1,523 research outputs found
Detecting adaptive evolution in phylogenetic comparative analysis using the Ornstein-Uhlenbeck model
Phylogenetic comparative analysis is an approach to inferring evolutionary
process from a combination of phylogenetic and phenotypic data. The last few
years have seen increasingly sophisticated models employed in the evaluation of
more and more detailed evolutionary hypotheses, including adaptive hypotheses
with multiple selective optima and hypotheses with rate variation within and
across lineages. The statistical performance of these sophisticated models has
received relatively little systematic attention, however. We conducted an
extensive simulation study to quantify the statistical properties of a class of
models toward the simpler end of the spectrum that model phenotypic evolution
using Ornstein-Uhlenbeck processes. We focused on identifying where, how, and
why these methods break down so that users can apply them with greater
understanding of their strengths and weaknesses. Our analysis identifies three
key determinants of performance: a discriminability ratio, a signal-to-noise
ratio, and the number of taxa sampled. Interestingly, we find that
model-selection power can be high even in regions that were previously thought
to be difficult, such as when tree size is small. On the other hand, we find
that model parameters are in many circumstances difficult to estimate
accurately, indicating a relative paucity of information in the data relative
to these parameters. Nevertheless, we note that accurate model selection is
often possible when parameters are only weakly identified. Our results have
implications for more sophisticated methods inasmuch as the latter are
generalizations of the case we study.Comment: 38 pages, in press at Systematic Biolog
Statistical Inference for Partially Observed Markov Processes via the R Package pomp
Partially observed Markov process (POMP) models, also known as hidden Markov
models or state space models, are ubiquitous tools for time series analysis.
The R package pomp provides a very flexible framework for Monte Carlo
statistical investigations using nonlinear, non-Gaussian POMP models. A range
of modern statistical methods for POMP models have been implemented in this
framework including sequential Monte Carlo, iterated filtering, particle Markov
chain Monte Carlo, approximate Bayesian computation, maximum synthetic
likelihood estimation, nonlinear forecasting, and trajectory matching. In this
paper, we demonstrate the application of these methodologies using some simple
toy problems. We also illustrate the specification of more complex POMP models,
using a nonlinear epidemiological model with a discrete population,
seasonality, and extra-demographic stochasticity. We discuss the specification
of user-defined models and the development of additional methods within the
programming environment provided by pomp.Comment: In press at the Journal of Statistical Software. A version of this
paper is provided at the pomp package website: http://kingaa.github.io/pom
Choices and trade-offs in inference with infectious disease models.
Inference using mathematical models of infectious disease dynamics can be an invaluable tool for the interpretation and analysis of epidemiological data. However, researchers wishing to use this tool are faced with a choice of models and model types, simulation methods, inference methods and software packages. Given the multitude of options, it can be challenging to decide on the best approach. Here, we delineate the choices and trade-offs involved in deciding on an approach for inference, and discuss aspects that might inform this decision. We provide examples of inference with a dataset of influenza cases using the R packages pomp and rbi
Microgravity Drill and Anchor System
This work is a method to drill into a rock surface regardless of the gravitational field or orientation. The required weight-on-bit (WOB) is supplied by a self-contained anchoring mechanism. The system includes a rotary percussive coring drill, forming a complete sampling instrument usable by robot or human. This method of in situ sample acquisition using micro - spine anchoring technology enables several NASA mission concepts not currently possible with existing technology, including sampling from consolidated rock on asteroids, providing a bolt network for astronauts visiting a near-Earth asteroid, and sampling from the ceilings or vertical walls of lava tubes and cliff faces on Mars. One of the most fundamental parameters of drilling is the WOB; essentially, the load applied to the bit that allows it to cut, creating a reaction force normal to the surface. In every drilling application, there is a minimum WOB that must be maintained for the system to function properly. In microgravity (asteroids and comets), even a small WOB could not be supported conventionally by the weight of the robot or astronaut. An anchoring mechanism would be needed to resist the reactions, or the robot or astronaut would push themselves off the surface and into space. The ability of the system to anchor itself to a surface creates potential applications that reach beyond use in low gravity. The use of these anchoring mechanisms as end effectors on climbing robots has the potential of vastly expanding the scope of what is considered accessible terrain. Further, because the drill is supported by its own anchor rather than by a robotic arm, the workspace is not constrained by the reach of such an arm. Yet, if the drill is on a robotic arm, it has the benefit of not reflecting the forces of drilling back to the arm s joints. Combining the drill with the anchoring feet will create a highly mobile, highly stable, and highly reliable system. The drilling system s anchor uses hundreds of microspine toes that independently find holes and ledges on a rock to create an anchor. Once the system is anchored, a linear translation mechanism moves the drill axially into the surface while maintaining the proper WOB. The linear translation mechanism is composed of a ball screw and stepper motor that can translate a carriage with high precision and applied load. The carriage slides along rails using self-aligning linear bearings that correct any axial misalignment caused by bending and torsion. The carriage then compresses a series of springs that simultaneously transmit the load to the drill along the bit axis and act as a suspension that compensates for the vibration caused by percussive drilling. The drill is a compacted, modified version of an off-the-shelf rotary percussive drill, which uses a custom carbide-tipped coring bit. By using rotary percussive drilling, the drill time is greatly reduced. The percussive action fractures the rock debris, which is removed during rotation. The final result is a 0.75-in. (.1.9- cm) diameter hole and a preserved 0.5- in. (.1.3-cm) diameter rock core. This work extends microspine technology, making it applicable to astronaut missions to asteroids and a host of robotic sampling concepts. At the time of this reporting, it is the first instrument to be demonstrated using microspine anchors, and is the first self-contained drill/anchor system to be demonstrated that is capable of drilling in inverted configurations and would be capable of drilling in microgravity
Statistical Inference for Spatiotemporal Partially Observed Markov Processes via the R Package spatPomp
We consider inference for a class of nonlinear stochastic processes with
latent dynamic variables and spatial structure. The spatial structure takes the
form of a finite collection of spatial units that are dynamically coupled. We
assume that the latent processes have a Markovian structure and that
unit-specific noisy measurements are made. A model of this form is called a
spatiotemporal partially observed Markov process (SpatPOMP). The R package
spatPomp provides an environment for implementing SpatPOMP models, analyzing
data, and developing new inference approaches. We describe the spatPomp
implementations of some methods with scaling properties suited to SpatPOMP
models. We demonstrate the package on a simple Gaussian system and on a
nontrivial epidemiological model for measles transmission within and between
cities. We show how to construct user-specified SpatPOMP models within
spatPomp
Systems and Methods for Gravity-Independent Gripping and Drilling
Systems and methods for gravity independent gripping and drilling are described. The gripping device can also comprise a drill or sampling devices for drilling and/or sampling in microgravity environments, or on vertical or inverted surfaces in environments where gravity is present. A robotic system can be connected with the gripping and drilling devices via an ankle interface adapted to distribute the forces realized from the robotic system
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