Comparative assessment of methods for short-term forecasts of COVID-19 hospital admissions in England at the local level.

BACKGROUND: Forecasting healthcare demand is essential in epidemic settings, both to inform situational awareness and facilitate resource planning. Ideally, forecasts should be robust across time and locations. During the COVID-19 pandemic in England, it is an ongoing concern that demand for hospital care for COVID-19 patients in England will exceed available resources. METHODS: We made weekly forecasts of daily COVID-19 hospital admissions for National Health Service (NHS) Trusts in England between August 2020 and April 2021 using three disease-agnostic forecasting models: a mean ensemble of autoregressive time series models, a linear regression model with 7-day-lagged local cases as a predictor, and a scaled convolution of local cases and a delay distribution. We compared their point and probabilistic accuracy to a mean-ensemble of them all and to a simple baseline model of no change from the last day of admissions. We measured predictive performance using the weighted interval score (WIS) and considered how this changed in different scenarios (the length of the predictive horizon, the date on which the forecast was made, and by location), as well as how much admissions forecasts improved when future cases were known. RESULTS: All models outperformed the baseline in the majority of scenarios. Forecasting accuracy varied by forecast date and location, depending on the trajectory of the outbreak, and all individual models had instances where they were the top- or bottom-ranked model. Forecasts produced by the mean-ensemble were both the most accurate and most consistently accurate forecasts amongst all the models considered. Forecasting accuracy was improved when using future observed, rather than forecast, cases, especially at longer forecast horizons. CONCLUSIONS: Assuming no change in current admissions is rarely better than including at least a trend. Using confirmed COVID-19 cases as a predictor can improve admissions forecasts in some scenarios, but this is variable and depends on the ability to make consistently good case forecasts. However, ensemble forecasts can make forecasts that make consistently more accurate forecasts across time and locations. Given minimal requirements on data and computation, our admissions forecasting ensemble could be used to anticipate healthcare needs in future epidemic or pandemic settings

Inferring within-flock transmission dynamics of highly pathogenic avian influenza H5N8 virus in France, 2020.

Following the emergence of highly pathogenic avian influenza (H5N8) in France in early December 2020, we used duck mortality data from the index farm to investigate within-flock transmission dynamics. A stochastic epidemic model was fitted to the daily mortality data and model parameters were estimated using an approximate Bayesian computation sequential Monte Carlo (ABC-SMC) algorithm. The model predicted that the first bird in the flock was infected 5 days (95% credible interval, CI: 3-6) prior to the day of suspicion and that the transmission rate was 4.1 new infections per day (95% CI: 2.8-5.8). On average, ducks became infectious 4.1 h (95% CI: 0.7-9.1) after infection and remained infectious for 4.3 days (95% CI: 2.8-5.7). The model also predicted that 34% (50% prediction interval: 8%-76%) of birds would already be infectious by the day of suspicion, emphasizing the substantial latent threat this virus could pose to other poultry farms and to neighbouring wild birds. This study illustrates how mechanistic models can help provide rapid relevant insights that contribute to the management of infectious disease outbreaks of farmed animals. These methods can be applied to future outbreaks and the resulting parameter estimates made available to veterinary services within a few hours

Comparative assessment of methods for short-term forecasts of COVID-19 hospital admissions in England at the local level

Background: Forecasting healthcare demand is essential in epidemic settings, both to inform situational awareness and facilitate resource planning. Ideally, forecasts should be robust across time and locations. During the COVID-19 pandemic in England, it is an ongoing concern that demand for hospital care for COVID-19 patients in England will exceed available resources. Methods: We made weekly forecasts of daily COVID-19 hospital admissions for National Health Service (NHS) Trusts in England between August 2020 and April 2021 using three disease-agnostic forecasting models: a mean ensemble of autoregressive time series models, a linear regression model with 7-day-lagged local cases as a predictor, and a scaled convolution of local cases and a delay distribution. We compared their point and probabilistic accuracy to a mean-ensemble of them all and to a simple baseline model of no change from the last day of admissions. We measured predictive performance using the weighted interval score (WIS) and considered how this changed in different scenarios (the length of the predictive horizon, the date on which the forecast was made, and by location), as well as how much admissions forecasts improved when future cases were known. Results: All models outperformed the baseline in the majority of scenarios. Forecasting accuracy varied by forecast date and location, depending on the trajectory of the outbreak, and all individual models had instances where they were the top- or bottom-ranked model. Forecasts produced by the mean-ensemble were both the most accurate and most consistently accurate forecasts amongst all the models considered. Forecasting accuracy was improved when using future observed, rather than forecast, cases, especially at longer forecast horizons. Conclusions: Assuming no change in current admissions is rarely better than including at least a trend. Using confirmed COVID-19 cases as a predictor can improve admissions forecasts in some scenarios, but this is variable and depends on the ability to make consistently good case forecasts. However, ensemble forecasts can make forecasts that make consistently more accurate forecasts across time and locations. Given minimal requirements on data and computation, our admissions forecasting ensemble could be used to anticipate healthcare needs in future epidemic or pandemic settings

Digest: Disentangling plumage and behavior contributions to iridescent signals

This article is a digest of Simpson, R. K., and K. J. McGraw. 2018. Experimental trait mis-matches uncover specificity of evolutionary links between multiple signaling traits and their interactions in hummingbirds. Evolution, doi: 10.1111/evo.13662, https://onlinelibrary.wiley.com/doi/10.1111/evo.13662International audienceTo what extent do plumage properties and behavior interact to produce visual signals? Simpson and McGraw (2018) propose an elegant and novel experimental set‐up to dissociate behavior and color and assess their relative effects in the resulting iridescent signal. They find that modification of either component leads to a modification of the resulting signal as seen by the receiver, suggesting that sexual selection acts simultaneously on both signal components

Origin, functions and evolution of iridescence in birds : the example of hummingbirds

The study of colour can offer valuable insights into the fine details of evolutive mechanisms. It is indeed a complex trait, which can evolve along several dimensions, and which is controlled by multiple selective pressures with often opposed effects. Yet, there is one class of colours that has received few attention from evolutionary biologists: iridescent colours. This is due to the inherent complexity of these colours and the fact that their sole quantitative measurement is a challenge in itself. During my PhD, I worked with physicists and biologists and I used optical theory to propose a new measurement method for iridescent colours. I then validated this method empirically by showing that it produced reliable and repeatable estimates for both hummingbirds and morpho butterflies. My work during these three years has also focused on the development of other methodological tools and software for the study of colours. I also focused more precisely on iridescent colours in hummingbirds. I mainly investigated two sides of this topic and tried to find out (i) the proximal causes of iridescence in hummingbirds: how do they produce the striking colours they are renowned for? (ii) the distal causes of iridescence: what are the evolutionary mechanisms which control the evolution of iridescence at the community level. I found out that the structures producing iridescence in hummingbirds are way more diverse than what we previously thought. They even display an usual type of structure which has not been described in any other group yet. I also showed that at the interspecific level, iridescent colours on the back of hummingbirds tend to be similar among species occupying the same communities, which suggests a possible role of the environment in the evolution of these colours, possibly for camouflage against predators.La couleur constitue un trait particulièrement intéressant pour étudier les mécanismes de l'évolution car il s'agit d'un trait complexe, qui peut évoluer dans plusieurs dimensions, et qui est soumis à des nombreuses pression évolutives, qui agissent généralement dans des directions opposées. Parmi les couleurs, il existe une classe qui a reçu relativement peu d'attention de la part des biologistes évolutifs jusqu'ici du fait de sa complexité et de la difficulté à la mesurer de manière fiable et comparable entre espèces : les couleurs iridescentes. Les couleurs iridescentes sont habituellement définies comme des couleurs qui changent selon l'angle d'observation ou d'illumination. Au cours de cette thèse, j'ai collaboré avec des biologistes et des physiciens et j'ai utilisé la théorie optique pour construire une nouvelle méthode de mesure pour ces couleurs, que j'ai ensuite testée sur les colibris et les morphos. J'ai également développé d'autres outils méthodologiques et des librairies logicielles pour l'étude des couleurs. Je me suis ensuite intéressé plus précisément aux couleurs iridescentes des colibris et à leur origine (i) proximale : par quels mécanismes les colibris produisent-ils leurs couleurs extraordinaires ? (ii) distale : quels sont les processus qui contrôlent l'évolution de ces couleurs à l'échelle de la communauté toute entière. J'ai découvert que les structures responsables de l'iridescence chez les colibris présentent bien plus de diversité que ce qu'on pensait jusqu'ici et ils ont également un type de structure qui n'a pour l'instant été observé dans aucun autre groupe. J'ai aussi montré qu'à l'échelle interspécifique, les couleurs iridescentes présentes sur le dos sont similaires parmi les espèces qui habitent la même communauté, ce qui suggère une sélection par l'environnement, pour le camouflage par exemple

Origine et fonctions des couleurs iridescentes chez les colibris

The study of colour can offer valuable insights into the fine details of evolutionary mechanisms. It is indeed a complex trait, which can evolve along several dimensions, and which is controlled by multiple selective pressures with often opposed effects. Yet, there is one class of colours that has received few attention from evolutionary biologists: iridescent colours. This is due to the inherent complexity of these colours and the fact that their sole quantitative measurement is a challenge in itself. During my PhD, I worked with physicists and biologists and I used optical theory to propose a new measurement method for iridescent colours. I then validated this method empirically by showing that it produced reliable and repeatable estimates for both hummingbirds and \textit{Morpho} butterflies. My work during these three years has also focused on the development of other methodological tools and software for the study of colours. I also focused more precisely on iridescent colours in hummingbirds. I mainly investigated two sides of this topic and tried to find out (i) the proximate causes of iridescence in hummingbirds: how do they produce the striking colours they are renowned for? (ii) the ultimate causes of iridescence: what are the evolutionary mechanisms which control the evolution of iridescence at the community level? I found out that the structures producing iridescence in hummingbirds are way more diverse than what we previously thought. They even display an usual type of structure which has not been described in any other group yet. I also showed that at the interspecific level, iridescent colours on the back of hummingbirds tend to be similar among species occupying the same communities, which suggests a possible role of the environment in the evolution of these colours, possibly for camouflage against predators. On the other hand, colours on the belly tend to be more similar than expected by change among co-occurring species, which suggests a role of selection for communication.La couleur constitue un trait particulièrement intéressant pour étudier les mécanismes de l'évolution car il s'agit d'un trait complexe, qui peut évoluer dans plusieurs dimensions, et qui est soumis à de nombreuses pressions évolutives, qui agissent généralement dans des directions opposées. Parmi les couleurs, il existe une classe qui a reçu relativement peu d'attention de la part des biologistes évolutifs jusqu'ici du fait de sa complexité et de la difficulté à la mesurer de manière fiable et comparable entre espèces : les couleurs iridescentes. Les couleurs iridescentes sont habituellement définies comme des couleurs qui changent selon l'angle d'observation ou d'illumination. Au cours de cette thèse, j'ai collaboré avec des biologistes et des physiciens et j'ai utilisé la théorie optique pour construire une nouvelle méthode de mesure pour ces couleurs, que j'ai ensuite testée sur les colibris et les papillons \textit{Morpho}. J'ai également développé d'autres outils méthodologiques et des librairies logicielles pour l'étude des couleurs. Je me suis ensuite intéressé plus précisément aux couleurs iridescentes des colibris et à leur origine (i) proximale : par quels mécanismes les colibris produisent-ils leurs couleurs extraordinaires ? (ii) ultime : quels sont les processus qui contrôlent l'évolution de ces couleurs à l'échelle de la communauté toute entière ? J'ai découvert que les structures responsables de l'iridescence chez les colibris présentent bien plus de diversité que ce qu'on pensait jusqu'ici et ils ont également un type de structure qui n'a pour l'instant été observé dans aucun autre groupe. J'ai aussi montré qu'à l'échelle interspécifique, les couleurs iridescentes présentes sur le dos sont similaires parmi les espèces qui habitent la même communauté, ce qui suggère une sélection par l'environnement, pour le camouflage par exemple, alors que celles sur le ventres sont plus différentes qu'attendu au hasard, ce qui suggère une sélection pour la communication

Origine, fonctions et évolution de l'iridescence chez les oiseaux : exemple chez les colibris

La couleur constitue un trait particulièrement intéressant pour étudier les mécanismes de l'évolution car il s'agit d'un trait complexe, qui peut évoluer dans plusieurs dimensions, et qui est soumis à des nombreuses pression évolutives, qui agissent généralement dans des directions opposées. Parmi les couleurs, il existe une classe qui a reçu relativement peu d'attention de la part des biologistes évolutifs jusqu'ici du fait de sa complexité et de la difficulté à la mesurer de manière fiable et comparable entre espèces : les couleurs iridescentes. Les couleurs iridescentes sont habituellement définies comme des couleurs qui changent selon l'angle d'observation ou d'illumination. Au cours de cette thèse, j'ai collaboré avec des biologistes et des physiciens et j'ai utilisé la théorie optique pour construire une nouvelle méthode de mesure pour ces couleurs, que j'ai ensuite testée sur les colibris et les morphos. J'ai également développé d'autres outils méthodologiques et des librairies logicielles pour l'étude des couleurs. Je me suis ensuite intéressé plus précisément aux couleurs iridescentes des colibris et à leur origine (i) proximale : par quels mécanismes les colibris produisent-ils leurs couleurs extraordinaires ? (ii) distale : quels sont les processus qui contrôlent l'évolution de ces couleurs à l'échelle de la communauté toute entière. J'ai découvert que les structures responsables de l'iridescence chez les colibris présentent bien plus de diversité que ce qu'on pensait jusqu'ici et ils ont également un type de structure qui n'a pour l'instant été observé dans aucun autre groupe. J'ai aussi montré qu'à l'échelle interspécifique, les couleurs iridescentes présentes sur le dos sont similaires parmi les espèces qui habitent la même communauté, ce qui suggère une sélection par l'environnement, pour le camouflage par exemple.The study of colour can offer valuable insights into the fine details of evolutive mechanisms. It is indeed a complex trait, which can evolve along several dimensions, and which is controlled by multiple selective pressures with often opposed effects. Yet, there is one class of colours that has received few attention from evolutionary biologists: iridescent colours. This is due to the inherent complexity of these colours and the fact that their sole quantitative measurement is a challenge in itself. During my PhD, I worked with physicists and biologists and I used optical theory to propose a new measurement method for iridescent colours. I then validated this method empirically by showing that it produced reliable and repeatable estimates for both hummingbirds and morpho butterflies. My work during these three years has also focused on the development of other methodological tools and software for the study of colours. I also focused more precisely on iridescent colours in hummingbirds. I mainly investigated two sides of this topic and tried to find out (i) the proximal causes of iridescence in hummingbirds: how do they produce the striking colours they are renowned for? (ii) the distal causes of iridescence: what are the evolutionary mechanisms which control the evolution of iridescence at the community level. I found out that the structures producing iridescence in hummingbirds are way more diverse than what we previously thought. They even display an usual type of structure which has not been described in any other group yet. I also showed that at the interspecific level, iridescent colours on the back of hummingbirds tend to be similar among species occupying the same communities, which suggests a possible role of the environment in the evolution of these colours, possibly for camouflage against predators

Estimation of colour volumes as concave hypervolumes using α‐shapes

International audience1. Organisms often display multiple colours patches and for many analyses, it may be useful to take into account all these patches at the same time, and reconstruct the colour volume of the organisms. Stoddard et al. (2008) proposed to use convex hulls to reconstruct the colour volume of a species. Convex hull volume has since then often been used as an index of colourfulness, and the intersection of multiple convex hulls is used to study the colour similarity between two objects.2. In this article, I outline the limitations of convex hulls in this context. In particular, multiple studies have reported that the convex hull overestimates the actual colour volume. I argue for the use of a more general tool, developed as a more exible extension of the convex hulls: α‐shapes. Depending on the parameter α, α‐shapes can reconstruct concave (i.e. non‐convex) volumes with voids or pockets, that are better suited for the estimation of colour volumes.3. To determine the optimal value of the parameter α, I point out two expected properties of multidimensional trait spaces, which translate into two conditions providing a lower and upper bound on α, and I propose technical tools to identify the α value satisfying these two conditions. Using colour data from the whole bird community from the biological station of the Nouragues, French Guiana, I show that using α‐shapes rather than convex hulls results in possibly major differences in the estimation of the colour volume.4. I discuss possible future developments of this new framework in both colour science, as well as other areas of ecology dealing with multidimensional trait spaces, such as community ecology where α‐shape volumes could serve as a replacement for the functional richness FRic, or morphometrics

fundiversity: a modular R package to compute functional diversity indices

International audienceFunctional diversity is widely used and widespread. However, the main packages used to compute functional diversity indices are not flexible and not adapted to the volume of data used in modern ecological analyses. We here present fundiversity, an R package that eases the computation of classical functional diversity indices. It leverages parallelization and memoization (caching results in memory) to maximize efficiency with data with thousands of columns and rows. We also did a performance comparison with packages that provide analog functions. In addition to being more flexible, fundiversity was always an order of magnitude quicker than alternatives. fundiversity aims to be a lightweight, efficient tool to compute functional diversity indices, which can be used in a variety of contexts. Because it has been designed following clear principles, it is easy to extend. We hope the wider community will adopt it and we welcome all contributions

fundiversity: Easy Computation of Functional Diversity Indices

Computes six functional diversity indices: Functional Divergence (FDiv), Function Evenness (FEve), Functional Richness (FRic), Functional Richness intersections (FRic_intersect), Functional Dispersion (FDis), Rao's entropy (Q) (reviewed in Villéger et al. 2008 ). Provides efficient, modular, and parallel functions to compute functional diversity indices. (preprint: