Model averaging in ecology Dormann, Carsten F.; Calabrese, Justin M.; Guillera-Arroita, Gurutzeta ...
Ecological monographs,
November 2018, Letnik:
88, Številka:
4
Journal Article
Recenzirano
Odprti dostop
In ecology, the true causal structure for a given problem is often not known, and several plausible models and thus model predictions exist. It has been claimed that using weighted averages of these ...models can reduce prediction error, as well as better reflect model selection uncertainty. These claims, however, are often demonstrated by isolated examples. Analysts must better understand under which conditions model averaging can improve predictions and their uncertainty estimates. Moreover, a large range of different model averaging methods exists, raising the question of how they differ in their behaviour and performance. Here, we review the mathematical foundations of model averaging along with the diversity of approaches available. We explain that the error in model-averaged predictions depends on each model's predictive bias and variance, as well as the covariance in predictions between models, and uncertainty about model weights. We show that model averaging is particularly useful if the predictive error of contributing model predictions is dominated by variance, and if the covariance between models is low. For noisy data, which predominate in ecology, these conditions will often be met. Many different methods to derive averaging weights exist, from Bayesian over information-theoretical to cross-validation optimized and resampling approaches. A general recommendation is difficult, because the performance of methods is often context dependent. Importantly, estimating weights creates some additional uncertainty. As a result, estimated model weights may not always outperform arbitrary fixed weights, such as equal weights for all models. When averaging a set of models with many inadequate models, however, estimating model weights will typically be superior to equal weights. We also investigate the quality of the confidence intervals calculated for model-averaged predictions, showing that they differ greatly in behaviour and seldom manage to achieve nominal coverage. Our overall recommendations stress the importance of non-parametric methods such as cross-validation for a reliable uncertainty quantification of model-averaged predictions.
Predictive performance is important to many applications of species distribution models (SDMs). The SDM ‘ensemble’ approach, which combines predictions across different modelling methods, is believed ...to improve predictive performance, and is used in many recent SDM studies. Here, we aim to compare the predictive performance of ensemble species distribution models to that of individual models, using a large presence–absence dataset of eucalypt tree species. To test model performance, we divided our dataset into calibration and evaluation folds using two spatial blocking strategies (checkerboard‐pattern and latitudinal slicing). We calibrated and cross‐validated all models within the calibration folds, using both repeated random division of data (a common approach) and spatial blocking. Ensembles were built using the software package ‘biomod2’, with standard (‘untuned’) settings. Boosted regression tree (BRT) models were also fitted to the same data, tuned according to published procedures. We then used evaluation folds to compare ensembles against both their component untuned individual models, and against the BRTs. We used area under the receiver‐operating characteristic curve (AUC) and log‐likelihood for assessing model performance. In all our tests, ensemble models performed well, but not consistently better than their component untuned individual models or tuned BRTs across all tests. Moreover, choosing untuned individual models with best cross‐validation performance also yielded good external performance, with blocked cross‐validation proving better suited for this choice, in this study, than repeated random cross‐validation. The latitudinal slice test was only possible for four species; this showed some individual models, and particularly the tuned one, performing better than ensembles. This study shows no particular benefit to using ensembles over individual tuned models. It also suggests that further robust testing of performance is required for situations where models are used to predict to distant places or environments.
Over the past few years, interest in health research has increased, making improved health a global goal for 2030. The purpose of such research is to ensure healthy lives and promote wellbeing across ...individuals of all ages. It has been shown that nutrition plays a key role in the prevention of some chronic diseases such as obesity, cardiovascular disease, diabetes, and cancer. One of the aspects that characterises a healthy diet is a high intake of vegetables and fruits, as both are flavonoid-rich foods. Flavonoids are one of the main subclasses of dietary polyphenols and possess strong antioxidant activity and anti-carcinogenic properties. Moreover, some population-based studies have described a relationship between cancer risk and dietary flavonoid intake. In this context, the goal of this review was to provide an updated evaluation of the association between the risk of different types of cancers and dietary flavonoid intake. We analysed all relevant epidemiological studies from January 2008 to March 2019 using the PUBMED and Web of Science databases. In summary, this review concludes that dietary flavonoid intake is associated with a reduced risk of different types of cancer, such as gastric, breast, prostate, and colorectal cancers.
This book offers a homogeneous presentation of the many faces of non-equilibrium thermodynamics. The first part is devoted to a description of the nowadays thermodynamic formalism recognized as the ...classical theory of non-equilibrium processes. This part of the book may serve as a basis to an introductory course dedicated to first-year graduate students in sciences and engineering. The classical description can however not be complete, as it rests on the hypothesis of local equilibrium. This has fostered the development of many theories going beyond local equilibrium and which cannot be put aside. The second part of the book is concerned with these different approaches, and will be of special interest for PhD students and researchers. For the sake of homogeneity, the authors have used the general structure and methods presented in the first part. Indeed, besides their differences, all these formalisms are not closed boxes but present some overlappings and parallelisms which are emphasized in this book. For pedagogical reasons, some problems have been analysed within the different formalisms to underline their differences and their convergences.
An increasing fraction of today's social interactions occur using online social media as communication channels. Recent worldwide events, such as social movements in Spain or revolts in the Middle ...East, highlight their capacity to boost people's coordination. Online networks display in general a rich internal structure where users can choose among different types and intensity of interactions. Despite this, there are still open questions regarding the social value of online interactions. For example, the existence of users with millions of online friends sheds doubts on the relevance of these relations. In this work, we focus on Twitter, one of the most popular online social networks, and find that the network formed by the basic type of connections is organized in groups. The activity of the users conforms to the landscape determined by such groups. Furthermore, Twitter's distinction between different types of interactions allows us to establish a parallelism between online and offline social networks: personal interactions are more likely to occur on internal links to the groups (the weakness of strong ties); events transmitting new information go preferentially through links connecting different groups (the strength of weak ties) or even more through links connecting to users belonging to several groups that act as brokers (the strength of intermediary ties).
As a consequence of the accelerated globalization process, today major cities all over the world are characterized by an increasing multiculturalism. The integration of immigrant communities may be ...affected by social polarization and spatial segregation. How are these dynamics evolving over time? To what extent the different policies launched to tackle these problems are working? These are critical questions traditionally addressed by studies based on surveys and census data. Such sources are safe to avoid spurious biases, but the data collection becomes an intensive and rather expensive work. Here, we conduct a comprehensive study on immigrant integration in 53 world cities by introducing an innovative approach: an analysis of the spatio-temporal communication patterns of immigrant and local communities based on language detection in Twitter and on novel metrics of spatial integration. We quantify the Power of Integration of cities -their capacity to spatially integrate diverse cultures- and characterize the relations between different cultures when acting as hosts or immigrants.
Bioelectronic devices must be fast and sensitive to interact with the rapid, low-amplitude signals generated by neural tissue. They should also be biocompatible and soft, and should exhibit long-term ...stability in physiologic environments. Here, we develop an enhancement-mode, internal ion-gated organic electrochemical transistor (e-IGT) based on a reversible redox reaction and hydrated ion reservoirs within the conducting polymer channel, which enable long-term stable operation and shortened ion transit time. E-IGT transient responses depend on hole rather than ion mobility, and combine with high transconductance to result in a gain-bandwidth product that is several orders of magnitude above that of other ion-based transistors. We used these transistors to acquire a wide range of electrophysiological signals, including in vivo recording of neural action potentials, and to create soft, biocompatible, long-term implantable neural processing units for the real-time detection of epileptic discharges. E-IGTs offer a safe, reliable and high-performance building block for chronically implanted bioelectronics, with a spatiotemporal resolution at the scale of individual neurons.
Abstract
The range of technologies currently used in biodiversity conservation is staggering, with innovative uses often adopted from other disciplines and being trialed in the field. We provide the ...first comprehensive overview of the current (2020) landscape of conservation technology, encompassing technologies for monitoring wildlife and habitats, as well as for on-the-ground conservation management (e.g., fighting illegal activities). We cover both established technologies (routinely deployed in conservation, backed by substantial field experience and scientific literature) and novel technologies or technology applications (typically at trial stage, only recently used in conservation), providing examples of conservation applications for both types. We describe technologies that deploy sensors that are fixed or portable, attached to vehicles (terrestrial, aquatic, or airborne) or to animals (biologging), complemented with a section on wildlife tracking. The last two sections cover actuators and computing (including web platforms, algorithms, and artificial intelligence).
Carbon dioxide accumulation is a major concern for the ecosystems, but its abundance and low cost make it an interesting source for the production of chemical feedstocks and fuels. However, the ...thermodynamic and kinetic stability of the carbon dioxide molecule makes its activation a challenging task. Studying the chemistry used by nature to functionalize carbon dioxide should be helpful for the development of new efficient (bio)catalysts for atmospheric carbon dioxide utilization. In this work, the ability of Desulfovibrio desulfuricans formate dehydrogenase (Dd FDH) to reduce carbon dioxide was kinetically and mechanistically characterized. The Dd FDH is suggested to be purified in an inactive form that has to be activated through a reduction-dependent mechanism. A kinetic model of a hysteretic enzyme is proposed to interpret and predict the progress curves of the Dd FDH-catalyzed reactions (initial lag phase and subsequent faster phase). Once activated, Dd FDH is able to efficiently catalyze, not only the formate oxidation (k cat of 543 s–1, K m of 57.1 μM), but also the carbon dioxide reduction (k cat of 46.6 s–1, K m of 15.7 μM), in an overall reaction that is thermodynamically and kinetically reversible. Noteworthy, both Dd FDH-catalyzed formate oxidation and carbon dioxide reduction are completely inactivated by cyanide. Current FDH reaction mechanistic proposals are discussed and a different mechanism is here suggested: formate oxidation and carbon dioxide reduction are proposed to proceed through hydride transfer and the sulfo group of the oxidized and reduced molybdenum center, Mo6+S and Mo4+-SH, are suggested to be the direct hydride acceptor and donor, respectively.
Dietary guidelines universally advise adherence to plant-based diets. Plant-based foods confer considerable health benefits, partly attributable to their abundant micronutrient (e.g., polyphenol) ...content. Interest in polyphenols is largely focused on the contribution of their antioxidant activity to the prevention of various disorders, including cardiovascular disease and cancer. Polyphenols are classified into groups, such as stilbenes, flavonoids, phenolic acids, lignans and others. Lignans, which possess a steroid-like chemical structure and are defined as phytoestrogens, are of particular interest to researchers. Traditionally, health benefits attributed to lignans have included a lowered risk of heart disease, menopausal symptoms, osteoporosis and breast cancer. However, the intake of naturally lignan-rich foods varies with the type of diet. Consequently, based on the latest humans' findings and gathered information on lignan-rich foods collected from Phenol Explorer database this review focuses on the potential health benefits attributable to the consumption of different diets containing naturally lignan-rich foods. Current evidence highlight the bioactive properties of lignans as human health-promoting molecules. Thus, dietary intake of lignan-rich foods could be a useful way to bolster the prevention of chronic illness, such as certain types of cancers and cardiovascular disease.
PDF
