Empirical Dynamic Modelling Identifies different Responses of Aedes Polynesiensis Subpopulations to Natural Environmental Variables

Explaining empirical dynamic modelling using verbal, graphical and mathematical approaches

Empirical dynamic modelling (EDM) is becoming an increasingly popular method for understanding the dynamics of ecosystems. It has been applied to laboratory, terrestrial, freshwater and marine systems, used to forecast natural populations and has addressed fundamental ecological questions. Despite its increasing use, we have not found full explanations of EDM in the ecological literature, limiting understanding and reproducibility. Here we expand upon existing work by providing a detailed introduction to EDM. We use three progressively more complex approaches. A short verbal explanation of EDM is then explicitly demonstrated by graphically working through a simple example. We then introduce a full mathematical description of the steps involved. Conceptually, EDM translates a time series of data into a path through a multi-dimensional space, whose axes are lagged values of the time series. A time step is chosen from which to make a prediction. The state of the system at that time step corresponds to a 'focal point' in the multi-dimensional space. The set (called the library) of candidate nearest neighbours to the focal point is constructed, to determine the nearest neighbours that are then used to make the prediction. Our mathematical explanation explicitly documents which points in the multi-dimensional space should not be considered as focal points. We suggest a new option for excluding points from the library that may be useful for short-term time series that are often found in ecology. We focus on the core simplex and S-map algorithms of EDM. Our new R package, pbsEDM, enhances understanding (by outputting intermediate calculations), reproduces our results and can be applied to new data. Our work improves the clarity of the inner workings of EDM, a prerequisite for EDM to reach its full potential in ecology and have wide uptake in the provision of advice to managers of natural resources.

Spatial predictive risk mapping of lymphatic filariasis residual hotspots in American Samoa using demographic and environmental factors

BACKGROUND

American Samoa successfully completed seven rounds of mass drug administration (MDA) for lymphatic filariasis (LF) from 2000-2006. The territory passed the school-based transmission assessment surveys in 2011 and 2015 but failed in 2016. One of the key challenges after the implementation of MDA is the identification of any residual hotspots of transmission.

METHOD

Based on data collected in a 2016 community survey in persons aged ≥8 years, Bayesian geostatistical models were developed for LF antigen (Ag), and Wb123, Bm14, Bm33 antibodies (Abs) to predict spatial variation in infection markers using demographic and environmental factors (including land cover, elevation, rainfall, distance to the coastline and distance to streams).

RESULTS

In the Ag model, females had a 26.8% (95% CrI: 11.0-39.8%) lower risk of being Ag-positive than males. There was a 2.4% (95% CrI: 1.8-3.0%) increase in the odds of Ag positivity for every year of age. Also, the odds of Ag-positivity increased by 0.4% (95% CrI: 0.1-0.7%) for each 1% increase in tree cover. The models for Wb123, Bm14 and Bm33 Abs showed similar significant associations as the Ag model for sex, age and tree coverage. After accounting for the effect of covariates, the radii of the clusters were larger for Bm14 and Bm33 Abs compared to Ag and Wb123 Ab. The predictive maps showed that Ab-positivity was more widespread across the territory, while Ag-positivity was more confined to villages in the north-west of the main island.

CONCLUSION

The findings may facilitate more specific targeting of post-MDA surveillance activities by prioritising those areas at higher risk of ongoing transmission.

Susceptible host availability modulates climate effects on dengue dynamics

Experiments and models suggest that climate affects mosquito-borne disease transmission. However, disease transmission involves complex nonlinear interactions between climate and population dynamics, which makes detecting climate drivers at the population level challenging. By analysing incidence data, estimated susceptible population size, and climate data with methods based on nonlinear time series analysis (collectively referred to as empirical dynamic modelling), we identified drivers and their interactive effects on dengue dynamics in San Juan, Puerto Rico. Climatic forcing arose only when susceptible availability was high: temperature and rainfall had net positive and negative effects respectively. By capturing mechanistic, nonlinear and context-dependent effects of population susceptibility, temperature and rainfall on dengue transmission empirically, our model improves forecast skill over recent, state-of-the-art models for dengue incidence. Together, these results provide empirical evidence that the interdependence of host population susceptibility and climate drives dengue dynamics in a nonlinear and complex, yet predictable way.

State dependence: Does a prior injury predict a future injury?

The sports medicine literature is filled with associations between injury and causal factors. However, those results have been inconsistent. We're left wondering which of our athletes might need more attention and where our efforts might be best spent. Resistance to injury is the result of interaction between many variables. These variables are interdependent with dynamic relationships which can be sometimes correlated, at times anti-correlated and from time to time show no relationship with injury risk. Relationships we may have seen yesterday do not necessarily hold true for today and we should not use those to infer what will happen. This perspective piece builds on prior works and describes how the complex interaction between injury determinants presents in other systems, why determinants are not stable and instead vary over time due to internal and external forcing and why our prediction ability remains limited even when determinants are identified. Patterns built from frequent time series data in conjunction with nonlinear dynamical methods can offer us a new approach to thinking about injury prediction.

Machine learning and dengue forecasting: Comparing random forests and artificial neural networks for predicting dengue burden at national and sub-national scales in Colombia

The robust estimate and forecast capability of random forests (RF) has been widely recognized, however this ensemble machine learning method has not been widely used in mosquito-borne disease forecasting. In this study, two sets of RF models were developed at the national (pooled department-level data) and department level in Colombia to predict weekly dengue cases for 12-weeks ahead. A pooled national model based on artificial neural networks (ANN) was also developed and used as a comparator to the RF models. The various predictors included historic dengue cases, satellite-derived estimates for vegetation, precipitation, and air temperature, as well as population counts, income inequality, and education. Our RF model trained on the pooled national data was more accurate for department-specific weekly dengue cases estimation compared to a local model trained only on the department's data. Additionally, the forecast errors of the national RF model were smaller to those of the national pooled ANN model and were increased with the forecast horizon increasing from one-week-ahead (mean absolute error, MAE: 9.32) to 12-weeks ahead (MAE: 24.56). There was considerable variation in the relative importance of predictors dependent on forecast horizon. The environmental and meteorological predictors were relatively important for short-term dengue forecast horizons while socio-demographic predictors were relevant for longer-term forecast horizons. This study demonstrates the potential of RF in dengue forecasting with a feasible approach of using a national pooled model to forecast at finer spatial scales. Furthermore, including sociodemographic predictors is likely to be helpful in capturing longer-term dengue trends.