Anders Henry Nielsen

TMB: Automatic differentiation and laplace approximation

TMB is an open source R package that enables quick implementation of complex nonlinear random effect (latent variable) models in a manner similar to the established AD Model Builder package (ADMB, admb-project.org). In addition, it offers easy access to parallel computations. The user defines the joint likelihood for the data and the random effects as a C++ template function, while all the other operations are done in R; e.g., reading in the data. The package evaluates and maximizes the Laplace approximation of the marginal likelihood where the random effects are automatically integrated out. This approximation, and its derivatives, are obtained using automatic differentiation (up to order three) of the joint likelihood. The computations are designed to be fast for problems with many random effects (~10^6) and parameters (~10^3). Computation times using ADMB and TMB are compared on a suite of examples ranging from simple models to large spatial models where the random effects are a Gaussian random field. Speedups ranging from 1.5 to about 100 are obtained with increasing gains for large problems. The package and examples are available at this http URL

The influence of finite Larmor radius effects on the radial interchange motions of plasma filaments

The influence of finite Larmor radius (FLR) effects on the perpendicular convection of isolated particle density filaments driven by interchange motions in magnetized plasmas is investigated using a two-moment gyrofluid model. By means of numerical simulations on a two-dimensional, bi-periodic domain perpendicular to the magnetic field, it is demonstrated that the radial velocities of the blob-like filaments are roughly described by the inertial scaling, which prescribes a velocity proportional to the square root of the summed electron and ion pressures times the square root of the blob width. Due to FLR effects, the poloidal up-down symmetry in the particle density field observed in the zero Larmor radius limit is broken. The symmetry breaking implies a poloidal motion of the blobs in the B×∇B direction. At later times, the direction of the poloidal motion is reversed when the blob is decelerated. It is shown that the spatial structure of the blobs depends on the ratio of the ion gyroradius to the initia...

Accuracy of Spectral and Finite Difference Schemes in 2D Advection Problems

In this paper we investigate the accuracy of two numerical procedures commonly used to solve 2D advection problems: spectral and finite difference (FD) schemes. These schemes are widely used, simulating, e.g., neutral and plasma flows. FD schemes have long been considered fast, relatively easy to implement, and applicable to complex geometries, but are somewhat inferior in accuracy compared to spectral schemes. Using two study cases at high Reynolds number, the merging of two equally signed Gaussian vortices in a periodic box and dipole interaction with a no-slip wall, we will demonstrate that the accuracy of FD schemes can be significantly improved if one is careful in choosing an appropriate FD scheme that reflects conservation properties of the nonlinear terms and in setting up the grid in accordance with the problem.

Fast fitting of non‐Gaussian state‐space models to animal movement data via Template Model Builder

State-space models (SSM) are often used for analyzing complex ecological processes that are not observed directly, such as marine animal movement. When outliers are present in the measurements, special care is needed in the analysis to obtain reliable location and process estimates. Here we recommend using the Laplace approximation combined with automatic differentiation (as implemented in the novel R package Template Model Builder; TMB) for the fast fitting of continuous-time multivariate non-Gaussian SSMs. Through Argos satellite tracking data, we demonstrate that the use of continuous-time t-distributed measurement errors for error-prone data is more robust to outliers and improves the location estimation compared to using discretized-time t-distributed errors (implemented with a Gibbs sampler) or using continuous-time Gaussian errors (as with the Kalman filter). Using TMB, we are able to estimate additional parameters compared to previous methods, all without requiring a substantial increase in computational time. The model implementation is made available through the R package argosTrack.

Three dimensional simulations of plasma filaments in the scrape off layer: A comparison with models of reduced dimensionality

This paper presents simulations of isolated 3D filaments in a slab geometry obtained using a newly developed 3D reduced fluid code, written using the BOUT++ framework. First, systematic scans were performed to investigate how the dynamics of a filament are affected by its amplitude, perpendicular size, and parallel extent. The perpendicular size of the filament was found to have a strong influence on its motions, as it determined the relative importance of parallel currents to polarization and viscous currents, whilst drift-wave instabilities were observed if the initial amplitude of the blob was increased sufficiently. Next, the 3D simulations were compared to 2D simulations using different parallel closures; namely, the sheath dissipation closure, which neglects parallel gradients, and the vorticity advection closure, which neglects the influence of parallel currents. The vorticity advection closure was found to not replicate the 3D perpendicular dynamics and overestimated the initial radial acceleratio...

Effects of sharp vorticity gradients in two-dimensional hydrodynamic turbulence

The appearance of sharp vorticity gradients in two-dimensional hydrodynamic turbulence and their influence on the turbulent spectra is considered. We have developed the analog of the vortex line representation as a transformation to the curvilinear system of coordinates moving together with the di-vorticity lines. Compressibility of this mapping can be considered as the main reason for the formation of the vorticity discontinuities at high Reynolds numbers. For two-dimensional turbulence in the case of strong anisotropy the vorticity discontinuities can generate spectra with the fall-off at large

Archived DNA reveals fisheries and climate induced collapse of a major fishery.

k

Numerical scalings of the decay lengths in the scrape-off layer

proportional to

Blob dynamics in the TORPEX experiment: a multi-code validation

k^{-3}

The influence of blobs on neutral particles in the scrape-off layer

resembling the Kraichnan spectrum for the enstrophy cascade. For turbulence with weak anisotropy the