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Register a new userIs your phylogeny informative? Measuring the power of comparative methods
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Phylogenetic comparative methods may fail to produce meaningful results when either the underlying model is inappropriate or the data contain insufficient information to inform the inference. The ability to measure the statistical power of these methods has become crucial to ensure that data quantity keeps pace with growing model complexity. Through simulations, we show that commonly applied model choice methods based on information criteria can have remarkably high error rates; this can be a problem because methods to estimate the uncertainty or power are not widely known or applied. Furthermore, the power of comparative methods can depend significantly on the structure of the data. We describe a Monte Carlo based method which addresses both of these challenges, and show how this approach both quantifies and substantially reduces errors relative to information criteria. The method also produces meaningful confidence intervals for model parameters. We illustrate how the power to distinguish different models, such as varying levels of selection, varies both with number of taxa and structure of the phylogeny. We provide an open-source implementation in the pmc (Phylogenetic Monte Carlo) package for the R programming language. We hope such power analysis becomes a routine part of model comparison in comparative methods.
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In the course of animal development, the shape of tissue emerges in part from mechanical and biochemical interactions between cells. Measuring stress in tissue is essential for studying morphogenesis and its physical constraints. Experimental measurements of stress reported thus far have been invasive, indirect, or local. One theoretical approach is force inference from cell shapes and connectivity, which is non-invasive, can provide a space-time map of stress and relies on prefactors. Here, to validate force- inference methods, we performed a comparative study of them. Three force-inference methods, which differ in their approach of treating indefiniteness in an inverse problem between cell shapes and forces, were tested by using two artificial and two experimental data sets. Our results using different datasets consistently indicate that our Bayesian force inference, by which cell-junction tensions and cell pressures are simultaneously estimated, performs best in terms of accuracy and robustness. Moreover, by measuring the stress anisotropy and relaxation, we cross-validated the force inference and the global annular ablation of tissue, each of which relies on different prefactors. A practical choice of force-inference methods in distinct systems of interest is discussed.
It is generally accepted that, when moving in groups, animals process information to coordinate their motion. Recent studies have begun to apply rigorous methods based on Information Theory to quantify such distributed computation. Following this perspective, we use transfer entropy to quantify dynamic information flows locally in space and time across a school of fish during directional changes around a circular tank, i.e. U-turns. This analysis reveals peaks in information flows during collective U-turns and identifies two different flows: an informative flow (positive transfer entropy) based on fish that have already turned about fish that are turning, and a misinformative flow (negative transfer entropy) based on fish that have not turned yet about fish that are turning. We also reveal that the information flows are related to relative position and alignment between fish, and identify spatial patterns of information and misinformation cascades. This study offers several methodological contributions and we expect further application of these methodologies to reveal intricacies of self-organisation in other animal groups and active matter in general.
Bayesian methods - either based on Bayes Factors or BIC - are now widely used for model selection. One property that might reasonably be demanded of any model selection method is that if a model ${M}_{1}$ is preferred to a model ${M}_{0}$, when these two models are expressed as members of one model class $mathbb{M}$, this preference is preserved when they are embedded in a different class $mathbb{M}$. However, we illustrate in this paper that with the usual implementation of these common Bayesian procedures this property does not hold true even approximately. We therefore contend that to use these methods it is first necessary for there to exist a natural embedding class. We argue that in any context like the one illustrated in our running example of Bayesian model selection of binary phylogenetic trees there is no such embedding.
The number of $n$-gaussoids is shown to be a double exponential function in $n$. The necessary bounds are achieved by studying construction methods for gaussoids that rely on prescribing $3$-minors and encoding the resulting combinatorial constraints in a suitable transitive graph. Various special classes of gaussoids arise from restricting the allowed $3$-minors.
Two separate statistical tests are described and developed in order to test un-binned data sets for adherence to the power-law form. The first test employs the TP-statistic, a function defined to deviate from zero when the sample deviates from the power-law form, regardless of the value of the power index. The second test employs a likelihood ratio test to reject a power-law background in favor of a model signal distribution with a cut-off.
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