whittle-Matérn SPDE, the variance is Γ(ν) σ2 = , ν = α − d/2, Γ(α)κ2ν (4π)d/2 the marginal spatial spectrum for the heat model is 1 1 Su (k)= Su (k,ω)dω = d , R 4πγ (2π) (κ2 + kkk2)α+1 Z which is a scaled Whittle spectrum for a Matérn covariance with smoothness ν = α + 1 − d/2. If α = 0, d = 2, then ν = 0, which is just outside of the allowed range of the Matérn family. However, for every t, u(·, t) is a generalised random field with s s′ 1 1 s′ s singular kernel K ( , )= 4πγ 2π K0(κk − k). Finn Lindgren - [email protected] Stochastic PDEs and Markov random fields with ecological applications Intro SPDE GMRF Examples Boundaries Excursions References Generalised Spectrum Markov Simple heat equation (cont) To help understand the temporal properties, take the Fourier transform in only the spatial directions: ∂ W(k, t) γ + κ2 + kkk2 u(k, t)= , ∂t (κ2 + kkk2)α/2 f so for each spatial frequency k, thee temporal evolution of u(k, t) is an Ornstein-Uhlenbeck process with covariance e 1 κ2 + kkk2 exp −|t| .